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Premature termination codon readthrough restores progranulin expression in preclinical models of frontotemporal… Frew, Jonathan 2021

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PREMATURE TERMINATION CODON READTHROUGH RESTORES PROGRANULIN EXPRESSION IN PRECLINICAL MODELS OF FRONTOTEMPORAL DEMENTIA AND NEURONAL CEROID LIPOFUSCINOSIS  by  Jonathan Frew B.Sc., The University of British Columbia, 2016  A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF   DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Experimental Medicine)   UNIVERSITY OF BRITISH COLUMBIA  (Vancouver) April 2021  © Jonathan Frew, 2021 ii  The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the dissertation entitled: Premature termination codon readthrough restores progranulin expression in preclinical models of frontotemporal dementia and neuronal ceroid lipofuscinosis  submitted by Jonathan Frew  in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Experimental Medicine  Examining Committee: Haakon B. Nygaard, Neurology Supervisor  Robin G-Y. Hsiung, Neurology Supervisory Committee Member  Stephanie Willerth, Biomedical Engineering Supervisory Committee Member Eric Jan, Biochemistry & Molecular Biology University Examiner Neil Cashman, Neurology University Examiner    Additional Supervisory Committee Members: Michel Roberge, Biochemistry & Molecular Biology iii  Abstract Frontotemporal dementia (FTD) is a devastating and progressive disorder and a common form of early-onset dementia. There are currently no disease-modifying therapies available, signifying the need for new therapeutic approaches. Progranulin (PGRN) haploinsufficiency due to autosomal dominant mutations in the progranulin gene (GRN) is a major cause of familial FTD (FTD-GRN), with nearly a quarter of these genetic cases resulting from a nonsense mutation. Nonsense mutations introduce premature termination codons (PTCs) that can be therapeutically targeted by compounds allowing readthrough, and aminoglycoside antibiotics are known to be potent PTC readthrough drugs. When this research project was initiated, restoring PGRN through PTC readthrough had not been explored as a therapeutic intervention in FTD-GRN.   We used human induced pluripotent cell (hiPSC) lines bearing clinical nonsense mutations spanning the GRN coding region (S116X+/-, R418X+/-, R493X-/- KI) to evaluate G418 and novel PTC readthrough enhancer (CDX-series) combination treatments. Our aim was to demonstrate proof-of-concept GRN PTC readthrough and lower the required dose of G418 to address the known toxicity of traditional aminoglycoside PTC readthrough agents.  Screening in HEK293 cells expressing nonsense mutant (S116X, R418X, R493X) GRN expression constructs found PTC readthrough combination treatment with G418 and CDX5-288 enhancer most potently induced GRN readthrough. We demonstrated in vivo iv  proof-of-concept GRN PTC readthrough by performing single intracerebroventricular (ICV) injections of G418 with or without CDX5-288 enhancer in our GRN R493X adeno-associated virus-based mouse model. Combination treatment in hiPSC-derived isogenic R493X-/- KI cortical neurons significantly restored PGRN levels and normalized overexpression of the mature form of the lysosomal enzyme cathepsin D.   We attempted to achieve in vivo PTC readthrough of GrnR493X through repeated ICV administrations of G418 in GrnR493X/R493X mice. However, G418 doses capable of eliciting PTC readthrough in these mice were associated with significant neurotoxicity. We next conducted further neuropathological characterization of lysosomal dysfunction, neuroinflammation, and neurodegeneration in GrnR493X/R493X mice, identifying several phenotypes recently reported in Grn-/- mice, including decreased thalamic excitatory neuronal density. Taken together, our findings suggest that PTC readthrough may be a potential therapeutic strategy for FTD caused by GRN nonsense mutations and support further investigations into novel readthrough drugs with improved tolerability.     v  Lay Summary Neurodegenerative diseases represent a growing burden to Canadian society. Frontotemporal dementia (FTD) is a neurodegenerative syndrome that is the second most common cause of early-onset dementia after Alzheimer’s disease. Approximately 25% of FTD cases are caused by mutations in the progranulin gene (GRN), meaning that patients only have 50% of the normal levels of the progranulin protein (PGRN). A nonsense mutation is a type of loss-of-function mutation that causes a protein to be cut short in length by a process known as premature termination. Nonsense mutations in GRN cause approximately 7.5-10% of FTD cases (FTD-GRN). We have discovered drugs that silence the effect of nonsense mutations by preventing premature termination. The goal of this work was to test whether these drugs promote full-length PGRN production in cells derived from FTD-GRN patients and in FTD-GRN mouse models. This work is important because there are currently no effective treatments for FTD. vi  Preface Parts of chapters 3 and 4 were published in the following articles:  1) Frew, J., Baradaran-Heravi, A., Balgi, A.D., Wu, X., Yan, T.D., Arns, S., Shidmoossavee, F.S., Tan, J., Jaquith, J.B., Jansen-West, K.R., Lynn, F.C., Gao, F.B., Petrucelli, L., Feldman, H.H., Mackenzie, I.R., Roberge, M., Nygaard, H.B. (2020). Premature termination codon readthrough upregulates progranulin expression and improves lysosomal function in preclinical models of GRN deficiency. Molecular Neurodegeneration, 15(21). https://doi.org/10.1186/s13024-020-00369-5. This article was minimally modified to fit formatting guidelines of this thesis and was reused under the Spring Nature Creative Commons license (CC BY 4.0).  2) Frew, J., Wu, X., Hsiung, G.Y., Feldman H.H., Mackenzie, I.R., Nygaard, H.B. (2019). Generation of an induced pluripotent stem cell line (UBCi001-A) from a presymptomatic individual carrying the R418X progranulin gene mutation. Stem Cell Research, 41(101582). https://doi.org/10.1016/j.scr.2019.101582. This article was minimally modified to fit formatting guidelines of this thesis and was reused under the Elsevier B.V. Creative Commons license (CC BY-NC-ND 4.0).   The design of all research, data analysis, and manuscript preparation were an original intellectual product of the author, myself, with the guidance and mentorship of Dr. Haakon B. Nygaard. I performed all experiments myself with the following exceptions: • GRN expression vector cloning and HEK293 experiments that generated data presented in Figures 3-1, 3-2, and 3-4 were performed by A. Baradaran-Heravi and A.D Balgi. vii  • AAV-GRN-R493X-V5 vector packaging was performed by K.R. Jansen-Weston. • AAV-GRN-R493X-V5 RIPA-soluble mouse brain lysate V5 automated capillary electrophoresis western analysis presented in Figure 3-7 was performed by A.D Balgi. • hiPSC CRISPR/Cas9 gene editing guidance was provided by F.C. Lynn. • X. Wu prepared DNA samples for Sanger sequencing. • T.D Yan assisted with some hiPSC tissue culture work. • S. Arns, F.S. Shidmoossavee, J. Tan, and J.B Jaquith were involved in the synthesis of CDX-series compound derivatives.   Parts of chapter 5 were published in the following article: 1) Frew, J., Nygaard, H.B. (2021). Neuropathological and behavioural characterization  of aged Grn R493X progranulin-deficient frontotemporal dementia knock-in mice. Acta  Neuropathologica Communications (in press). This article was minimally modified to fit  formatting guidelines of this thesis and was reused under the Elsevier B.V. Creative  Commons license (CC BY 4.0).  The design of all research, data analysis, and manuscript preparation were an original intellectual product of the author, myself, with the guidance and mentorship of Dr. Haakon B. Nygaard. I performed all experiments myself with the following exception: • Dr. Kunho Choi isolated and treated Grn+/+ and GrnR493X/R493X MEFs and conducted the Pgrn linker-1 antibody PTC readthrough western blot assay presented in Figure 5-16 (unpublished data). viii  Animal studies were performed in compliance with the Canadian Council on Animal Care and were approved by the University of British Columbia (UBC) Animal Care Committee under protocols A19-0623 (FTD mouse model breeding), A19-0062 (generation of mouse embryonic fibroblasts), A17-0225 (AAV injection of P0 C57BL/6J pups) and A16-0161 (CNS delivery of PTC readthrough drugs). hiPSC studies were in compliance with the Tri-Council Policy Statement on ‘Ethical Conduct for Research Involving Humans’, as well as ICH Good Clinical Practice Guidelines and were approved by the UBC under protocol HO7-03022. I have successfully completed the following Canadian Council on Animal Care courses: Rodent Biology and Husbandry, Introduction to Rodent Anesthesia Inhalable and Injectable, Introduction to Rodent Aseptic Surgery – Full Sterile and Sterile Tip (Online animal care training program certificate number: 6870-14). I have also completed the UBC Laboratory Biological Safety Course (certificate number: 2019-swyay).   ix  Table of Contents  Abstract ......................................................................................................................... iii Lay Summary ................................................................................................................. v Preface .......................................................................................................................... vi Table of Contents ......................................................................................................... ix List of Tables .............................................................................................................. xvi List of Figures ........................................................................................................... xvii List of Symbols .......................................................................................................... xxi List of Abbreviations ................................................................................................. xxii Acknowledgements ................................................................................................. xxvii Dedication ................................................................................................................. xxix Chapter 1: An introduction to frontotemporal lobar degeneration, progranulin neurobiology, and premature termination codon readthrough ................................ 1 1.1 Frontotemporal lobar degeneration ................................................................... 1 1.1.1 History of FTLD ............................................................................................. 1 1.1.2 Clinical presentations of FTD ........................................................................ 2 1.1.3 Neuropathology of FTLD ............................................................................... 3 1.1.4 Genetics of FTLD .......................................................................................... 4 1.1.5 FTLD caused by PGRN haploinsufficiency .................................................... 6 1.1.6 Genetic modifiers of FTLD-GRN ................................................................... 8 1.1.7 Clinical and neuropathological phenotypes of FTLD-GRN and CLN11 ....... 12 1.2 PGRN neurobiology ........................................................................................ 14 x  1.2.1 PGRN structure ........................................................................................... 15 1.2.2 PGRN expression in the brain ..................................................................... 15 1.2.3 PGRN regulation in the brain ....................................................................... 18 1.2.4 Mouse models of Grn-deficiency  ................................................................ 24 1.2.4.1 Neuroinflammation ............................................................................... 24 1.2.4.2 Lysosomal dysfunction ......................................................................... 28 1.2.4.3 Dysregulated lipid metabolism ............................................................. 31 1.2.4.4 Neural connectivity deficits and neurodegeneration ............................. 33 1.2.5 hiPSC-derived CNS models of GRN-deficiency .......................................... 37 1.2.6 Proposed mechanisms of neurodegeneration in FTLD-GRN ...................... 41 1.2.7 Therapeutic development for the treatment of FTLD-GRN .......................... 47 1.3 Premature termination codon readthrough ..................................................... 48 1.3.1 Aminoglycoside PTC readthrough ............................................................... 52 1.3.2 Aminoglycoside toxicity ............................................................................... 54 1.3.3 Promising PTC readthrough drugs .............................................................. 56 1.3.4 PTC readthrough enhancers ....................................................................... 59 1.3.5 Nonsense mediated mRNA decay .............................................................. 60 1.3.6 PTC readthrough in cellular models of FTLD-GRN ..................................... 62 1.4 Thesis research questions .............................................................................. 63 Chapter 2: Materials and methods ............................................................................. 67 2.1 Mice ................................................................................................................ 67 2.2 Cells ................................................................................................................ 67 2.2.1 HEK293 ....................................................................................................... 67 xi  2.2.2 Mouse embryonic fibroblasts ....................................................................... 68 2.3 Expression vectors .......................................................................................... 68 2.3.1 Vector mutagenesis ..................................................................................... 68 2.3.2 Transfection ................................................................................................. 69 2.3.3 AAV vector packaging ................................................................................. 69 2.3.4 In vitro transduction ..................................................................................... 70 2.4 Antibodies ....................................................................................................... 71 2.5 Drug treatments .............................................................................................. 73 2.5.1 In vitro.......................................................................................................... 73 2.5.2 AAV mouse model ....................................................................................... 73 2.5.3 GrnR493X/R493X mouse model ......................................................................... 74 2.6 Western blot .................................................................................................... 74 2.6.1 Conventional western blot ........................................................................... 74 2.6.2 ProteinSimple Wes ...................................................................................... 75 2.7 hiPSC models ................................................................................................. 76 2.7.1 hiPSC reprogramming ................................................................................. 76 2.7.2 hiPSC culture .............................................................................................. 76 2.7.3 hiPSC trilineage differentiation .................................................................... 77 2.7.4 hiPSC CNS lineage differentiation ............................................................... 77 2.7.5 Karyotyping analysis ................................................................................... 78 2.8 CRISPR/Cas9 gene editing............................................................................. 78 2.9 Multielectrode array electrophysiology ............................................................ 79 2.10 ELISA .............................................................................................................. 80 xii  2.11 qPCR .............................................................................................................. 81 2.12 Mouse genotyping ........................................................................................... 81 2.13 Histology ......................................................................................................... 82 2.13.1 Immunocytochemical staining and quantification ........................................ 82 2.13.2 Brain immunofluorescence microscopy and quantification .......................... 83 2.13.3 Brightfield microscopy ................................................................................. 87 2.14 Surgical procedures ........................................................................................ 87 2.14.1 Intracerebroventricular injection of AAV particles ........................................ 87 2.14.2 Bolus intracerebroventricular injection of drugs ........................................... 87 2.14.2.1 AAV-GRN-R493X-V5 mice ................................................................... 87 2.14.2.2 Grn+/+ and GrnR493X/R493X mice .............................................................. 88 2.14.3 Intracerebroventricular iPRECIO® pump implantation in Grn+/+ and GrnR493X/R493X mice ................................................................................................. 89 2.15 Open-field behavioural assay .......................................................................... 90 2.16 Brain collection of processing ......................................................................... 90 2.16.1 AAV mouse model ....................................................................................... 90 2.16.2 GrnR493X/R493X baseline characterization ...................................................... 91 2.16.3 Vehicle/G418 treated Grn+/+ and GrnR493X/R493X mice ................................... 92 2.17 Statistical analysis ........................................................................................... 92 Chapter 3:  Exogenous PTC readthrough of nonsense mutant GRN expression constructs .................................................................................................................... 94 3.1 Introduction ..................................................................................................... 94 3.2 Results ............................................................................................................ 96 xiii  3.2.1 PTC readthrough in transiently transfected HEK293 cells ........................... 96 3.2.2 PTC readthrough in stably transfected HEK293 cells ................................ 100 3.2.3 PTC readthrough in HEK293 cells transduced with AAV-GRN-R493X-V5 viral particles ........................................................................................................ 102 3.2.4 Technical demonstration of CNS P0 delivery of AAV particles and bolus ICV injection in adult mice ........................................................................................... 104 3.2.5 PTC readthrough in AAV-GRN-R493X-V5 mice ........................................ 107 3.3 Discussion..................................................................................................... 109 Chapter 4: Generation of FTLD-GRN hiPSC lines and endogenous PTC readthrough of GRN nonsense mutant hiPSC-derived CNS cell types ................ 111 4.1 Introduction ................................................................................................... 111 4.2 Results .......................................................................................................... 114 4.2.1 Generation of WT and FTLD-GRN patient-derived hiPSC lines ................ 114 4.2.2 Generation of an isogenic GRN R493X homozygous knock-in hiPSC line using CRISPR/Cas9 gene editing ........................................................................ 114 4.2.3 Characterization of hiPSC line pluripotency .............................................. 115 4.2.4 Differentiation of WT and GRN-deficient hiPSC lines into cortical neurons and astrocytes ...................................................................................................... 121 4.2.5 PTC readthrough in GRN-deficient hiPSC-derived cortical neurons ......... 128 4.2.6 PTC readthrough rescues lysosomal dysfunction in R493X-/- KI hiPSC-derived cortical neurons ....................................................................................... 137 4.2.7 PTC readthrough in R493X-/- KI hiPSC-derived astrocytes ........................ 141 xiv  4.2.8 Impact of G418 on PGRN expression in WT hiPSC-derived cortical neurons and astrocytes ...................................................................................................... 149 4.3 Discussion..................................................................................................... 153 Chapter 5: Phenotypic characterization of the GrnR493X/R493X mouse model and dose-limiting in vivo toxicity of G418 ...................................................................... 159 5.1 Introduction ................................................................................................... 159 5.2 Results .......................................................................................................... 160 5.2.1 Pgrn expression in the brains of aged GrnR493X/R493X mice ......................... 160 5.2.2 Lysosomal dysfunction in the brains of aged GrnR493X/R493X mice .............. 165 5.2.3 Neuroinflammation and astrogliosis in the ventral thalamus of aged GrnR493X/R493X mice ................................................................................................ 177 5.2.4 Partial preservation of inhibitory synaptic density in the thalamus of aged GrnR493X/R493X mice ............................................................................................... 185 5.2.5 Reduced thalamic excitatory neuron density in the brains of aged GrnR493X/R493X mice ............................................................................................... 188 5.2.6 Aged male GrnR493X/R493X mice exhibit an increased anxiety phenotype .... 190 5.2.7 PTC readthrough in GrnR493X/R493X MEFs ................................................... 198 5.2.8 G418-induced toxicity in GrnR493X/R493X mice limits therapeutic potential ... 201 5.3 Discussion..................................................................................................... 216 Chapter 6: Conclusions ............................................................................................ 223 6.1 Contributions to the fields of FTLD-GRN and CLN11 ................................... 223 6.1.1 In vitro and in vivo PTC readthrough of exogenously expressed nonsense mutant human GRN expression constructs .......................................................... 223 xv  6.1.2 In vitro and in vivo PTC readthrough in human and mouse models endogenously expressing nonsense mutant GRN ............................................... 224 6.2 Final conclusions .......................................................................................... 226 6.3 Future directions ........................................................................................... 227 References ................................................................................................................. 231 xvi  List of Tables Table 1-1 Primary antibodies ........................................................................................ 71  xvii  List of Figures Figure 1-1 Brain regulation of extracellular PGRN proteolysis ...................................... 22 Figure 1-2 Nonsense mutation readthrough .................................................................. 51 Figure 1-3 Graphical overview of experimental models................................................. 66 Figure 3-1 Induction of PTC readthrough by G418 and CDX5 enhancers in cells stably expressing nonsense mutant GRN-V5 .......................................................................... 97 Figure 3-2 Induction of PTC readthrough by G418 in transiently transfected cells expressing nonsense mutant GRN-V5 .......................................................................... 99 Figure 3-3 Chemical structures of CDX5-196 and CDX5-288 ..................................... 101 Figure 3-4 Induction of PTC readthrough in cells transduced with increasing titers of AAV-GRN-R493X-V5 .................................................................................................. 103 Figure 3-5 Technical demonstration of AAV P0 ICV injection method ........................ 105 Figure 3-6 Technical demonstration of bolus ICV injection method in adult mice ....... 106 Figure 3-7 Induction of PTC readthrough in AAV-R493X-GRN-V5 mice ..................... 108 Figure 4-1 Generation of isogenic CRISPR/Cas9 gene edited R493X-/- KI hiPSC line from WT ...................................................................................................................... 116 Figure 4-2 PGRN immunofluorescence in WT and R493X-/- KI hiPSC-derived cortical neurons ....................................................................................................................... 118 Figure 4-3 Characterization of WT and GRN-deficient hiPSC lines ............................ 119 Figure 4-4 Differentiation and characterization of cortical neurons and astrocytes derived from WT and GRN-deficient hiPSCs .............................................................. 122 Figure 4-5 Characterization of hiPSC-derived cortical neuron synaptic development and neural network formation ............................................................................................. 124 xviii  Figure 4-6 Co-culturing hiPSC-derived cortical neurons with hiPSC-derived astrocytes accelerates electrophysiological maturation and neural network formation................. 126 Figure 4-7 Baseline expression and secretion of PGRN in WT hiPSC-derived cortical neurons and astrocytes ............................................................................................... 130 Figure 4-8 Detecting PGRN in WT and R493X-/- KI hiPSC-derived cortical neurons by western blot ................................................................................................................. 131 Figure 4-9 Induction of PTC readthrough by G418 and enhancers in hiPSC-derived cortical neurons bearing FTLD-GRN nonsense mutations .......................................... 132 Figure 4-10 Quantification of G418-induced neuronal cytotoxicity .............................. 134 Figure 4-11 Selective increase of nonsense mutant GRN mRNA in R493X-/- KI hiPSC-derived cortical neurons in response to PTC readthrough treatments ........................ 136 Figure 4-12 GRN PTC readthrough rescues FTLD-GRN/CLN11 lysosomal pathological CTSD maturation phenotype in R493X-/- KI hiPSC-derived cortical neurons .............. 139 Figure 4-13 qPCR analysis of GRN mRNA levels in WT hiPSC-derived cortical neurons and astrocytes ............................................................................................................. 143 Figure 4-14 Induction of PTC readthrough by G418 and enhancers in R493X-/- KI hiPSC-derived astrocytes demonstrated by western blot ............................................ 144 Figure 4-15 Induction of PTC readthrough by G418 and enhancers in R493X-/- KI hiPSC-derived astrocytes demonstrated by ELISA ..................................................... 147 Figure 4-16 Selective increase of nonsense mutant GRN mRNA in R493X-/- KI hiPSC-derived astrocytes in response to PTC readthrough treatments ................................. 148 Figure 4-17 G418-mediated disruption of PGRN homeostasis in WT hiPSC-derived astrocytes .................................................................................................................... 151 xix  Figure 5-1 GrnR493X/R493X genotyping............................................................................ 162 Figure 5-2 Pgrn expression in the brains of aged GrnR493X/R493X mice ......................... 163 Figure 5-3 Lysosomal dysfunction in the ventral thalamus and CA3 hippocampal region of aged GrnR493X/R493X mice .......................................................................................... 167 Figure 5-4 Enlarged lysosomes in the ventral thalamus and CA3 hippocampal region of aged GrnR493X/R493X mice .............................................................................................. 169 Figure 5-5 Global lysosomal dysfunction in the brains of aged GrnR493X/R493X mice ..... 171 Figure 5-6 Neuronal TDP-43 proteinopathy is localized to the ventral thalamus of aged GrnR493X/R493X mice ....................................................................................................... 174 Figure 5-7 Absence of global p-TDP-43 proteinopathy in the brains of aged GrnR493X/R493X mice ....................................................................................................... 176 Figure 5-8 Neuroinflammation in the ventral thalamus of aged GrnR493X/R493X mice ..... 180 Figure 5-9 Microglial skeletal analysis method ............................................................ 182  Figure 5-10 Severe astrogliosis in the ventral thalamus and CA3 hippocampal region of aged GrnR493X/R493X mice .............................................................................................. 183 Figure 5-11 Inhibitory synaptic density is preserved in the thalamus of aged GrnR493X/R493X mice ....................................................................................................... 186 Figure 5-12 Reduced thalamic Foxp2+ excitatory neuron density in the brains of aged GrnR493X/R493X mice ....................................................................................................... 189 Figure 5-13 Aged male GrnR493X/R493X mice exhibit an increased anxiety phenotype ... 192  Figure 5-14 GrnR493X/R493X brain lysosomal dysfunction does not exhibit a sex-specific phenotype ................................................................................................................... 194 xx  Figure 5-15 GrnR493X/R493X microgliosis and astrogliosis does not exhibit a sex-specific phenotype ................................................................................................................... 195 Figure 5-16 GrnR493X/R493X decreased thalamic excitatory neuron density and inhibitory synaptic pruning does not exhibit a sex-specific phenotype ........................................ 196 Figure 5-17 Induction of PTC readthrough by G418 and enhancers in GrnR493X/R493X MEFs ........................................................................................................................... 199 Figure 5-18 A single ICV injection of G418 may induce increased Pgrn expression in the brains of GrnR493X/R493X mice ........................................................................................ 203 Figure 5-19 Technical demonstration of bolus iPRECIO® pump-mediated ICV injections targeting the lateral ventricles ..................................................................................... 205 Figure 5-20 G418’s PTC readthrough activity is preserved despite prolonged incubation at physiologic temperature .......................................................................................... 206 Figure 5-21 Schematic describing iPRECIO® pump experiment infusion programs and toxicity outcomes in mice ............................................................................................ 208 Figure 5-22 Quantification of G418 concentration in the brains of Grn+/+ and GrnR493X/R493X mice treated ICV with G418 .................................................................. 209 Figure 5-23 Multiple iPRECIO® pump-mediated ICV infusions of 50 µg G418 may induce increased Pgrn expression in the brains of GrnR493X/R493X mice ....................... 210 Figure 5-24 Grn+/+ tolerate iPRECIO® pump ICV infusion of saline ............................. 213 Figure 5-25 Increased Pgrn expression induced by 2X repeated ICV G418 injections in the brains of GrnR493X/R493X mice .................................................................................. 214   xxi  List of Symbols µ  micron α  alpha β  beta δ  delta γ  gamma κ  kappa    xxii  List of Abbreviations    2-DOS  2-deoxystreptamine AAV   Adeno-associated virus AAVS1  Adeno-associated virus integration site 1 AD   Alzheimer’s disease ADAMTS7  A disintegrin and metalloproteinase with thrombospondin motifs 7 ADP   Adenosine diphosphate ALP   Autophagy-lysosomal pathway ALS   Amyotrophic lateral sclerosis  ANOVA  Analysis of variance ATP   Adenosine triphosphate ATRA   Vitamin A1 metabolite all-trans retinoic acid BBB   Blood-brain-barrier BDNF   Brain-derived neurotrophic factor  bvFTD  Behavioural variant frontotemporal dementia C/EBPβ  CCAAT-enhancer binding protein β C1qa   Complement C1q subcomponent subunit A C3b   Complement component C3b C9orf72  Chromosome 9 open reading frame 72 Cas9   CRISPR associated protein 9 CE   Cholesterol ester CF   Cystic fibrosis CLEAR   Coordinated lysosomal expression and regulation CLN11  Ceroid lipofuscinosis neuronal 11  CNS   Central nervous system CreER  Cre-estrogen receptor CRISPR  Clustered regularly interspaced short palindromic repeats crRNA  trans-activating CRISPR RNA CSF   Cerebrospinal fluid CSF1R  Colony stimulating factor 1 receptor CTF   C-terminal fragment CTIP2   COUP-TF-interacting protein 2 CTSB/D/L/S  Cathepsin B/D/L/S CX3CR1  CX3 chemokine receptor 1 DAG   Diacylglycerides DAM   Disease-associated microglia DAPI   4′,6-diamidino-2-phenylindole DIV   Day in vitro DLDH   Dementia lacking distinctive histopathology DMD   Duchenne muscular dystrophy DMEM  Dulbecco's Modified Eagle Medium DMSO  Dimethyl sulfoxide DN   Dystrophic neurites  xxiii  DNMT   DNA methyltransferase DPPII/7   Dipeptidyl peptidase II/7 DTT   Dithiothreitol EDTA   Ethylenediaminetetraacetic acid eGFP   Enhanced green fluorescent protein EJC   Exon junction complex ELISA   Enzyme-linked immunosorbent assay EP   Erythroid progenitor ER   Endoplasmic reticulum eRF1/3  Eukaryotic release factor 1/3  EWS   Ewing sarcoma FAM171A2  Family with sequence similarity 171 member A2 FBS   Fetal bovine serum FOXG/O/P1  Forkhead box protein G/O/P1 FTD   Frontotemporal dementia FTD-MND  Frontotemporal dementia with motor neuron disease FTLD   Frontotemporal lobar degeneration FUS   Fused in Sarcoma  GAD65  Glutamic acid decarboxylase 65-kilodalton isoform GAPDH  Glyceraldehyde 3-phosphate dehydrogenase GCase  Glucocerebrosidase GDNF   Glia cell-derived neurotrophic factor GFAP   Glial fibrillary acidic protein GNS   N-acetylglucosamine-6-sulfatase  GOF   Gain-of-function GPNMB  Glycoprotein NMB gRNA   Guide RNA GRNs   Granulin peptides GWAS   Genome-wide association studies HEK293  Human embryonic kidney 293 cells HEXB   Hexosaminidase subunit beta hiPSC   Human induced pluripotent stem cells HPRT1  Hypoxanthine phosphoribosyltransferase 1 Hsp70   Heat shock protein 70 IBA1   Allograft inflammatory factor 1 ICV   Intracerebroventricular IF   Immunofluorescence  IFNγ   Interferon gamma IKBKB  Inhibitor of NF-κB subunit beta IL-10   Interleukin 10 IL-1β   Interleukin 1 beta kDa   Kilodaltons KO   Knockout LAMP1  Lysosomal-associated membrane LC   Locus ceruleus xxiv  LC3-I/II  Microtubule-associated proteins I/II light chain 3B LD   Lipid-droplet LOF   Loss-of-function LPS   Lipopolysaccharide LRP1   Low density lipoprotein receptor-related protein 1 M6PR   Mannose 6-phosphate receptor MAC   Membrane attack complex MAP2   Microtubule-associated protein 2 MAPK   Mitogen-activated protein kinase MAPT   Microtubule-associated protein tau MCM   Microglia conditioned media MEA   Multielectrode array MEF   Mouse embryonic fibroblast miRNA  Micro-RNA Mitoribosome Mitochondrial ribosome mPFC   Medial prefrontal cortex MSN   Medium spiny neurons mTOR C1  Mammalian target of rapamycin complex 1 N2a   Neuro2a NA   Nucleus accumbens NCI   Neuronal cytoplasmic inclusions NCL   Neuronal ceroid lipofuscinosis NF-κB   Nuclear factor kappa beta nfvPPA  Non-fluent variant primary progressive aphasia NII    Neuronal intranuclear inclusions NMD   Nonsense-mediated mRNA decay NPC   Neuronal progenitor cells OCD   Obsessive-compulsive disorder ORF   Open reading frame PBS   Phosphate-buffered saline PCR   Polymerase chain reaction PFA   Paraformaldehyde PFU   Plaque-forming unit PGRN   Progranulin PGRN/GRNs  Full-length PGRN, truncated PGRN, and GRN peptides PI3K   Phosphoinositide 3-kinase PKB   Protein kinase B PKCδ   Protein kinase C delta PLO/L   Poly-L-ornithine / laminin Poly I:C  Polyinosinic:polycytidylic acid PP2A   Protein phosphatase 2 PSAP   Prosaposin PTC   Premature termination codon p-TDP-43  Phosphorylated TAR DNA-binding protein 43 xxv  qPCR   Quantitative polymerase chain reaction rec. PGRN  Recombinant PGRN RF   Release factor RIPA   Radioimmunoprecipitation assay  RNAi   RNA interference ROS   Reactive oxygen species RT   Room temperature S1BF   Barrel field region of the rodent primary somatosensory cortex S6K2   S6 kinase beta SAP   Saposin SCARB2  Scavenger receptor class B member 2 SDS-PAGE  Sodium dodecyl sulfate polyacrylamide gel electrophoresis SEM   Standard error of mean siRNA   Small interfering RNA SLPI   Secretory leukocyte protease inhibitor SMAD   Small mothers against decapentaplegic SNP    Single nucleotide polymorphism snRNA-seq   Single-nuclei RNA-sequencing  SORT1  Sortilin SOX1/17  SRY-related HMG-box 1/17 ssODN  Single-stranded oligonucleotide svPPA  Semantic-variant primary progressive aphasia  TAF15  TBP associated factor 15 TAG   Triacylglycerides TARDBP  TAR DNA-binding protein 43 gene TBR1   T-box brain transcription factor 1 TBS   Tris-buffered saline TCA   Tricarboxylic acid TDP-43  TAR DNA-binding protein 43 TFEB   Transcription factor EB TGF-β  Transforming growth factor beta TGFβR-1  Transforming growth factor beta receptor 1 TLR4   Toll-like receptor 4 TMEM106B  Transmembrane protein 106B TNFR1/2  Tumor necrosis factor receptor 1/2 TNFα   Tumor necrosis factor alpha TP53/p53  Tumor protein p53 TPP1   Tripeptidyl-peptidase 1 TUJ1   Neuron specific class III beta-tubulin UBC   University of British Columbia UPF1/2/3  Up-frameshift suppressor 1/2/3 UTR   Untranslated region V-ATPase  Vacuolar-type ATPase VGAT   Vesicular gamma-aminobutyric amino acid transporter VGLUT1  Vesicular glutamate transporter 1 xxvi  VPL   Ventral posterolateral VPM   Ventral posteromedial  VT   Vehicle-treated WB   Western blot WHP   Woodchuck hepatitis virus Wnt   Wingless-related integration site WPRE  WHP post-transcriptional regulatory element WT   Healthy control hiPSC line  xxvii  Acknowledgements I conducted this research and wrote this dissertation on the unceded traditional ancestral territories of the Coast Salish peoples, including the Qayqayt (the only First Nation without a land base), the xʷməθkʷəy̓əm (Musqueam), the skwxwú7mesh (Squamish) and the səl̓ilwətaɁɬ (Tsleil-Waututh). As a Canadian decedent of white colonial settlers, I acknowledge the historical and ongoing injustices against indigenous people and am committed to the lifelong practices of decolonization and reconciliation.   I offer my tremendous gratitude to my supervisor Dr. Haakon Nygaard for his incredible support, guidance, and generosity throughout my graduate studies. I am grateful for the trust he had in me to establish his new lab's scientific foundation. His encouragement, thoughtful feedback, and belief in my abilities helped me develop the resilience required to face major challenges I encountered throughout my graduate studies. I thank my committee member Dr. Michel Roberge, whose frequent collaborative and insightful discussions greatly improved the work presented in this thesis. I would also like to thank my current and former committee members, Dr. Stephanie Willerth, Dr. Robin Hsiung, and Dr. Christian Naus, for their invaluable guidance.  I also thank the Nygaard lab members, past and present, who created a lab environment that nurtured my scientific curiosity and contributed to my ultimate success in accomplishing my research goals. In no particular order, thank you: Tyler Yan, Dr. Brianne Kent, Dr. Xiajuan Wu, Julia Boyle, Katina Mak, Hannah Pae, Chris Lee, Ariel Frame, Clara Dutton-Kneaves, Meghan Chen, Kiana Yau, and Adrienne Kinman. Many xxviii  thanks also to past and present Roberge lab members, especially to Dr. Aruna Balgi, Dr. Alireza Baradaran-Heravi, and Dr. Kunho Choi.   Thank you to the Weston Brain Institute, who provided funds for the research presented in this thesis. I would also like to thank the Canadian Institute for Health Research for providing salary support through the Canada Graduate Scholarships – Master’s program.   Special thanks are owed to my family, especially to my parents Mark and Debbie Frew, who have always believed in me. I was so lucky to have you both so close by for emotional support and encouragement throughout all the successes and failures that defined this journey. Last but certainly not least, I would like to also thank my wife, Madison Galts, for her unconditional love and support, cheering me on every step of the way.    xxix  Dedication I dedicate this thesis to my wife Madison for the endless sacrifices she happily made to support me throughout this challenging endeavor, and to my late grandpa Roy whose battle with Alzheimer’s disease inspired me to pursue graduate studies in the field of neurodegeneration.   1  Chapter 1: An introduction to frontotemporal lobar degeneration, progranulin neurobiology, and premature termination codon readthrough  1.1 Frontotemporal lobar degeneration Frontotemporal lobar degeneration (FTLD) is the underlying pathology uniting a clinically, genetically, and pathologically heterogeneous group of disorders that primarily affect the frontal, temporal, and parietal lobes. FTLD causes a spectrum of clinical presentations of frontotemporal dementia (FTD), including progressive changes in behaviour, personality, executive function, and language. 75-80% of FTD patient symptomatic onset occurs before age 65, and FTLD has an incidence of 10-30 per 100,000 individuals aged 45-65 years old (1). FTLD is the 2nd most common cause of early-onset dementia (2). There are currently no approved therapies that can stop or alter the progression of this disease. Symptomatic management with selective serotonin reuptake inhibitors and other antipsychotics represents the only available form of pharmacological intervention for FTD patients (3).  1.1.1 History of FTLD Pathology resembling FTLD has been clinically described for over a century; however, it was often misdiagnosed as Alzheimer’s disease (AD) or other psychiatric disorders (4). Arnold Pick was first to characterize a now rare form of FTLD, Pick’s disease, diagnosed post-mortem pathologically by the observation of neuronal ballooning (Pick 2  cells) and intraneuronal argentophilic inclusion bodies (Pick bodies) in the absence of AD plaques/tangles (5-7). In the early 1980s, American neurologists believed it was essentially impossible to distinguish between Pick’s disease and AD using either clinical or radiological measures (8). Meanwhile, neurologists in Europe had observed a behavioural phenotype not classically associated with AD and developed a clinical rating scale to differentiate between AD and Pick’s disease / ‘frontal degeneration of non-Alzheimer’s type’ (9,10). It was later discovered that many FTLD cases in America had been misdiagnosed as AD, likely due to a lack of awareness of its distinct clinical presentation (11). In 1994, European clinicians published a consensus report on the clinical and neuropathological criteria for FTLD; thus, solidifying its recognition as a separate condition from AD dementia (2). More recently, advances in DNA sequencing, neuropathological indicators, and radiographic technologies have further revealed the complex clinical heterogeneity underlying FTLD.  1.1.2 Clinical presentations of FTD There are three main clinical subtypes of FTD: behavioural variant (bvFTD), semantic variant primary progressive aphasia (svPPA), and non-fluent variant progressive non-fluent aphasia (nfvPPA). Few cases present in a relatively pure form, with most patients developing overlapping syndromes throughout disease progression. bvFTD is characterized by atrophy of the frontal, anterior temporal, and lateral parietal lobes resulting in various degrees of social disinhibition, loss of sympathy/empathy, and increased apathy (12). svPPA is characterized by a consistent asymmetric atrophy pattern in the anterior temporal lobe leading to an inability to access conceptual 3  knowledge (12). nfvPPA is characterized primarily by atrophy of the left hemisphere, disrupting smooth speech articulation, and grammatical proficiency (12). Fluorodeoxyglucose positron emission tomography imaging measuring glucose uptake in FTLD patients’ brains has identified deficits in cerebral glucose metabolism as an early marker of disease progression (13). Further, 15% of patients with FTLD express comorbidity in the form of motor neuron disease (14,15), resembling amyotrophic lateral sclerosis (ALS), highlighting the significant overlap of genetic, clinical, and pathological characteristics shared by these two disorders (16). In general, the prognosis for FTLD patients is poor, leading to death within 3-10 years following diagnosis (17).  1.1.3 Neuropathology of FTLD Post mortem analysis of clinically diagnosed FTLD patients’ brains has led to the identification of four major types of abnormal aggregated protein accumulation in neurons and glia. Approximately 45% of clinically diagnosed FTLD cases develop neuronal intracytoplasmic inclusions (NCI) that are composed of the microtubule-associated protein tau (FTLD-tau) (18). FTLD-tau can be further divided into two subtypes, with the hallmark either being round tau-positive Pick bodies observed in Pick’s disease or neurofibrillary tangle-like structures observed in corticobasal syndrome and progressive supranuclear palsy (19). Tau-negative FTLD cases were initially classified as dementia lacking distinctive histopathology (DLDH) (20), though it was later discovered that the majority of these DLDH cases possessed ubiquitin-positive inclusions (21,22).   4  A few years later, the elusive ubiquitinated protein that constitutes the aggregates in about 50% of FTLD cases was discovered to be the RNA/DNA binding protein TAR DNA-binding protein 43 (TDP-43) (23,24). TDP-43 aggregates can appear as neuronal cytoplasmic inclusions (NCI), neuronal intranuclear inclusions (NII), and dystrophic neurites (DN) in the cortices of FTLD patients (FTLD-TDP). The ratio and prevalence of these different TDP-43 aggregates distinguish FTLD-TDP type A-D sub-classifications (25). Subtype A cases have a near-equal ratio of NCI and DN; in type B, NCI predominates over DN; type C is applied when DN predominates over NCI, and type D when NII is the most common form of TDP-43 pathology. The discovery that chromosome 9 open reading frame 72 (C9orf72) hexanucleotide expansion mutations cause the majority of familial FTLD cases has led to the identification of distinct histopathological hallmarks. In addition to TDP-43 pathology, these patients develop sense and antisense C9orf72 expanded repeat RNA foci (26), and translation of the hexanucleotide expansion derived mRNA results in the cytoplasmic accumulation of dipeptide repeat proteins (27). The remaining 5% of FTLD patient brains accumulate protein inclusions (NCI and sometimes NII) consisting of Fused in Sarcoma (FUS) protein and sometimes other members of the FET (FUS, EWS, and TAF15) family of proteins (FTLD-FUS) (28).   1.1.4 Genetics of FTLD An estimated 40% of FTLD cases are familial, with patients often presenting with a history of similar diseases within their family (29). Furthermore, a clear autosomal dominant inheritance pattern has been observed in ~10% of cases, thus indicating 5  genetics play a key role in disease pathogenesis (29). Certain FTD clinical phenotypes exhibit differential inheritance patterns; for example, svPPA is rarely familial, while bvFTD can be either familial or sporadic in nature (29). The three most prevalent genes confirmed to cause familial FTLD are MAPT, GRN, and C9orf72. There are 44 known pathogenic MAPT mutations, causing between 5-20% of familial FTLD cases (30,31). There are two main types of MAPT mutations: 1) mutations that disrupt splicing of exon 10 that result in an increased ratio of 4R:3R tau isoforms (32) that lead to accumulation of 4R insoluble tau aggregates forming neurofibrillary tangles; 2) missense mutations throughout the gene that reduce the ability of all tau isoforms to bind to microtubules, increasing the pool of unbound tau accelerating 3R/4R tau aggregation into Pick bodies (33). After identifying MAPT mutations on chromosome 17q21, there were still numerous FTLD cases that had been linked to 17q21 but were null for mutations in MAPT (34). Subsequently, loss-of-function (LOF) mutations in GRN were discovered in these patients within a 6.2 Mb segment of 17q21 that also contained the MAPT locus (35,36). Approximately 5-20% of familial FTLD cases are caused by GRN haploinsufficiency (FTLD-GRN) (37). Most heterozygous pathogenic GRN mutations lead to a > 50% loss in progranulin protein (PGRN) levels/function leading to disease through haploinsufficiency (38).   In the years following the identification of causal FTLD-GRN mutations, there was still a significant proportion of FTLD patients that exhibited clear autosomal dominant pattern of inheritance with unknown genetic origin. In 2011, researchers identified the GGGGCC hexanucleotide repeat expansion in the non-coding region of the C9orf72 6  gene as a key driver of familial FTLD and ALS (39,40). The majority (~25%) of familial FTLD cases are caused by C9orf72 hexanucleotide expansions (41), with patients carrying 100-1000 repeats compared to 2-20 repeats in healthy control populations (38). It has been demonstrated that transcripts bearing the GGGGCC repeat sequences can be translated through an unconventional repeat-associated non-ATG initiated form of translation, which results in the accumulation of dipeptide repeats (27). The mechanism driving neurodegeneration in C9orf72 repeat expansion carriers is still up for debate, with findings from numerous disease models supporting both LOF and gain-of-function (GOF) pathogenic processes (42,43). Interestingly, mutations in TARDBP (TDP43) are rarely associated with FTLD-TDP pathology (19). Meanwhile, several rare mutations in genes associated with autophagolysosomal pathways (CHMP2B, VCP, SQSTM1, TBK1) have been shown to cause a small minority of FTLD-TDP cases (44-47). This suggests that disrupted proteolytic mechanisms play a major role in the establishment of FTLD-TDP pathology. Lastly, most FTLD-FUS cases appear to lack clear genetic origin and are believed to be sporadic in nature (19).   1.1.5 FTLD caused by PGRN haploinsufficiency As discussed in section 1.1.4, heterozygous mutations in GRN on chromosome 17q21 cause a familial form of FTLD. Going forward, we will refer to symptomatic GRN haploinsufficient mutation carriers as having FTLD-GRN and will refer to models of GRN deficiency as FTLD-GRN models. All pathogenic GRN mutations have either been confirmed or are predicted to produce a LOF allele (48). Of the known 79 known pathogenic GRN mutations, ~84% are either nonsense or frameshift mutations that 7  introduce premature termination codons (PTCs) (49-51). However, less common missense and deletion mutations have also been identified that can: disrupt mRNA maturation leading to nuclear mRNA degradation (52); prevent initiation of protein translation at the start codon (53); destroy the signal peptide sequence critical for protein secretion (54); and, eliminate key cysteine residues that do not decrease total protein/mRNA levels but cause impaired protein function and processing into granulin peptides (GRNs) (55).   FTLD-GRN has a variable age of onset, ranging from 35-89 years of age. This presents a significant challenge for designing clinical trials since even family members bearing the same GRN mutation can develop symptoms at significantly different ages (56). Extrapolating the incidence of FTLD (see section 1.1) using the proportion of FTLD patients bearing GRN mutations (~4%) implies a global incidence of 0.5-1.5 FTLD-GRN cases per 100,000 people (36,57). This finding, along with the lack of clinical correlation between age of onset and PGRN plasma/cerebrospinal fluid (CSF) concentration (58), implies that other factors such as disease modulating genetic variants or environmental conditions may play a role in determining age of onset. The vast majority of FTLD-GRN patients express 70-80% less serum PGRN than control subjects (59). These patient PGRN levels are lower than expected, given the heterozygous LOF nature of FTLD-GRN mutations. Reprogramming FTLD-GRN patient fibroblasts that express < 50% GRN mRNA levels compared to healthy control cells into human induced pluripotent stem cells (hiPSCs) increased GRN mRNA back to the expected 50% level (60). Pluripotent reprogramming resets a differentiated cell’s epigenetic signature; therefore, 8  suggesting that epigenetic mechanisms may be responsible for the additional basal suppression of PGRN expression in FTLD-GRN mutation carriers.   1.1.6 Genetic modifiers of FTLD-GRN A host of genetic elements have been associated with the age of onset and disease progression in FTLD-GRN. The majority of these factors are either known to influence lysosomal function, are involved in the regulation of GRN expression, or participate in direct protein-protein interactions with PGRN (61). Most of these genetic markers have been identified through genome-wide association studies (GWAS); thus, it is important to recognize the limitations of interpreting these disease-associated risk loci. The original variant or single nucleotide polymorphism (SNP) identified by a GWAS is rarely confirmed to be the true causal variant resulting in the molecular modification that confers greater disease risk (62); this is because there are usually 10s-100s of variants in strong linkage disequilibrium with the sentinel SNP at the specified genetic locus, representing a set of co-inherited variants or haplotypes. There is the potential for any of these co-inherited variants to be the true underlying cause of altered disease risk. It is also important to consider that the risk-haplotype can often span multiple genes, further complicating the identification of the gene to which a certain GWAS signal belongs.  TMEM106B is a single-pass integral membrane glycoprotein localized to late endosomes and lysosomes and is important for regulating lysosomal size, motility, and responsiveness to stress (63). TMEM106B and PGRN have both been shown to co-localize in the endolysosomal compartment in various cell types (64).  9  SNPs in TMEM106B have been shown to have protective effects on FTLD-GRN disease progression (65,66). The minor allele of the non-coding TMEM106B SNP rs1990662 has been detected at a low frequency in FTLD-GRN patients compared to healthy controls, suggesting GRN mutation carriers expressing the minor allele may exhibit delayed symptomatic onset (65,66). Further, the frontal cortices of FTLD-TDP patients and unaffected individuals carrying the major allele exhibit significantly elevated TMEM106B mRNA levels compared to those with the minor allele (65). Remarkably, the age of onset was delayed by an average of 13 years in FTLD-GRN patients homozygous for the rs1990662 “protective” TMEM106B allele (67). These patients were also found to possess significantly higher plasma PGRN levels than those homozygous for the “risk” allele, possibly explaining their slower disease progression (67).   More recently, TMEM106B SNP rs1990620, an additional non-coding “risk” allele, has been identified in complete linkage disequilibrium with the sentinel SNP (rs1990622) that functionally increases recruitment of the chromatin-organizing protein CTCF to downstream regulatory sequences of the TMEM106B locus, positively regulating transcription levels (68). The “protective” allele of the lone TMEM106B coding region SNP rs3173615 or p.T185S (also in linkage disequilibrium with rs1990662) has been shown to impart faster protein turnover, resulting in an overall decrease in TMEM106B expression (64). Together these findings suggest that these “risk” alleles confer genetic susceptibility through increased TMEM106B gene expression or GOF mechanism. Finally, independent of TMEM106B SNPs, FTLD-GRN patients exhibit reduced levels (< 50%) of the TMEM106B targeting miRNA-312 cluster members (miRNA-132, miRNA-10  132*, miRNA-212) compared to controls, resulting in the derepression of TMEM106B expression (69), further strengthening the hypothesis that reducing TMEM106B expression may be beneficial in FTLD-GRN patients (70).  The first GWAS study to search for genetic modulators of CSF PGRN levels identified a SNP (rs708384) in another gene encoding a transmembrane protein, FAM171A2, for which the minor allele (A allele) was significantly linked to lower CSF PGRN levels in a dose-dependent manner (71). FAM171A2 is highly expressed in cerebral vascular endothelium and microglia in the mouse brain (71). HEK293 cells transfected with the minor allele exhibited higher FAM171A2 expression levels compared to the major allele (71). Overexpression of FAM171A2 in human umbilical vein endothelial cells decreased PGRN expression and secretion, and siRNA knock-down of FAM171A2 significantly increased PGRN expression (71). Little is known about the function of the single-pass type I membrane protein FAM171A2; therefore, the precise mechanisms underlying its regulation of PGRN expression are currently unclear (71).  The discovery of genetic variability within the GRN allele itself has led to the identification of novel mechanisms that modify GRN expression levels. In particular, the minor T-allele rs5848, a SNP in the 3’ untranslated region (UTR) of GRN, has been shown to affect the predicted binding site of miRNA-659 (72). The presence of the minor T-allele enhances the binding affinity of miRNA-659, thus expediting the rate of GRN mRNA turnover (72). Homozygous carriers of rs5848 exhibit decreased serum and CSF PGRN levels (58,72,73), though there is mixed evidence correlating this genotype with an increased risk of developing non-GRN linked FTLD-TDP (74). Moreover, FTLD-GRN 11  patients with the common R493X GRN mutation carrying the A-allele of SNP rs9897526 found 21 bp downstream of the GRN intron 2 splice donor site of their intact allele exhibit delayed disease progression (75). Though the precise mechanism for this delay is currently unclear, its proximity to the splice site suggests it may alter the maturation and stability of GRN mRNA. Additional non-coding regions of the GRN allele have also been implicated in regulating GRN expression, including the methylation state of the GRN promoter which is inversely correlated with GRN expression in lymphoblasts and post-mortem brain tissue derived from FTLD patients (76,77). Expression of DNA methyltransferase 3a (DNMT3a) mRNA is upregulated in the brain tissue of FTLD-TDP patients compared to controls and thus may be responsible for hypermethylation of the GRN locus (76). Also, overexpressing DNMT3a in lymphoblasts resulted in decreased GRN expression, which could be reversed through treatment with a DNMT inhibitor (76). Improving the understanding of the epigenetic regulation of GRN expression may lead to the identification of novel therapeutic targets.  Several proteins are known to interact directly with PGRN, which mainly function to regulate its trafficking and cellular localization. Sortilin (SORT1) is a type I membrane glycoprotein and high-affinity neuronal receptor for PGRN, mediating PGRN endocytosis and delivery to the lysosome, therefore regulating extracellular PGRN concentrations (78). Sort1-/- knockout (KO) mice exhibit elevated (2.5-5X) brain and serum levels of PGRN (78). The minor C-allele SORT1 SNP (rs646776) is associated with decreased serum PGRN levels, with each allele copy generating a subsequent ~15% decrease, though it is unlikely that this SNP influences CNS PGRN levels since it 12  primarily alters hepatic SORT1 expression levels (79). Prosaposin (PSAP), another protein that interacts with PGRN, is a precursor protein that is localized to the lysosome, where it is processed into saposin (SAP) activators that are critical for glycosphingolipid degradation (80). Further, PSAP facilitates the SORT1-independent delivery of extracellular PGRN to lysosomes, made evident by the 5X increase in serum PGRN levels in Psap-/- mice (81). At a genetic level, more copies of the PSAP minor T-allele SNP (rs1867977) were correlated with decreased plasma PGRN levels in healthy controls (82). Additional PGRN binding partners have been identified with roles regulating extracellular PGRN levels, including members of the endoplasmic reticulum (ER) chaperone network, such as calreticulin and disulfide isomerases ERp57 and ERp5 (83). These factors likely play a key role in orchestrating the PGRN folding process by forming several disulfide bonds throughout the cysteine-rich polypeptide.  1.1.7 Clinical and neuropathological phenotypes of FTLD-GRN and CLN11 FTLD-GRN includes a wide range of clinical presentations, including bvFTD, nfvPPA, svPPA, Parkinson’s disease-like syndromes such as corticobasal syndrome, and an amnestic disorder resembling AD (84). The most common clinical presentation in FTLD-GRN patients is bvFTD, though there is also a high prevalence of nfvPPA (35,85). Clinical symptoms of bvFTD in FTLD-GRN cases commonly include behavioural disinhibition and increased apathy (35), while nfvPPA symptoms include effortful inconsistent speech and agrammatism (86). Extrapyramidal motor dysfunction is rare in FTLD-GRN but occurs with high prevalence in particular families beginning with muscular rigidity and akinesia, eventually progressing to an inability to walk (35,87). 13  Generally, disease duration ranges from 3 to 12 years (84). The common neuropathological hallmarks in FTLD-GRN include global atrophy of the frontal, temporal, and, in some cases, the parietal lobes (85), hypometabolism of frontotemporal cortices (88), significant white matter degeneration (89), FTLD-TDP type A pathology in neocortical layer II (90,91), microgliosis (92), and pathological features associated neuronal ceroid lipofuscinosis (NCL) including elevated expression of lysosomal enzymes (93). Interestingly, only the unaffected FTLD-GRN post-mortem brain regions show a clear reduction in PGRN protein levels compared to healthy control samples, whereas atrophied regions show similar PGRN levels to controls (94). The elevated PGRN in diseased brain regions may be derived from infiltrating microglial populations, known to secrete high levels of PGRN.   The growing interest in understanding the contribution of lysosomal dysfunction to FTLD-GRN disease progression stems from the recent discovery of a rare form of NCL caused by homozygous GRN LOF mutations, CLN11 (95). Two GRN-null siblings were the first identified cases of CLN11, presenting with early adulthood-onset NCL, developing progressive retinal dystrophy, cognitive decline, cerebellar ataxia, and recurrent myoclonic seizures. Eleven CLN11 cases have now been identified, exhibiting a range of early- to late-onset phenotypes (96). The first neuropathological characterization of an early-onset case (died age 27) found severe cerebellar atrophy, numerous lipofuscin deposits in hippocampal and temporal cortical neurons, and early signs of cytoplasmic translocation of TDP-43 with a lack of classic FTLD-GRN inclusions (96). Therefore, these findings demonstrate that GRN-mutation dosage 14  strongly impacts the severity and age of disease onset and suggest that FTLD-GRN may neuropathologically resemble a mild form of NCL (95).  1.2 PGRN neurobiology In a quest to characterize novel granulocyte peptides with unknown immunoregulatory functions, Bateman et al. discovered several GRNs in a minor subfraction of cysteine-rich peptides purified from human leukocyte extracts (97). Key sequences of these approximately 6 kDa cysteine-rich peptides are highly conserved between species suggesting a long evolutionary history. Phylogenetic analysis of the GRN motif suggests it evolved only once ~1.5 billion years ago in a primordial unicellular eukaryote predating the divergence of the plant and animal kingdoms (98). These GRNs are believed to have played a role in early cell signaling mechanisms, predating the evolution of classical growth factor pathways such as Wnt, Hedgehog, and TGF-β (99,100). Given PGRNs ancient evolutionary origin, it is not surprising that it is a key player in a diverse array of biological phenomena, including proliferation (101), wound healing (102), immunoregulation (103), embryogenesis (104,105), neurodegeneration (35,92), and autophagy-lysosomal function (106,107). The identification of GRNs in such a variety of biological contexts resulted in an equally divergent nomenclature; therefore, PGRN (108) is known synonymously as granulin-epithelin precursor (109), proepithelin (110), PC cell-derived growth factor (111), acrogranin (112), and epithelial transforming growth factor (113).   15  1.2.1 PGRN structure  The human progranulin gene is located on chromosome 17q21 and consists of 12 coding exons (114). Full-length PGRN is an 88 kDa multifunctional secreted glycoprotein made up of 7.5 cysteine-rich repeat units known as GRN modules (para-GRN & GRN1-7) separated by short intervening spacer/linker sequences and an N-terminal 17 amino acid signal peptide for secretion (111). Post-translational glycosylation of PGRN contributes 20 kDa to the 68 kDa 593 amino acid polypeptide. It is a member of the cysteine-rich mini protein family, which are generally known to function as hormones, growth factors, ion channel modulators, or enzyme inhibitors. As its name suggests, PGRN is a pro-protein, which cleavage gives rise to individual 6 kDa GRNs. The highly conserved GRN modules consist of 4 pairs of cysteines plus 2 additional cysteine residues at each amino/carboxyl-terminal (CX5-6 CX5CCX8CCX6CC XDXXHCCPX4CX5-6C) for a total of 12 cysteines, except for GRN-1 and para-GRN, which possess 10 and 6 cysteine residues, respectively. Though no tertiary structures have been established for full-length PGRN, some of the GRNs (GRN-2, -4, and -5) have been crystallographically solved, identifying that these cysteine residues significantly contribute to PGRNs rigid peptide backbone. The globular structure of individual GRNs is composed of a core of 6 disulfide bridges forming a parallel stack of 4 beta-hairpins that twists through a left-handed super-helix (115,116).   1.2.2 PGRN expression in the brain  During early murine embryonic neurodevelopment (E15.5), Grn expression is limited to small cell populations throughout the developing brain, often associated with 16  neurovasculature and epithelial populations (117). Neuronal Grn expression gradually increases from E15.5 to P7, though it does not appear to be critical for neocortical development since immature neurons migrating to the cortical plate (E15.5) lack Pgrn immunoreactivity (117). Post-mitotic mature cortical neurons begin to show progranulin positivity at P0, which increases into adulthood (117). Brightly Pgrn immunoreactive Iba1+ amoeboid microglia are also scattered throughout the embryonic and postnatal mouse brain from E15.5 to P14, often localized along developing white matter tracts (117). In adult mice, Pgrn is expressed widely throughout the neocortex and hippocampus, with immunoreactivity observed most prominently in large pyramidal cells in cortical layers V/VI and the CA3 hippocampal region (117). Moderate Pgrn expression is also observed in the thalamus, hypothalamus, amygdala, and midbrain, with little to no expression in the striatum and brain stem (117). Additionally, only the large Purkinje neurons of the cerebellum are positive for Pgrn staining. Interestingly, this Pgrn expression is achieved despite a lack of a neuronal Grn expression observed throughout the adult cerebellum, possibly indicating that Purkinje cell Pgrn may be derived from distal brain regions (117).   Intracellularly, PGRN is primarily localized to lysosomal-associated membrane protein 1 (LAMP1) positive early lysosomes, the Golgi apparatus, and in vesicles immediately adjacent to and partially overlapping with Ras-related protein Rab7+ late endosomes (78,92). Recent findings suggest that once transported to the lysosome, full-length PGRN undergoes rapid proteolysis into stable GRNs (118). Given that most anti-PGRN antibodies also detect a subset of GRNs, it is likely that a significant proportion of 17  intracellular PGRN immunoreactivity likely represents cleaved GRNs.   Histological characterization of CNS cell type-specific Pgrn expression patterns has shown that both neurons and microglia express Pgrn, though relative staining intensity is much greater in microglia (117). GFAP-positive astrocytes, on the other hand, have been shown to exhibit no Pgrn immunoreactivity in the adult mouse brain (117). Nevertheless, subsequent western blot analysis of astrocyte- and neuron-enriched whole mouse brain lysate fractions and single-nuclei RNA-sequencing (snRNA-seq) of Grn+/+ mouse thalami have both observed similar baseline Pgrn/Grn expression levels in both astrocyte and neuronal populations (119,120). Moreover, cultured primary human astrocytes (121) and our own hiPSC-derived astrocytes (122) have both been shown to express and secrete PGRN; thus, suggesting that astrocyte Pgrn expression in the adult mouse brain may have been below the threshold of histological detection in the previous study (117).   Conditional neuronal- and microglia-specific Grn KO mouse models have further delineated individual cell types' contributions to total brain Pgrn expression levels. A conditional neuronal floxed Grn KO mouse achieved through Nestin promoter-driven Cre recombinase expression resulted in a 50% reduction in CNS Pgrn and no detectable Pgrn in primary neuronal cultures, implying that approximately half of mouse CNS Pgrn originates in neurons (123,124). The initial attempts to generate conditional-microglia Grn KO mice, on the other hand, proved more difficult with primary microglia cultures and isolated adult microglia only exhibiting a 50% decrease in Grn mRNA/Pgrn 18  expression (125-128). However, a subsequent study using the tamoxifen-inducible Cre-estrogen receptor (CreER) fusion protein KO system driven by the microglial promoter Cx3Cr1 achieved a 95% reduction in isolated adult microglial Grn mRNA expression and a 26% decrease in overall brain Pgrn levels (129). Thus, suggesting that microglia produce approximately a quarter of total CNS Pgrn, despite representing only 10% of mouse brain cells (130); therefore, the remaining unaccounted for ~25% of CNS Pgrn expression is likely collectively produced by astrocytes, endothelial cells, and oligodendrocytes (120).   1.2.3 PGRN regulation in the brain  Mature neurons are post-mitotic and dependent on a high basal rate of autophagy compared to non-neuronal cells since toxic metabolites and misfolded proteins cannot be diluted through serial cell division. Transcription factor EB (TFEB) is a master regulator of autophagy mediating the activation of the coordinated lysosomal expression and regulation (CLEAR) gene network resulting in increased lysosomal biogenesis and expression of lysosomal enzymes (131). The GRN gene possesses two TFEB binding sites upstream of its coding sequence (131,132); therefore, GRN expression can be upregulated by activation of TFEB (132,133). Inhibiting the key negative regulator of autophagy, mTORC1, which functions to maintain TFEBs cytosolic localization (134), increases PGRN expression in several cell lines, though importantly not in neuronal cell types (135). Activating autophagy with the disaccharide trehalose through a mTORC1-independent mechanism has been shown to increase GRN expression in hiPSC-derived neurons in a partially TFEB-dependent manner (135).  19   Additionally, a genome-wide RNAi screen performed in the Neuro2A (N2a) mouse neuroblastoma cell line identified that several genes regulating GRN expression were enriched for autophagy-lysosomal pathways (ALPs) involved in both transcriptional and post-transcriptional mechanisms (136). For example, when expression of the autophagy regulator Foxo1 transcription factor was suppressed, Pgrn levels were increased by 1.7-fold in N2a cells (136). Moreover, siRNA knockdown of Foxo1 in primary mouse cortical neurons increased both Grn expression and Pgrn secretion, and simultaneous siRNA knockdown of both Foxo1 and Grn prevented the accumulation of enlarged lysosomal vesicles observed following siRNA-mediated Grn knockdown alone (136). The opposing effects of TFEB and FOXO1 ALP transcription factor activation on the regulation of Grn expression highlights the complex role PGRN plays in regulating lysosomal biology, which will be explored further in the following sections.   Microglia constantly survey the brain parenchyma for damaged or unnecessary neurons and synapses, infectious agents, and abnormal chemical stimuli. The GRN gene is highly expressed in the myeloid lineage and is strongly upregulated in response to brain and spinal cord injury (117,137). The GRN promoter region also contains several CCAAT-enhancer-binding protein β (C/EBPβ) response elements (138). The C/EBPβ transcription factor is commonly activated by the action of upstream pro-inflammatory cytokines such as IL-6, known to induce GRN expression (139,140). The vitamin A1 metabolite all-trans retinoic acid (ATRA) has also been shown to induce upregulation of GRN mRNA expression, specifically in cells of myeloid origin (141). Though the GRN 20  allele lacks a canonical retinoic acid response element in its promoter, ATRA may activate downstream transcription factors capable of upregulating GRN transcription (141). Interestingly, treating primary human fetal microglia cultures with pro-inflammatory cytokines (IL-1β + IFNγ) and endotoxins (LPS, Poly I:C) was shown to significantly suppress GRN/PGRN expression at the transcript and protein level (121). Additionally, this study also demonstrated an opposing phenomenon in primary human fetal astrocyte cultures, which despite lower baseline PGRN levels, significantly upregulated GRN/PGRN expression in response to stimulation with either IL-1β + IFNγ or Poly I:C (121). LPS treatment was omitted because human astrocytes lack TLR4 co-receptor CD14 expression necessary for LPS-induced TLR4 activation (142). Differential expression of alternative splice variants has also been implicated in the regulation of GRN expression. Alternatively spliced GRN transcripts harboring a long 5’UTR sequence (219 nucleotides) containing two upstream open reading frames (ORFs) exhibit translational repression and lower mRNA stability compared to transcripts bearing short 5’UTRs (38-93 nucleotides) that lack upstream ORFs (143).  Upon GRN mRNA translation and translocation into the ER, PGRN is post-translationally processed. Here, PGRN interacts with ER chaperones to ensure correct protein folding through disulfide bond formation and undergoes regulated glycosylation (144,145), which is essential for its sorting through the secretory pathway (146). After transit through the trans-Golgi network, PGRN is either secreted into the extracellular environment (147) or localized to the endolysosomal network via SORT1-dependent or SORT1-independent transport mechanisms (78,81,148). Once secreted, full-length 21  PGRN can also undergo reuptake or be taken up by neighboring cells resulting in lysosomal delivery; therefore, the relative abundance of endocytic PGRN receptors (SORT1, LRP1, M6PR) in the plasma membrane plays a key role in regulating the levels of intracellular PGRN/GRNs (78,81,148). Lysosomal PGRN can be cleaved into individual GRNs by the lysosomal protease cathepsin L (CTSL) and at least one additional unknown lysosomal enzyme that may be activated by cathepsin B (CTSB) (149,150). As previously discussed in section 1.1.6, extracellular PGRN has been shown to interact with another pro-protein, PSAP, which promotes PGRN homodimer and oligomer formation and regulates the extracellular levels of PGRN (82). The ratio of secreted full-length PGRN to individual GRNs is regulated by the secretory leukocyte protease inhibitor (SLPI) (103). SLPI forms a complex with full-length PGRN preventing its conversion into GRNs by extracellular proteases (e.g., elastase, metalloprotease ADAMTS-7, proteinase 3), which functions to promote an anti-inflammatory and wound healing response (103). SLPI is upregulated by neurons and astrocytes in response to either neurological damage or stimulation with pro-inflammatory cytokines (121,151) and, therefore, may function to regulate PGRN biology in the brains of FTLD-GRN patients.    22                         Figure 1-1 Brain regulation of extracellular PGRN proteolysis. Upon detecting cellular damage/pathogen associated molecular patterns, microglia secrete proinflammatory cytokines into the extracellular space. This induces upregulation and secretion of SLPI by neurons and astrocytes. Microglia secrete the majority of extracellular PGRN, which can be degraded into GRNs by extracellular proteases (elastase, ADAMST-7, proteinase 3), however, neuron/astrocyte-derived SLPI can bind to PGRN and protect it from proteolysis into GRNs, enhancing PGRNs anti-inflammatory function.    23  As highlighted in section 1.1.6, genetic variance in TMEM106B has been identified as a major modifier of FTLD-GRN disease progression (66). The TMEM106B type-II transmembrane protein is highly expressed in neurons and is localized to the endolysosomal compartment, where it controls the size, number, motility, and trafficking of lysosomes in both neuronal and non-neuronal cell types (63,152,153). Overexpression of TMEM106B in neurons has been shown to induce lysosomal dysfunction resulting in enlarged vacuolar lysosomes with impaired acidification and a reduced endocytic degradative capacity (63,152,154). Contrary to the GOF risk hypothesis proposed based on SNP data, excess Tmem106b in N2a cells has been shown to cause intra- and extracellular accumulation of PGRN (152). Further, exogenously delivered TMEM106B expression in primary cortical mouse neurons significantly increased TFEB nuclear localization activating expression of the CLEAR gene network, providing a potential mechanism for TMEM106B-dependent positive regulation of CNS PGRN expression (63).   Nevertheless, recent in vivo evidence from Tmem106b KO and overexpression studies in the context of Grn-deficiency suggest that both resulted in detrimental consequences to disease progression (155-158), therefore complicating exploration into the potential therapeutic benefits of disrupting TMEM106B function. Another transmembrane protein, FAM171A2, expressed in murine cerebral vascular endothelial cells and microglia, has recently been demonstrated to regulate CSF PGRN levels (71). FAM171A2 overexpression and knockdown induced suppression and increased levels of PGRN, respectively, indicating an inverse proportional relationship between FAM171A2 and 24  PGRN expression levels (71). Therefore, the mechanisms driving FAM171A2-mediated regulation of CSF PGRN levels are currently under active investigation.  1.2.4 Mouse models of Grn-deficiency  Over the past 15 years, significant progress has been made characterizing the role of PGRN in the CNS through the use of Grn KO mouse models. Although FTLD-GRN is caused by GRN haploinsufficiency, Grn+/- mouse models have not replicated the majority of the pathological hallmarks observed in this variant of FTLD-TDP (159). Therefore, most studies have focused on models bearing homozygous deletion of Grn expression (Grn-/-), which better recapitulate FTLD-GRN pathological progression (92,93,106,107,159-164) but would be more accurately described as a model of the rare form of NCL (CLN11) caused by homozygous LOF GRN mutations. The characterization of Grn-/- mice has uncovered that PGRN is an essential regulator of neuroinflammation, autophagy, and synaptic pruning in the CNS.  1.2.4.1 Neuroinflammation Microgliosis is a hallmark of FTLD-GRN, in which the affected brain regions are populated with increased numbers of hyperactivated microglia with thick processes and an enlarged soma. Therefore, major research efforts have sought to better understand the role of PGRN in regulating inflammatory processes. Cultured Grn-/- and GrnR493X/R493X macrophages and microglia express and secrete elevated pro-inflammatory cytokines in response to treatment with inflammatory mediators, likely due to their suppressed levels of Il-10 expression and exaggerated NF-κB activation 25  (125,129,161). These excessive pro-inflammatory phenotypes can be acutely rescued through exogenous delivery of murine Grn (125,165). Extraordinarily, Grn-/- microglia stimulated with LPS + IFNγ were found to secrete elevated levels of Il-10 into the culture medium, despite lower levels of Il-10 mRNA, reflecting differential regulation at the transcriptional and secretory levels (125). Nevertheless, increased Il-10 secretion was insufficient to reduce the increased pro-inflammatory state observed in Grn-/- microglia, possibly indicating that Grn-/- microglia are less responsive to the anti-inflammatory action of Il-10 signaling (125). Treatment of Grn+/+ rat primary cortical neurons with human PGRN increased expression and secretion of cytokines/chemokines associated with chemoattraction, including Il-10 (166). Grn-/- hippocampal slices are significantly more sensitive to microglia-mediated neurotoxicity than Grn+/+; however, this phenotype can be replicated in Grn+/+ slices by inhibiting Il-10 function (161). These findings highlight PGRNs essential role in suppressing hyperinflammatory immune responses.  Pgrn-deficient microglia and macrophages overexpress and secrete excessive quantities of TNFα (125,161). Several reports have suggested that Pgrn mediates its anti-inflammatory effects by extracellularly disrupting TNFα signaling through direct inhibition of its plasma membrane receptors (TNFR1/2) (167,168); however, the veracity of this direct binding hypothesis has been challenged (169-171). Whether PGRN directly modulates TNFα signaling through TNFR1/2 binding competition or an unknown indirect mechanism, several studies have clearly established that PGRN and the multi-GRN derivative Atsttrin negatively regulate TNFα expression and function (167,172-174). Conditioned media obtained from activated (LPS + IFNγ) primary Grn-/- microglia 26  induced a greater increase in cell death in Grn+/+ primary cortical neurons than media derived from Grn+/+ microglia, suggesting that activated Grn-deficient microglia may secrete neurotoxic factors (125). A recent publication by the Huang lab further elucidated this process, establishing that elevated levels of complement proteins (C1qa and C3b) in primary Grn-/- microglia conditioned media (MCM) are at least partially responsible for increased primary cortical neuronal death compared to Grn+/+ MCM (120). Since inhibition of membrane attack complex (MAC) formation completely blocked Grn-/- MCM-induced neurotoxicity, it is likely that the additional toxicity promoting factors in Grn-/- MCM may be downstream complement pathway components involved in MAC assembly (120).  Modelling complete loss of Pgrn in vivo consistently results in significant astro- and microgliosis established as early as 7 months of age, which then rapidly accelerates throughout the aging process (159,161,162,164,165). The most neuroinflammation-prone regions in Grn-/- mouse brain include the cerebral cortex, CA3 hippocampal region, and ventral posteromedial (VPM)/ventral posterolateral (VPL) thalamic nuclei. Furthermore, a region of cortical layer IV in Grn-/- mice (S1BF) innervated by the highly pathologically vulnerable VPM/VPL thalamic nuclei has also been shown to exhibit increased microgliosis (164). Interestingly, a recent study examining differentially expressed genes in primary Grn-/- microglia identified significant enrichment for the overexpression of cell cycle-related genes, suggestive of an increased proliferative capacity in line with the observed microgliosis phenotype (175). The VPM/VPL regions of the thalamus in aged Grn-/- mice have also been shown to accumulate deposits of the 27  complement proteins C1qa and C3b, which when disrupted (Grn-/-;C1qa-/- and Grn-/-;C1qa-/-;C3-/- mice) partially reduces the severity of thalamic microgliosis (92,120). Grn-/- microglia also exhibit impaired motility as evidenced by their decreased chemotaxis towards ADP/ATP gradients and limited process extensions/retractions observed at baseline and post-laser-induced injury (129). The loss of Pgrn has also been shown to increase the sensitivity of Grn-/- mice to both chemically- and physically-induced CNS damage resulting in exaggerated neuroinflammation and increased neurotoxicity compared to Grn+/+ (125,176). Grn-/- mice acutely infected with Listeria monocytogenes (L. monocytogenes) mount a dysfunctional innate immune response that fails to efficiently clear the bacterial burden in various organs (106,161).  The previously held notion that microglia only exist in the binary categorization of either resting or activated (M1 vs. M2) has been disputed by transcriptomic analyses, which have identified greater biological complexity in the form of several unique homeostatic and disease-associated microglia (DAM) gene expression signatures (177). Several studies have transcriptomically characterized aged Grn-/- brains identifying upregulated genes related to innate immunity, including several cytotoxic factors (92,107,164). Additionally, the aforementioned snRNA-seq study of microdissected Grn+/+ and Grn-/- thalami identified drastic and dynamic microglia-specific transcriptional changes throughout disease progression, characterized by downregulation of homeostatic genes and overexpression of genes associated with inflammation, lysosomal function, and neurodegeneration (120). Moreover, a similar 11 gene DAM signature emerged following quantification of differentially expressed genes in Grn+/+ and Grn-/- primary 28  microglia cultures, including the downregulation of the homeostatic genes Tgfbr1 and Csf1r (175). Intriguingly, conditionally depleting either neuronal or microglia Grn expression fails to replicate any of the major neuropathological hallmarks observed in Grn-/- mice. This may be because only partial microglial Grn KO (LysM promoter-driven) was achieved compared to nearly complete penetrance in conditional neuronal KO models (123,124,127,128). However, a recent effort achieved a more robust depletion of Grn expression using the tamoxifen-inducible CreER system driven by the microglial-specific Cx3Cr1 promoter and observed behavioural deficits in aged mice resembling Grn-/- phenotypes (129). Cumulatively, these findings suggest that PGRN plays a major role in suppressing aberrant microglial activation throughout the aging process.  1.2.4.2 Lysosomal dysfunction Since the identification and characterization of CLN11, a rare form of NCL caused by homozygous GRN mutations, there has been growing research interest in uncovering the role of PGRN in lysosomal function. Lysosomal abnormalities are among the first observable phenotypes in Grn-/-, developing months before chronic hyperinflammation and microgliosis (107,119,120,178). 3 month old Grn-/- hippocampal neurons exhibit increased lysosomal size and abundance, often presenting with lamellar pseudomembranous inclusions characteristic of NCL (107). Transcriptomic and proteomic analysis of 2 month old Grn-/- mice cerebral cortex identified significant upregulation of several key lysosomal enzymes (Hexb, Tpp1, Ctsb, Ctsl, Dpp7) (179). Lipofuscin accumulation, a hallmark of NCL, commonly observed in neuropathological hot spots of aged Grn-/- brains (159,163-165), has been observed in the thalamus of 2 29  month old Grn-/- mice (179). Moreover, 2-3 month old Grn-/- mice exhibit major deficiency in xenophagy (ability to clear intracellular pathogens) following intravenous infection with L. monocytogenes, with increased bacterial burdens detected in the brain, liver, and spleen in Grn-/- mice 1 week post-infection (106,161). Lipidomic analysis of 2-3 month old Grn-/- brains has detected decreased levels of both di-18:1 and di-22:6 bis(monoacylglycerol)phosphates, lipid species known to stimulate lysosomal hydrolase activity important for lysosomal sphingolipid degradation (Denali Therapeutics, Alzheimer’s Association International Conference 2020). However, these studies failed to identify which specific cell populations are most responsible for driving lysosomal dysfunction.   Following the discovery that aged Grn-/- mice brains exhibit elevated levels of NCL related proteins, such as SapD (PSAP peptide product), cathepsin D (Ctsd), Lamp1, Tmem106b, and subunit C of mitochondrial ATP synthase (93), the Capell lab sought to determine whether a particular CNS cell type plays an outsized role in the establishment of these lysosomal pathologies. Western blot analysis of whole-brain lysates derived from aged 20 month old Grn-/- mice found an increase in the maturation rate of cathepsin enzymes (Ctsd, Ctsb, and Ctsl), resulting in increased enzyme activity that is absent in 3 month old Grn-/- mice (119). However, characterizing microglial enriched lysate fractions from young Grn-/- brains revealed decreased cathepsin maturation levels, indicated by the accumulation of the pro-forms of Ctsd, Ctsb, Ctsl, and Ctss, not observed in Grn+/+ microglial lysates (119). Furthermore, these young Grn-/- derived microglial enriched fractions also possessed increased lysosomal proteins Lamp1 and 30  SapD. On the other hand, the microglial depleted fractions produced from young Grn-/- and Grn+/+ express similar levels of the pro- and mature-forms of cathepsins and exhibit no increase in Lamp1 or SapD (119). Strikingly, throughout the aging process (3 months to 12 months), dysregulation of Ctsd and Ctsb maturation patterns appeared to be partially normalized in Grn-/- microglia, while non-microglial cells compensated for the early decreased degradative capacity of microglia by increasing their respective Ctsd enzyme activity (119). Therefore, providing evidence supporting microglia as the primary drivers of the early lysosomal pathology in Grn-/- mice. These results are supported by several CNS cell type-specific transcriptomic analyses suggesting that microglia-specific transcriptomic signatures in Pgrn-deficient brains exhibit the highest degree of differential gene expression, transitioning from a homeostatic to disease state characterized by significant endolysosomal dysfunction (92,106,120).   The development of FTLD-TDP type A pathology in FTLD-GRN patients is thought to be caused by an inability to proteolytically process nuclear and cytoplasmic aggregated TDP-43 granules. Significant research efforts have been conducted to explore PGRNs role in regulating the autophagolysosomal pathway to better understand this pathological hallmark. Grn-deficient mice have been shown to accumulate neuronal cytoplasmic inclusions of both TDP-43 and the ubiquitin-binding autophagosome cargo protein p62, most notably in the thalamus and hippocampus (93,120,161,164,165). This selective vulnerability was elegantly demonstrated by infecting both Grn+/+ and Grn-/- primary cortical neurons with an adeno-associated virus (AAV) vector expressing the aggregation-prone C-terminal fragment (CTF) of TDP-43. This resulted in an increase in 31  TDP-43 CTF levels in Grn-/- neurons that could be rescued by recombinant (rec.) Pgrn treatment and phenotypically replicated in Grn+/+ neurons by inhibiting autophagosome degradation (106). Activation of autophagy by serum/amino acid starvation in primary Grn-/- microglia and cortical neuron cultures has been used to further highlight their propensity for overexpression of lysosomal genes/proteins (180) and impaired autophagosome clearance (106), both of which could also be reversed through exogenous delivery of rec. Pgrn. Grn-/- primary cortical neurons and Grn-/- cortical tissue have been found to express reduced levels of phosphorylated 5’ AMP-activated protein kinase alpha, a key positive regulator of autophagy; therefore, PGRN may positively regulate upstream autophagolysosomal signaling pathways (106). Together these findings suggest that impaired autophagy caused by PGRN deficiency plays a central role in TDP-43 pathology.  1.2.4.3 Dysregulated lipid metabolism Lipidomic analysis of the frontal cortices of aged (12 month old) Grn-/- mice identified the accumulation of polyunsaturated triacylglycerides (TAGs) and cholesterol esters (CEs), accompanied by a corresponding reduction in diacylglycerides (DAGs) and phosphatidylserines of increasing chain length and number of unsaturated bonds (107). Thus, suggesting that PGRN/GRNs are involved in the regulation of long-chained polyunsaturated fatty acid metabolism. This hypothesis is further supported by the observed Grn-/- specific transcriptomic differential downregulation of DAG-specific lipid hydrolases, providing a potential mechanism for PGRN-dependent positive regulation of the enzymatic conversion of phosphatidic acid into DAGs (107). Long polyunsaturated 32  TAG-rich lipid-droplets (LDs) are produced in cells of myeloid origin in response to inflammation and stress; intriguingly, a recent study identified GRN as a primary negative regulator of LD formation (181). Additionally, they found that 9-10 month old Grn-/- mice hippocampi contain increased levels of LD-accumulating microglia, a process previously identified in a Drosophila model of neurodegeneration (182). Grn-/- LD-rich microglia exhibited decreased phagocytic activity and secreted elevated levels of pro-inflammatory cytokines following LPS stimulation compared to LD-low Grn-/- microglia. Since lysosomal dysfunction precedes the establishment of pro-inflammatory phenotypes in Grn-/- brains and LDs are known sites of cytokine production and storage (183), altered lipid metabolism caused by GRN deficiency may prime microglia for hyperinflammation throughout the aging process.   Huang et al. recently conducted whole-brain proteomic network analysis in 3 and 19 month old Grn+/+ and Grn-/- mice. This unbiased quantitative proteomic analysis replicated previously described early lysosomal dysfunction phenotypes (179), detecting overexpression of lysosomal proteins (Gns, Scarb2, Hexb, Ctss); however, they also observed a substantial subset of lysosomal proteins that exhibited decreased expression (178). A significant proportion of the most downregulated proteins identified in 3 month old Grn-/- pooled brain lysates were enriched for proteins involved in lysosomal lipid catabolism, with functions ranging from regulation of lipogenesis and lipid homeostasis to enzymatic roles in lipid degradation pathways (178). The most significantly elevated protein in the aged Grn-/- cohort was the transmembrane type I glycoprotein Gpnmb (178), which exhibits diverse cellular functions and has been found 33  to exhibit increased expression in several neurodegenerative diseases (184). CNS Gpnmb expression was primarily observed in Iba1+ microglia and was most prominent in the thalamus of 19 month old Grn-/- mice (178). Though it is unclear whether Gpnmb plays a direct role in Grn-/- pathophysiology, results demonstrating that Gpnmb is upregulated in the murine CNS in response to direct inhibition of the lysosomal hydrolase glucocerebrosidase (GCase) suggest that it may be elevated in Grn-/- brains in response to lysosomal dysfunction (185). Moreover, this hypothesis is further strengthened by findings that Pgrn directly regulates GCase lysosomal localization and enzymatic activity levels (186,187). Interestingly, microglia expressing elevated levels of Gpnmb have been implicated in the demyelination process in multiple sclerosis (188), potentially explaining the significant decrease in myelin basic protein levels found in the aged Grn-/- brain (178), providing another plausible link between lysosomal dysfunction and the onset of chronic inflammation. Once again, the early establishment of lysosomal dysfunction was shown to precede the onset of neuroinflammatory processes, suggesting that disruptions to lysosomal lipid metabolism may represent a key instigating factor driving neurodegenerative processes in FTLD-GRN.   1.2.4.4 Neural connectivity deficits and neurodegeneration Microglia play a pivotal role in modulating neural networks during neurodevelopment and aging through a process known as synaptic pruning, by which microglia trogocytose (selective partial phagocytosis) the membranes of presynaptic boutons and axons (189). The disruption of microglial immunoregulation in the CNS of mouse models of Grn deficiency has profound downstream consequences on the neural activity of the 34  thalamocortical circuit, which may drive behavioural abnormalities (92). Electrophysiological recordings of hippocampal slice cultures have demonstrated reduced synaptic connectivity in Grn-/- mice, likely due to impaired synaptic plasticity resulting in an overall depression of activity (163). Additionally, the Leavitt laboratory also showed that the apical dendritic arbors of hippocampal CA1 region pyramidal neurons showed significantly lower spine density in Grn-/- compared to Grn+/+ (163). Grn-deficient primary microglia co-cultured with Grn+/+ primary cortical neurons engulfed higher levels of C1qa-tagged synapses resulting in lower synaptic density surrounding Grn-/- microglia (92). Grn-/- mice also exhibited decreased synaptic density in the ventral thalamus, which was first detected at 7 months of age and continues to decrease throughout the aging process (92). The rescue of synaptic loss in double Grn-/-;C1qa-/- and triple Grn-/-;C1qa-/-;C3-/- KO mice demonstrated that complement-mediated microglial synaptic pruning is responsible for this observed Grn-/--specific decrease in synaptic density (92,120).   These neurological aberrancies drive behavioural defects in both Grn+/- and Grn-/- mice (160,162,163,190). Two of the most well-characterized Grn-/- behavioural abnormalities include a chronic grooming phenotype resembling a form of obsessive-compulsive disorder (OCD) that results in an increased incidence of skin lesions and a male-specific increase in anxiety (92,160,163,165). Remarkably, the C1qa-dependent synaptic pruning in Grn-/- VPM/VPL thalamic nuclei has been shown to selectively target inhibitory synapses for elimination (92). The loss of inhibitory synapses in the thalamocortical circuit in Grn-/- mice results in electrophysiological hyperexcitability in 35  thalamic slice cultures, which may in part be responsible for their excessive grooming phenotype (92). Incredibly, both the hyperexcitability and chronic grooming Grn-/- phenotypes can be rescued by C1qa deletion (92).   Given the association of increased plasma TNFα levels in OCD patients (191) and the growing consensus that PGRN negatively regulates TNFα signaling, researchers sought to demonstrate the impact of Tnfα deficiency on the Grn-/- OCD phenotype (129). Since the cortico-basal ganglia circuit in the nucleus accumbens (NA) of ventral striatum has also been implicated in OCD patients (192), electrophysiological brain slice recordings were performed on the medium spiny neurons (MSNs) in the core of the NA, identifying a similar hyperexcitability phenotype (129). Extraordinarily, both hetero- and homozygous deletion of Tnfα rescued both the chronic grooming and NA MSNs hyperexcitability Grn-/- phenotypes (129). However, both Grn-/-;Tnfα+/- and Grn-/-;Tnfα-/- mice still possess defects in social behavioural observed in Grn-/-  mice, suggesting TNFα may only play an important role in the regulation of the neural circuits associated with compulsive behaviours (129). As mentioned in section 1.2.4.1, Krabbe et al. also observed this OCD-like chronic grooming phenotype in 8-10 month old tamoxifen-induced microglia-specific Grn KO mice, suggesting loss of microglial Pgrn may be sufficient to disrupt neural circuitry (129). Ikbkb encodes the inhibitor of NF-κB subunit beta required for NF-κB activation and therefore regulates the transcription factor responsible for upregulating inflammatory cytokines, including TNFα. To further evaluate the contribution of microglial-induced neuroinflammation to Grn-/- pathophysiology, they also generated the less penetrant (LysM promoter-driven) Cre/lox 36  microglial-specific KO mouse model targeting both Grnfl/fl and Ikbkbfl/fl (129). Despite only achieving an ~50% reduction in adult Cd11b+ microglia Grn mRNA levels, this LysM-Grnfl/fl mouse model exhibited both OCD and social behavioural abnormalities, that were rescued by simultaneous microglia-specific KO of Ikbkb (LysM-Grnfl/fl;Ikbkbfl/fl) (129). Thus, suggesting that the increased propensity for NF-κB activation in Grn-/- microglia (193) is at least partially responsible for their hyperinflammatory phenotype, which results in the overexpression of pro-inflammatory cytokines, including TNFα that drives the OCD phenotype.  Neurodegeneration in Grn-/- has been shown to occur primarily in the VPM/VPL thalamic nuclei, and therefore may also contribute to the development of behavioural phenotypes (120,164). Interestingly, 19 month old Grn-/- thalamic snRNA-seq transcriptomes exhibited a strikingly lower quantity of nuclei expressing cell type-specific markers associated with excitatory neurons and a modest increase in the number of inhibitory neurons (120). Immunohistochemical verification of these findings confirmed that the loss of excitatory neurons could be detected by Pkcδ and Foxp2 staining in Grn-/- thalamus in both 12 and 19 month old Grn-/- mice (120). 19 month old Grn-/- thalamic Foxp2+ neurons were found surrounded by microglia containing intracellular Foxp2+ debris suggestive of microglial-mediated neurotoxicity and phagocytic clearance of dying excitatory neurons (120). The selective vulnerability of Grn-/- excitatory primary cortical neurons to Grn-/- MCM compared to Grn-/- GABAergic primary cortical neurons supports these findings (120). Extraordinarily, Grn-/-;C1qa-/-;C3-/- mice have near-complete protection of thalamic Pkcδ+ excitatory neurons, further signifying the 37  importance of complement-mediated neurodegenerative mechanisms in FTLD-GRN. Though the loss of VPM/VPL inhibitory synapses is apparent in 8,12, and 19 month old Grn-/- mice, the electrophysiological hyperexcitability phenotype was only assessed at 12 months old (92); therefore, it is possible that the hyperexcitability phenotype may be less prominent in 19 month old Grn-/- mice due to the continued neurodegeneration of thalamic Pkcδ+ and Foxp2+ excitatory neurons between 12 and 19 months of age (120). Furthermore, the increase in the number of thalamic nuclei expressing inhibitory neuron markers in Grn-/- mice from 12 to 19 months of age may represent a compensatory mechanism due to complement-mediated inhibitory synaptic pruning (92,120).  1.2.5 hiPSC-derived CNS models of GRN-deficiency Though rodent models have been essential for uncovering the CNS functions of Pgrn, one must be careful when directly applying these findings to the clinical manifestation of FTLD-GRN. The inability to translate vast amounts of data obtained in preclinical therapeutic interventions in AD mouse models into viable disease-modifying agents provides reason to be cautious projecting murine pathogenic mechanisms onto human disease (194). Until recently, post-mortem analysis was the primary option for studying human neurobiology; however, in 2007, the Yamanaka group developed a technology that could achieve human adult somatic cell reprogramming into hiPSCs (195), unlocking the potential to generate human cell types from any genetic background. Subsequently, researchers around the world worked to establish hiPSC differentiation protocols for a variety of cell types, including those present in CNS tissue such as 38  neurons, astrocytes, and microglia (196-198). To date, our group and several others have generated hiPSC lines from symptomatic and presymptomatic carriers of haploinsufficient GRN mutations and differentiated them into CNS cell types for FTLD-GRN disease modelling and preclinical drug development (60,122,135,199,200).  The first FTLD-GRN hiPSC line was generated from fibroblasts obtained from a patient carrying the heterozygous p.S116X mutation (designated S116X+/-) and was successfully differentiated into neurons and microglia (60). S116X+/- hiPSC-derived neurons expressed and secreted reduced levels of PGRN, exhibited increased sensitivity to the broad-spectrum kinase inhibitor staurosporine, and expressed decreased levels of the ribosomal Ser/Thr kinase S6K2 involved in PI3K/PKB and MAPK signaling pathways. Importantly, these latter two phenotypes could be rescued by lentiviral delivery of GRN expression (60). Another study generated hiPSC lines from three different FTLD-GRN patients carrying the same GRN IVS1+5G>C splice donor site mutation (199). Differentiation of healthy control and FTLD-GRN splice donor mutant hiPSC lines into cortical neurons uncovered that these GRN-deficient lines expressed significantly lower levels of cortical neuron markers (CTIP2, TBR1, FOXG1) at days in vitro (DIV) 40 compared to healthy control neurons. This inefficient cortical neuron maturation phenotype was corrected by genetically inserting GRN cDNA into the AAVS1 safe harbor locus of one of the FTLD-GRN lines (199). However, more recent studies, including those published by our lab using other cortical neuron differentiation methods, have failed to observe this defect in several FTLD-GRN hiPSC lines, including a homozygous knock-in GRN p.R493X mutant line (122,200,201). These findings 39  suggest that GRN haploinsufficiency does not disrupt all pathways required for inducing robust cortical neuron differentiation and that a more efficient differentiation technique may have been required to obtain similar differentiation efficiency across their healthy control and FTLD-GRN lines.  Valdez et al. generated an FTLD-GRN patient hiPSC line bearing the p.A9D signal peptide disrupting mutation that blocks PGRN post-translational glycosylation and secretion in order to assess lysosomal defects in patient-derived cortical neurons (54,200). Subsequently, they corrected this heterozygous GRN mutation using CRISPR/Cas9 gene editing to produce an isogenic control hiPSC line in order to eliminate any potential phenotypic contributions from disparate genetic backgrounds between the isogenic control and FTLD-GRN line. Aged GRN+/- hiPSC-derived cortical neurons exhibited decreased lysosomal proteolysis, resulting in the accumulation of intracellular electron-dense lipofuscin deposits and increased TDP-43 expression (200). This study also assessed CTSD enzyme maturation levels in both isogenic control and mutant hiPSC-derived cortical neurons. Both 35 and 100 DIV GRN+/- neurons exhibited increased levels of mature CTSD; notably, the ratio of mature to immature CTSD was significantly increased in the aged GRN+/- neurons (200). However, CTSD enzyme activity normalized to mature CTSD expression levels were significantly lower in both 35 and 100 DIV GRN+/- hiPSC-derived cortical neurons (200). Though not demonstrated in hiPSC-derived neurons, this study also added to the growing consensus suggesting that PGRN and CTSD are binding partners and that PGRN’s C-terminus and/or GRN-7 may promote CTSD maturation/activity (202,203). This finding is counterintuitive given the 40  increased levels of CTSD maturation frequently observed in the context of GRN-deficiency, although it is possible that the impact of general lysosomal dysfunction on CTSD maturation outweighs the effects of limited PGRN chaperone activity.  FTLD-GRN patient hiPSC-derived CNS tissue provides an invaluable resource for the preclinical development of new therapeutics aimed at elevating GRN/PGRN expression levels. For example, neurons derived from the S116X+/- hiPSC line have been used for the in vitro validation of the SORT1 antagonist 2-methyl-6-(phenylethynyl)-pyridine, which induced accumulation of extracellular PGRN in cell culture medium (204). As we will discuss in section 1.2.7, a SORT1 targeting approach using the AL001 anti-SORT1 antibody has recently begun phase 3 clinical trials for FTLD-GRN, highlighting the importance of preclinical validation in hiPSC models. Additionally, treatment of S116X+/- hiPSC-derived cortical neurons with suberoylanilide hydroxamic acid, a histone deacetylase inhibitor previously shown to upregulate GRN expression through epigenetic modification (205), has been shown to significantly increase intra- and extracellular PGRN expression from the intact allele (201). Another group, studying the therapeutic potential of the disaccharide trehalose, generated hiPSC lines from a healthy control and FTLD-GRN patient carrying the GRN p.R198GfsX19 mutation (135). They demonstrated that p.R198GfsX19 mutant hiPSC-derived neurons express slightly elevated levels of the LC3-II autophagosome marker compared to control neurons. Treatment of p.R198GfsX19 mutant hiPSC-derived neurons with the autophagy activator trehalose increased intracellular PGRN expression but further increased the levels of LC3-II (135). In chapter 4, we will describe studies we conducted in our lab 41  using novel GRN nonsense mutant hiPSC lines demonstrating the therapeutic potential of nonsense mutation readthrough drugs for the treatment of FTLD-GRN (122).  1.2.6 Proposed mechanisms of neurodegeneration in FTLD-GRN  The multifunctional nature of PGRN has complicated the elucidation of the key biological mechanisms driving FTLD-GRN pathophysiology. The pathological cascade resulting in FTLD-GRN symptomatic onset is multi-decade in nature, involving both biochemical and cellular phases that precede the clinical manifestation of FTLD-GRN (206,207). Drawing heavily upon the discoveries made in Grn-/- mice, it is likely that microglial lysosomal dysfunction is a key initial step in the disease process, preceding the establishment of neuroinflammation and gliosis (179). Götzl et al. elegantly demonstrated that disrupted microglial lysosomal function in Grn-/- mice is one of the earliest pathological events. Interestingly, the lysosomal dysfunction phenotype was not observed in non-microglial populations until the latter stages of disease progression. This may reflect both the heavy proteolytic strain associated with constantly sampling their extracellular microenvironment and the fact that microglia express the most PGRN in the brain on a per-cell basis (see section 1.2.2). The role of PGRN/GRNs in the regulation of lysosomal biology is multifaceted, with functions including activation of lysosomal proteases (119,202,208) and glycolipid hydrolases (186,187), promotion of lysosomal acidification (180), and the homeostatic maintenance of lysosomal morphology and biogenesis (93,107,178).   42  As discussed in section 1.2.4.3, GRN-deficiency has been increasingly linked to dysfunctional microglial lipid metabolism, as evidenced by abnormal accumulation of TAG and CE lipid species and LDs (107,181). These findings, combined with the mounting evidence that PGRN is a key regulator of autophagy (106,131,209), provide a potential mechanistic link to the eventual establishment of the pro-inflammatory DAM phenotype through immunometabolic disruption. Immunometabolism is a cellular process that regulates the way immune cells respond to environmental stimuli through the flexible reprogramming of metabolic pathways (210). Microglial metabolic plasticity is increasingly understood as a central node that controls the distinct states of microglial homeostasis and activation. For example, homeostatic microglia preferentially metabolize glucose through oxidative phosphorylation, while DAM are primarily dependent on glycolysis to fuel their pro-inflammatory activities (reviewed here (210,211)). Remarkably, transcriptomic analysis of LD-accumulating microglia isolated from 9 month old Grn-/- mice hippocampi were found to be hyperglycolytic, exhibiting significant disruption of metabolic pathways, including the TCA cycle and lipid metabolism (181). The loss of microglial PGRN/GRNs may disrupt metabolic flexibility, limiting the ability of microglia to revert back to a homeostatic state following initial pro-inflammatory activation (212). However, it is still unclear whether disturbances to Grn-/- microglial energetic pathways are a result of early lysosomal dysfunction or are an additional independent phenotype caused by the loss of multifunctional PGRN/GRNs. Regardless, the mechanisms driving dysfunctional microglial immunometabolism in FTLD-GRN warrant further investigation. 43  Neuroinflammation is a prominent feature of FTLD-GRN, with severe microgliosis observed in pathologically affected brain regions. Highly reactive pro-inflammatory microglia with enlarged somas and thick processes are the central drivers of FTLD-GRN pathogenesis. GRN-deficient DAM exhibit a transcriptomic signature unique to FTLD-GRN neurodegeneration, characterized by suppression of homeostatic microglial genes (Tgfbr1, Mef2c, P2ry12, etc.) and upregulation of microglial neurodegeneration-associated genes (Apoe, Csf1, Clec7a, etc.) (120,212). These activated DAM secrete elevated levels of pro-inflammatory mediators into the surrounding brain parenchyma, including complement cascade proteins C1QA and C3. Complement proteins have been shown to accumulate in the frontal cortices of FTLD-GRN patients and have also been detected at heightened levels in their CSF. Interestingly, the levels of complement proteins C1QA and C3B in FTLD-GRN patient CSF are negatively correlated with mini-mental status exam score, in which lower scores indicate greater cognitive decline (92). The Huang group’s research has strongly implicated these complement proteins in FTLD-GRN pathogenesis, identifying several mechanisms linking neuroinflammation to neurodegeneration (92,120). These include both selective targeting of inhibitory synapses for complement-mediated microglial synaptic pruning (92) and the formation of complement MAC on the excitatory neuronal cell surface that induces TDP-43 cytoplasmic translocation and neuronal cell death (120). Clinical validation of these disease processes discovered in mouse models has been obtained through an fMRI study on asymptomatic/prodromal GRN mutation carriers compared to healthy controls. This study identified enhanced connectivity across four major neural networks (salience, non-fluent variant primary progressive aphasia, perirolandic, and default mode), with the 44  unifying feature being thalamocortical hyperconnectivity (213), mirroring complement-mediated phenotypic observations in aged Grn-/- mice.  Examining the relationship between PGRN and the FTLD-GRN risk factor TMEM106B is essential for developing a comprehensive understanding of the basis of neuronal lysosomal dysfunction in FTLD-GRN. Neuronal TMEM106B lysosomal functions include maintaining lysosomal acidity through positive regulation of V-ATPase activity and regulating axonal transport of lysosomes (179,214). Current evidence suggests that TMEM106B risk alleles accelerate FTLD-GRN pathology through a GOF mechanism (see section 1.1.6). Overexpression of TMEM106B driven by a neuron-specific promoter in aged Grn+/+ mice identified tight regulation of TMEM106B protein levels, which exhibited no increase despite a several-fold increase in TMEM106B mRNA (155). However, TMEM106B overexpression in aged Grn-/- mice resulted in a 50% increase in TMEM106B levels compared to normal aged Grn-/- mice, providing further evidence that PGRN is involved in homeostatic negative regulation of TMEM106B levels (155). Overexpression of TMEM106B in aged Grn-/- mice accelerated lysosomal dysfunction in these mice (155), thus providing additional support for the GOF TMEM106B risk allele hypothesis. On the contrary, several recent publications have demonstrated that deletion of Tmem106b in a Grn KO background also exacerbates Grn-/- pathology (156,157,215). A more clinically relevant double heterozygous KO model (Grn+/-;Tmem106b+/-) was generated to assess whether a partial reduction in Tmem106b levels may rescue Grn+/- phenotypes, but this only normalized the activity of a single lysosomal enzyme (β-glucuronidase) (216). The current consensus suggests that 45  cortical neurons are particularly susceptible to excess or limited TMEM106B in the context of GRN-deficiency, and that tight spatiotemporal regulation of TMEM106B in neurons is required for neuronal lysosomal function.  As mentioned above, neuronal lysosomal dysfunction has been shown to develop in aged Grn-/- mice further along the pathological progression (119). It has been speculated that neurons may compensate for early decreased microglial autophagic capacity; although, it is also possible that microglia-derived secreted neuroinflammatory factors exacerbate this neuronal phenotype (120) or that neuronal autophagy is more resilient to the effects of GRN haploinsufficiency. Ultimately, disrupted neuronal proteolysis contributes to the major neuropathological hallmark of ubiquitin- and TDP-43-positive NCI and DN subtype A pathology in neocortical layer II of the frontal and temporal lobes of FTLD-GRN patients (90,91). As previously discussed in section 1.1.7, the neuropathological hot spots in FTLD-GRN patient brains exhibit greater GRN mRNA/PGRN levels than would be expected for a haploinsufficient condition (94). This is likely a consequence of severe microgliosis in the affected regions, given that activated microglia are known to upregulate GRN expression in response to pathological insults (137,217). However, it appears that the levels of upregulated microglial-derived GRN expression are insufficient to result in any meaningful impact on FTLD-GRN neurodegeneration.   In aged Grn-/- mice, delivery of AAV-Grn expression vectors to the medial prefrontal cortex (mPFC) increased neuronal Pgrn levels to 10X more than Grn+/+ baseline mPFC 46  expression levels (218). Despite only inducing a minor increase in neuronal Grn/Pgrn expression in the epicenter of Grn-/- pathology (thalamic VPM/VPL), exogenous delivery of Pgrn was capable of reducing thalamic microgliosis and lysosomal dysfunction 8-10 weeks post-viral injection (218). Importantly, this finding demonstrates that increasing neuronal Pgrn expression, even in the latter stages of disease progression, can disrupt neuropathology associated with Grn-deficiency. Given the multi-decade progression of FTLD-GRN neuropathology, it is possible that increased microglial GRN expression derived from the normal allele occurs too late in the disease process to provide therapeutic benefit or that the microglia-derived PGRN fails to reach the threshold concentration required for clinical improvement. It is currently unknown why particular brain regions are sparred, and others are vulnerable to the neurodegenerative effects of GRN haploinsufficiency, although neuroimaging studies have shed light on the earliest functional and metabolic brain changes observed in the presymptomatic stages of FTLD-GRN, which generally precedes grey/white matter atrophy (219). The pattern of disrupted glucose metabolism and altered network activity expands topographically from anterior to posterior as the disease progresses. The most consistent abnormalities are initially observed in medial/dorsal prefrontal and fronto-insular regions mapping onto the salience network, which plays key roles in social-emotional processing (219). Further exploration of the complex immunometabolic regulatory interactions between microglia and neurons/astrocytes may provide insights into the neuropathological basis for the selective vulnerability observed in these brain regions (210).  47  1.2.7 Therapeutic development for the treatment of FTLD-GRN There are currently no disease-modifying therapies that can slow down or reverse the progression of FTLD-GRN. The therapeutic efforts explored to date have aimed to increase GRN expression from the intact allele (135,201,205,220), increase PGRN’s extracellular half-life (204), and restore PGRN through exogenous delivery (218,221). Thus far, the proposed therapies have attempted to upregulate GRN/PGRN expression levels by alkalizing lysosomes to decrease lysosomal turnover of PGRN (222), calcium channel blockade (223), promoting the acetylation state of the GRN allele by modulating epigenetic regulation through deacetylase inhibition (201,205,220), disrupting the SORT1-PGRN axis to prevent the endocytosis and extend extracellular bioavailability of PGRN (204), activating autophagy in an mTOR- and TFEB independent manner (135), or directly delivering GRN to the CNS (218,221). Though several of these mechanisms have been tested clinically, only the anti-SORT1 antibody AL001 (Alector, INFRONT-3) and AAV GRN gene therapies PR006 (Prevail Therapeutics, PROCLAIM) and PBFT02 (Passage Bio Inc., upliFT-D) have currently demonstrated clinical potential (224-226).   Recent phase I/IIb clinical trial results presented at the 2020 Alzheimer’s Association International Conference showed that short- (single dose 60 mg/kb, 12 days, asymptomatic) and extended-treatment (3X 30 mg/kg, 4 weeks, symptomatic) of FTLD-GRN patients with the Alector’s AL001 human monoclonal anti-SORT1 antibody was well tolerated and significantly restored plasma and CSF PGRN levels to normal levels. PGRN CSF levels in 8 symptomatic FTLD-GRN patients remained in the normal range 8 weeks after receiving the final of the three doses, and extended treatment rescued 48  several pathological CSF biomarkers of lysosomal dysfunction (CTSB), neuroinflammation (osteopontin), and gliosis (chitotriosidase). These findings have initiated the development of a phase III clinical study (INFRONT-3) to assess the impact of AL001 on FTLD-GRN pathological progression. Symptom management is currently the only clinical option available to FTLD-GRN patients. Some patients expressing the behavioural variant of FTLD-GRN have been shown to respond positively to serotonin reuptake inhibitors and antipsychotic medications. For example, bvFTD symptoms such as irritability, agitation, and depression are improved by treatment with the serotonergic compound trazodone in a double-blind placebo-controlled crossover trial (227). There is a clear need for more research and preclinical development into novel therapies capable of treating or preventing FTLD-GRN.  1.3 Premature termination codon readthrough Nonsense mutations change an amino acid codon to a termination codon (UAG, UAA (228), or UGA (229)), resulting in the production of a truncated protein and mRNA destabilization (230). PTC readthrough is a process that suppresses nonsense mutations through the pairing of a near-cognate aminoacyl-tRNA at a PTC, allowing for the incorporation of an amino acid instead of termination, leading to translation of the full-length protein and increased nonsense mutant mRNA stability (Figure 1-2) (230-233). Under normal conditions, PTC readthrough occurs at a rate of ~1% of translation events (234,235), while suppression of natural stop codons occurs at a frequency of ≤ 0.1% (236,237). The rationale for the observed discrepancy between these rates is two-fold; the surrounding mRNA sequence context has been under evolutionary pressure to 49  select for efficient termination at natural stop codons (238-240), and the stabilization effect imparted by the proximity of stop codons to the poly(A) binding protein bound to the 3’ poly(A) tail which enables interaction with release factor (RF) eRF3 to enhance termination of translation (241,242).   Over the past several decades, significant efforts have been made to identify compounds that are capable of increasing the rate of PTC readthrough as a means to restore expression from nonsense mutant alleles back to normal levels for therapeutic gain. To date, many PTC readthrough-inducing drugs has been identified, developed, and tested clinically; the most common include aminoglycosides (natural (243,244) and synthetic derivatives (245-247)), negamycin analogs (248,249), and non-aminoglycoside compounds such as ataluren (formally known as PTC124) (250,251). Still, common concerns often raised against research into PTC readthrough as a disease-modifying therapy include the potential for negative impact on global translation efficiency and whether these efforts would increase suppression of normal stop codons at the end of ORFs. Failing to terminate translation at stop codons would significantly increase misfolded proteins due to C-terminal extensions, inevitably inducing the unfolded protein response. Such a response would be expected to cause upregulation of the inducible form of heat shock protein 70 (Hsp70) (252), however, treating fibroblasts with a high concentration of readthrough drugs only slightly increased Hsp70 expression (253) and had no impact on overall translation rates (254,255). On the contrary, results from a recent global ribosomal profiling study treating HEK293 cells with high concentrations (0.5 mg/mL) of aminoglycosides, observed increased ribosome 50  density within 3’UTRs in samples treated with G418 and paromomycin. This finding is indicative of readthrough of natural stop codons, highlighting the need to identify aminoglycoside readthrough enhancer compounds that may lower the concentration of aminoglycosides required to induce PTC readthrough (256).   According to a recent analysis of the Orphanet database (257), 3.5-5.9% of the human population is affected by rare genetic diseases, and of that, ~11% of all genetic disorders are caused by single base substitutions leading to the introduction of an in-frame PTC (258); thus, the potentially addressable patient population for PTC readthrough treatment is substantial. In the past 20 years, there have been numerous clinical trials conducted testing candidate PTC readthrough drugs in nonsense mutation bearing Duchenne muscular dystrophy (DMD) (244,251,259) and cystic fibrosis (CF) (260-263) patients. Though these trials have resulted in the approval of ataluren (known commercially as Translarna™) to treat children with DMD by the European Medicines Agency (264), the drug only provides marginal clinical benefit to a subset of nonsense mutation carriers. The success of previous clinical studies testing PTC readthrough drugs has been limited by low readthrough efficiencies (0.5-20% increase) failing to reach the therapeutic threshold required for meaningful disease-modification (265) and significant toxicity associated with the long-term treatment required to delay and/or prevent further disease progression (266-268). There is growing interest in applying a readthrough-based approach to neurodegenerative diseases that possess a significant proportion of nonsense mutation bearing patients, and in some cases exhibit a lower therapeutic threshold.   51                                       Figure 1-2 Nonsense mutation readthrough. A, Translation termination at a natural mRNA stop codon. B, Premature translation termination at a nonsense codon. C, Drug-induced PTC readthrough resulting in full-length translation of nonsense mutant mRNA. 52  1.3.1 Aminoglycoside PTC readthrough Aminoglycosides are bactericidal antibiotics consisting of two to three amino sugar groups joined to either a streptidine or 2-deoxystreptamine (2-DOS) ring by glycosidic linkages and are potent inhibitors of protein synthesis at high doses and reduce translational fidelity at low doses in Gram-negative bacteria (269,270). Aminoglycoside-mediated PTC readthrough has been thoroughly demonstrated in several mammalian cell lines and in vivo models expressing disease-associated nonsense mutations (reviewed here (271-273)). In 2-DOS aminoglycosides, this is achieved through binding to the 30S ribosomal subunit’s 16S rRNA decoding center, which is responsible for proof-reading codon-anticodon base-pairing complementarity (274). The eukaryotic 18S rRNA decoding center sequence differs from prokaryotic 16S rRNA at two key nucleotides, weakening the binding affinity of 2-DOS aminoglycosides by 25-50X (275,276). Therefore, eukaryotic ribosomes are less susceptible to translational inhibition by aminoglycosides at low doses, supporting their clinical use as therapeutic antibiotics targeting bacterial infections. The weaker affinity of aminoglycosides to the eukaryotic ribosomal decoding center is fundamental to their propensity to suppress nonsense mutations while minimizing the misincorporation of amino acids at sense codons (277).  The differential biochemical interactions between the eukaryotic ribosomal A-site and aminoacyl tRNAs / translational RFs in the presence and absence of aminoglycosides have been thoroughly investigated (reviewed here (278,279)). Translational fidelity is monitored by three universally conserved ribosomal rRNA nucleotides in helix 18 53  (G530) and 44 (A1492, A1493). For simplicity, rRNA residues will be numbered according to the numbering used in E. coli 16S rRNA. As mentioned above, the eukaryotic rRNA decoding center also contains non-conserved nucleotides; A1408G and G1491A base substitutions in helix 44 are responsible for the diminished aminoglycoside binding affinity (274,276). Upon forming a cognate codon-anticodon pair, A1492 and A1493 are flipped out into the minor groove of the codon-anticodon mini-helix core, and G530 transitions from a syn to anti conformation (280,281). This conformational change, often referred to as the ON-state, brings these proof-reading rRNA nucleotides in proximity to the codon-anticodon base-pairing event, allowing hydrogen bonding via 2’ OH groups to assess complementarity.   In contrast, natural stop codons and PTCs are instead recognized through a nucleotide-protein interaction with RFs, which trigger translational termination. The eukaryotic RF (eRF1) is capable of recognizing all three stop codons (282), while prokaryotes possess RF1 and RF2, which recognize UAG/UAA and UGA/UAA, respectively (283). These RFs share 3D structural homology with aminoacyl tRNAs and can directly recognize the three stop codons; however, there are subtle differences in how they interact with the ribosomal A-site. Unlike sense codons, only one of the A1492 or A1493 position nucleotides is flipped out of helix 44 (A1492 in prokaryotes vs. A1493 position in eukaryotes) in response to RF stop codon/PTC recognition, leaving the remaining adenine free to form a stacking interaction with A1913 of helix 69 on 23S rRNA which signals the RF to activate peptidyl transferase activity (284,285). The ribosomal A-site configuration where either one or both of the conserved adenines are directed towards 54  the helical core is known as the non-decoding or OFF-state, which has also been associated with the absence of a cognate tRNA (286,287).   Aminoglycoside binding to the 16S rRNA decoding center is stabilized by hydrogen bonds with G1408 and displaces both A1492 and A1493 from the helical core, similar to the ON-state induced by cognate tRNAs, which may introduce steric clash and disrupt potential base stacking interactions between A1493 and A1913, thus limiting the access of RFs to stop codons/PTCs (288,289). Furthermore, aminoglycoside-mediated displacement of A1493 has been shown to strongly shift its phosphate group, which relaxes the decoding pocket on the codon side (290). These conformation changes simultaneously increase the likelihood of near-cognate tRNA sampling in the ribosomal A-site and the accommodation of a single-nucleotide anticodon mismatch at PTCs, stimulating readthrough.  1.3.2 Aminoglycoside toxicity To prevent or delay the progression of any nonsense mutation-linked diseases, patients will likely require lifelong treatment with PTC readthrough-inducing drugs to maintain adequate expression from their nonsense alleles. Therefore, long-term tolerability with minimal toxicity and low rates of drug-associated adverse events are essential for the success of nonsense suppression therapy as a treatment for genetic disorders. Therefore, a major impediment to the clinical application of aminoglycosides as translational readthrough-inducing drugs has been the association of their prolonged use with significant nephro- and ototoxicity (reviewed here (267,291,292)). 55  Aminoglycoside-induced nephrotoxicity is a reversible process that results in both the necrosis and apoptosis of renal proximal tubular epithelial cells (293,294). In contrast, ototoxicity induced by aminoglycosides results in permanent bilateral sensorineural hearing loss by triggering apoptosis of vestibular and cochlear hair cells (295,296). Three main mechanisms contribute to aminoglycoside-induced toxicity: lysosomal phospholipidosis, accumulation of intracellular reactive oxygen species (ROS), and inhibition of mitochondrial protein synthesis.   Aminoglycoside antibiotics gain entry into cells through the endocytic membrane receptor, megalin, which is highly expressed on the apical membrane of epithelial cells in the renal proximal tubule (297) and stria vascularis marginal cells of the cochlear duct (298,299). Following endocytosis, most aminoglycosides enter the endolysosomal network, those destined for the lysosome become positively charged (300), allowing them to bind to negatively charged lysosomal membrane phospholipids. This affinity for the lysosomal membrane disrupts phospholipid turnover and inhibits phospholipase function, resulting in lysosomal phospholipidosis (266,301). Eventually, membrane damage becomes so severe that lysosomal membranes rupture (302), releasing aminoglycosides into the cytosol, causing the formation of ROS and subsequent oxidative damage (303,304) via iron-aminoglycoside complexes (305), and aminoglycoside-mediated mitochondrial dysfunction (306,307). Mitochondrial ribosomal (mitoribosomal) rRNA shares significant homology with prokaryotic rRNA; given that the mitoribosome is a remnant from a previously symbiotic bacteria, the mitoribosomal decoding site is more susceptible to aminoglycoside-mediated inhibition of protein 56  synthesis than the eukaryotic ribosome. Genetic analysis has revealed that individuals carrying specific SNPs in their mitochondrial DNA encoding the helix 44 decoding center that further enhance aminoglycoside-mitoribosomal affinity are at greater risk of aminoglycoside-induced ototoxicity (268,308,309). Molecularly characterizing the mechanisms of both PTC readthrough and aminoglycoside-induced toxicity have provided researchers with a rational basis for designing novel synthetic aminoglycosides with improved readthrough activity while minimizing toxicity.  1.3.3 Promising PTC readthrough drugs As discussed in section 1.3.2, there are several known clinical limitations to using aminoglycosides as potential PTC readthrough drugs (266-268). While natural aminoglycosides are currently not suitable for long-term human administration, efforts are underway to develop novel aminoglycoside derivatives with improved tolerability and PTC readthrough potency. Medicinal chemistry approaches for designing synthetic aminoglycosides have been largely focused on limiting their affinity for the prokaryotic and mitochondrial ribosomal decoding center while maintaining a weak affinity for eukaryotic ribosomes as a means to reduce toxicity. The aminoglycoside G418 (geneticin) is simultaneously the strongest readthrough inducer and most toxic of all natural aminoglycosides tested to date (234,310,311). Over the past 15 years, Baasov and co-workers have systematically and elegantly demonstrated which aminoglycoside chemical moieties of G418 are essential for its PTC readthrough activity and those responsible for its toxicity that may be expendable (312-316). In summary, these exceptional molecular remodeling studies confirmed that ring I is essential for G418-57  induced PTC readthrough activity, and its garosamine ring III is largely responsible for its significant toxicity.   Their 4th generation aminoglycoside derivative NB124 only differed from G418 by modifications to ring III, swapping the garosamine ring to a 5 amino ribose with an (S)-5’’-methly group and its ring II attachment position (C6 instead of C5). Compared to G418, these ring III alterations in NB124 dramatically reduced its affinity for both the mitochondrial and prokaryotic ribosomes (> 100X) while maintaining similar PTC readthrough efficiency (316). Following its initial synthesis, NB124 was acquired by Eloxx Pharmaceuticals and became one of their lead investigational therapeutic candidates (ELX-02). ELX-02 is a novel eukaryotic ribosomal selective glycoside that exhibits potent PTC suppression activity in several nonsense mutant disease models, comparable to G418 (317,318). Recent results of a phase I clinical trial have established that ELX-02 is safe and tolerated in healthy human subjects (246), thus prompting ongoing phase II clinical trials in CF and cystinosis patients harboring nonsense mutations (319-321). Despite the early success of ELX-02, Baasov et al. have continued their efforts to further structurally optimize aminoglycoside derivatives, applying a rational design strategy to maximize readthrough efficacy while minimizing nephro- and ototoxicity (317,322).    In parallel, significant research efforts have been made to identify PTC readthrough-inducing drugs of non-aminoglycoside antibiotic origin. The poor long-term tolerability of the aminoglycoside gentamicin highlighted the need for novel nonsense suppressors; 58  this search culminated in a high-throughput PTC readthrough screen of over 800,000 compounds identifying the small molecule oxadiazole, ataluren, as the most potent stimulator of a firefly luciferase-based PTC readthrough reporter assay (250). However, shortly following its discovery, evidence emerged demonstrating that ataluren binds to and stabilizes the firefly luciferase enzyme, which suggested that the ataluren ‘hit’ may have been the result of a PTC readthrough-independent mechanism (323,324). Several subsequent PTC readthrough studies failed to observe ataluren-induced PTC readthrough activity in various genetic contexts (325-327). On the other hand, multiple preclinical studies have confirmed ataluren-mediated PTC readthrough activity and observed lower toxicity levels compared to aminoglycosides (250,328-330). An additional mechanistic study unambiguously demonstrated that ataluren promotes the insertion of near cognate tRNAs at PTCs, similar to aminoglycosides (331). In further support of this interaction, co-treatment of both nonsense mutant cell cultures and CF patients with tobramycin, an aminoglycoside with a strong affinity for the eukaryotic ribosomal A site (332), has been discovered to competitively inhibit ataluren-induced readthrough (263,331). Confidence in ataluren’s therapeutic potential as a PTC readthrough drug ultimately resulted in multiple phase III clinical trials treating nonsense mutation carrying DMD and CF patients with ataluren but failed to significantly alter disease progression compared to placebo groups (251,263,333). Nevertheless, these varied results have led to the development of promising novel oxadiazole containing ataluren analogs with improved readthrough performance, currently under preclinical development (334-336).  59  1.3.4 PTC readthrough enhancers Our collaborators in the Roberge lab previously identified several readthrough enhancer compounds capable of synergistically increasing the potency of aminoglycoside-mediated suppression of nonsense mutations. In 2016, they discovered a novel class of aminoglycoside PTC readthrough enhancer compounds (CDX-series) using a high-throughput screen for nonsense suppression in yeast (337). The CDX-series compounds are N-substituted phthalimide derivatives that they further systematically functionalized to increase their potency. They demonstrated that co-treatment with CDX5-1 and G418 enhanced PTC readthrough in TP53 nonsense mutant HDQ-P1 cancer cells. At present, the mechanism underpinning the readthrough enhancement achieved by CDX compounds is unclear. However, qualitative observations suggest that combination treatment with G418 and CDX compounds inhibit proliferation in cell cultures; therefore, toxicity may limit clinical potential. In a subsequent study, the Roberge group also identified that the antimalaria drug mefloquine could potentiate aminoglycoside-induced PTC readthrough in several TP53 nonsense mutant cancer cell lines (338). Importantly, readthrough-derived full-length p53 retained biological function as observed through increased Ser15 phosphorylation in response to ionizing radiation. They demonstrated that mefloquine-induced readthrough enhancement is not achieved through increased extracellular uptake of G418 or increased lysosomal permeability to G418, suggesting that mefloquine may directly target translation machinery.   60  1.3.5 Nonsense mediated mRNA decay  The abundance of nonsense mutant mRNA transcripts is a determining factor of PTC readthrough efficiency. mRNA stability is regulated by several biological processes, including microRNA silencing, mRNA maturation, and nonsense-mediated mRNA decay (NMD). mRNAs bearing nonsense mutations are targeted for degradation by NMD, and PTC readthrough enables escape of nonsense mutant mRNA from degradation by NMD. NMD efficiency can vary up to 4-fold in the general population, likely resulting in a wide variance in basal PTC readthrough levels in individual nonsense mutation carriers (339). For this discussion, only the exon-junction complex (EJC)-dependent model of mammalian NMD will be presented, as EJC-independent NMD is not triggered by the presence of a PTC (reviewed here (233,340,341)). For a PTC containing mRNA to elude destruction by NMD, it must be translated through to at least 50-55 nucleotides upstream of the final exon-exon junction during its ‘pioneer’ round of translation. This degree of translation is sufficient because it removes al EJCs that are deposited 20-24 nucleotides upstream of every exon-exon junction during pre-mRNA splicing. During the translation of a nonsense mutant mRNA transcript, the NMD factors UPF1 and SMG1 kinase interact with eRF1 and eRF3 upon PTC recognition forming a pretermination complex. When a ribosome encounters a PTC with an intact downstream EJC (contains NMD factors UPF2 and UPF3), UPF1 can interact with UPF2/UPF3, which induces UPF1 phosphorylation by SMG1, thus marking the mRNA for degradation. This phosphorylation recruits additional NMD factors (SMG5, SMG6, SMG7, PP2A), forming an mRNA surveillance complex that facilitates the breakdown of the PTC-containing 61  mRNA. Concurrently, the PP2A phosphatase dephosphorylates UPF1, thus enabling the detection of additional nonsense mutant mRNAs.   The elucidation of the NMD pathway and understanding its role in suppressing the levels of nonsense mutant mRNAs has identified potential drug targets to inhibit NMD as an adjunct to PTC readthrough agents. Because the phosphorylation and subsequent dephosphorylation of UPF1 are the main rate-limiting steps driving NMD, interfering with these processes leads to efficient NMD inhibition. Thus far, several compounds have been identified that inhibit NMD by targeting the phosphorylation status of UPF1. For example, the natural substances caffeine and wortmannin both inhibit the SMG1 kinase, preventing the phosphorylation of UPF1, which rescues nonsense mutant mRNA from being tagged for degradation (342). Another group performed a virtual screen, capitalizing on the crystallographic resolution of the UPF1-SMG7 complex to identify commercially available compounds capable of binding to the SMG7 pocket critical for association with UPF1. This screen led to the identification of NMDI-14, which prevents phosphorylated UPF1 from recruiting the SMG5-SMG7 heterodimer, which together serves as an adapter for phosphatase PP2A-mediated UPF1 dephosphorylation (343).   Another compound, NMDI-1, inhibits NMD through a similar mechanism by disrupting the association between SMG5 and UPF1, which leads to the sequestration of hyperphosphorylated UPF1 (344); notably, NMDI-1 is a 1500X more potent NMD inhibitor than caffeine. In vivo co-administration of the NMD attenuator, NMDI-1, and 62  gentamicin in the IduaW392X/W392X mucopolysaccharidosis type I mouse model synergistically enhanced Idua enzyme activity and rescued glycosaminoglycan accumulation and lysosomal dysfunction (345). Despite the synergistic benefits of combining NMD inhibition and PTC readthrough treatment, it is important to consider the potential negative consequences of inhibiting NMD factors. For example, NMD factors have also been implicated in the transcriptomic regulation of ~10% of all mammalian mRNA (non-PTC bearing) transcripts (265), playing important roles in B and T cell maturation (346), as well as telomere maintenance (347). Therefore, efforts exploring the clinical application of NMD inhibition should proceed with caution, although, considering that a 4-fold variation in NMD efficiency has been observed in the general population, it is likely that some degree of NMD disruption may be tolerated.  1.3.6 PTC readthrough in cellular models of FTLD-GRN  Of the 79 known GRN mutations, 18 (23%) are single-base substitutions introducing nonsense mutations, and notably, the most common familial GRN mutation is the p.R493X nonsense mutation. These disease characteristics make FTLD-GRN an ideal candidate for PTC readthrough drug development. Following our abstract presented at the 11th International Conference in Frontotemporal Dementias in 2018, Kuang et al. corroborated parts of our findings, showing that aminoglycosides induced GRN nonsense mutation readthrough in cells transfected with nonsense mutant expression GRN constructs (348). They transfected N2a cells with C-terminally FLAG-tagged GRN nonsense mutant expression constructs (p.Q125X, p.Y229X, p.R493X) and confirmed gentamicin- and G418-mediated PTC readthrough of UGA nonsense codon (p.R493X), 63  while UAG/UAA codons (p.Q125X/p.Y229X) were unresponsive (348). Analysis of the subcellular localization of G418-induced PTC readthrough-derived full-length PGRN found co-localization with the lysosomal and Golgi apparatus similar to wild-type PGRN; thus, suggesting the readthrough product may function similarly to wild-type PGRN (348). Moreover, they reported evidence demonstrating escape of FLAG-tagged GRN R493X mRNA from NMD, resulting in a 2X increase in mRNA levels following a 24 h treatment with G418 (348). Two months later, we published our manuscript demonstrating G418-mediated PTC readthrough in HEK293 cells transfected with similar C-terminally tagged nonsense mutant GRN expression constructs, further improving upon these efforts by co-treating with novel readthrough enhancer drugs. The results from our studies demonstrating GRN PTC readthrough will be presented in detail in the subsequent chapters.  1.4 Thesis research questions The primary objectives of this thesis were to answer the following questions: 1) can we demonstrate in vitro and proof-of-concept in vivo GRN PTC readthrough of exogeneous nonsense mutant GRN expression constructs? 2) do FTLD-GRN and CLN11 hiPSC models of GRN-deficiency caused by nonsense mutations exhibit mutant lysosomal phenotypes? 3) can we demonstrate proof-of-concept PTC readthrough of endogenous pathogenic GRN mutations in both in vitro and in vivo models, and reverse disease-related phenotypes? 4) What behavioural and neuropathological phenotypes develop in the recently developed GrnR494X/R493X knock-in mouse model? A graphical overview and 64  summary of our experimental approach is described below (Figure 1-3).    65                                                                                                                                                                                                                                                                                                       66  Figure 1-3 Graphical overview of experimental models. Exogenous PTC readthrough was demonstrated in HEK293 cells transfected with several C-terminally V5-tagged GRN expression constructs, each bearing a causal FTLD-GRN pathological mutation. Stably transfected HEK293 lines provided an ideal model for screening PTC readthrough CDX-series enhancer compounds treated in combination with G418. The coding sequence of the R493X GRN-V5 expression construct was cloned into an AAV expression vector, which was used to generate AAV-GRN-R493X-V5 mice. Top readthrough enhancer compound CDX5-288 identified in HEK293 screening was used in combination with G418 to induce in vivo CNS PTC readthrough of the V5-tagged GRN R493X construct. To demonstrate PTC readthrough of endogenously expressed GRN, we established novel FTLD-GRN patient- and isogenic CRISPR/Cas9 gene editing-derived hiPSC models of GRN LOF caused by nonsense mutations. GRN nonsense mutant hiPSC-derived neurons and astrocytes were treated with top candidate PTC readthrough drug combinations and assessed for rescued PGRN expression. We also obtained and similarly treated aged GrnR493X/R493X mice with G418 to further establish proof-of-concept in vivo readthrough; however, high levels of toxicity prevented us from achieving long-term delivery of therapeutic dosages. Therefore, we limited the scope to a novel phenotypic characterization of this mouse model, assessing several neuropathological phenotypes previously reported in Grn-/- mice.    67  Chapter 2: Materials and methods  2.1 Mice C57BL/6J mice for AAV studies were acquired from Dr. Ann Marie Craig (Department of Psychiatry, Centre for Brain Health, UBC). GrnR493X/R493X mice on a C57BL/6J background, and C57BL/6J Grn+/+ mice were obtained from Jackson Laboratories (Stock# 029919 and #000664, respectively). Animal procedures were approved by the UBC Animal Care and Biosafety Committees. Mice were housed at the UBC Centre for Disease Modelling and Animal Research Unit facilities, where work outlined in institutionally approved breeding and experimental protocols (A19-0623, A19-0062, A16-0161, and A17-0225) was conducted. Mice were provided with a 12 h light/12 h dark cycle and allowed food and water ad libitum. All efforts were made to minimize suffering with minimally invasive procedures, and where necessary, isoflurane anesthesia was used.  2.2 Cells 2.2.1 HEK293 HEK293 cell studies were conducted in Dr. Roberge’s lab (Life Science Center, UBC) and cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific) + 1% Pen/Strep (Thermo Fisher Scientific).  68  2.2.2 Mouse embryonic fibroblasts Grn+/+ and GrnR493X/R493X mouse embryonic fibroblasts (MEFs) were isolated from E14.5 embryos. Briefly, dissected embryos were finely minced and digested in 0.25% Trypsin-EDTA (Thermo Fisher Scientific) at 37 °C for 10 min. This solution was centrifuged at 100 x g for 3.5 min, and the pellet was resuspended in 0.125% Trypsin-EDTA for further digestion at 37 °C for 25 min. Following the addition of FBS to neutralize the trypsin, the solution was vigorously pipetted with FBS and passed through a cell strainer for collection of a single cell suspension. This resulting suspension was centrifuged at 300 x g for 5 min, and the supernatant was discarded and replaced with DMEM-high glucose medium (Thermo Fisher Scientific) supplemented with 15% FBS + 1% Pen/Strep. The cells were counted and plated at a density of 1.5E7 cells per 150 mm plate and passaged once confluent. Early passage frozen stocks were prepared and thawed as needed for experiments.  2.3 Expression vectors 2.3.1 Vector mutagenesis Using GeneArt mutagenesis service (Thermo Fisher Scientific), the coding sequence of GRN was synthesized and cloned into pDONR221 Entry vector. Three base substitutions c.347C>A, c.1252C>T, and c.1477C>T were engineered into GRN using a targeted PCR-based strategy to generate p.S116X (UAA), p.R418X (UGA) and p.R493X (UGA) nonsense mutations. Finally, to generate expression clones, LR recombination reaction was used to recombine the wild-type and mutated samples from the Entry vectors into the pcDNA-6.2/V5-DEST vector (Thermo Fisher Scientific). These 69  C-terminal V5 tagged GRN expression constructs were used for HEK293 cell transfections.  2.3.2 Transfection HEK293 cells were transiently transfected with pcDNA6.2/V5-DEST vector expressing C-terminally V5-tagged mutated GRN with nonsense mutations (p.S116X, p.R418X, p.R493X) using Lipofectamine 2000 (Thermo Fisher Scientific). 24 h after transfection, each sample was split into two wells and either left untreated or treated with G418 (100 µg/mL). After 72 h, cells were lysed and subjected to automated capillary electrophoresis western analysis (Wes, ProteinSimple). To generate stable cell lines, HEK293 cells were transfected with pcDNA-6.2/V5-DEST vectors expressing mutant GRN as described above and subjected to blasticidin (Thermo Fisher Scientific) selection. Individual clones that were resistant to 15 μg/mL blasticidin were selected.  2.3.3 AAV vector packaging The packaging of AAV-GRN-R493X-V5 was performed by the Petrucelli group at the Mayo Clinic in Jacksonville, Florida. The coding sequence for V5-tagged p.R493X mutant GRN was cloned into the AAV expression vector pAM/CBA-EGFP-WPRE-BGH, AAV particles were packaged into serotype 9 capsid (AAV9), and purified using standard methods (349). Briefly, AAV was generated by co-transfection with the cis plasmids pF Delta6 and pRepCap9 into HEK293T cells. Cells were harvested 72 h after transfection, treated with 50 Units/ml Benzonase (Sigma-Aldrich), and lysed by freeze-thaw. The virus (AAV-GRN-R493X-V5) was then purified using a discontinuous 70  iodixanol gradient and buffer exchanged to PBS using an Amicon Ultra 100 Centrifugation device (EMD Millipore).  The genomic titer of each virus was determined by quantitative PCR using the ABI 7700 (Applied Biosystems) and primers specific to the WPRE.  The viral DNA samples were prepared for quantification by treating the virus with DNaseI (Invitrogen) and Proteinase K (Invitrogen), and samples were compared against a standard curve of supercoiled plasmid. AAV9-eGFP-Cre viral particles (AddGene, 105540-AAV9) were used to demonstrate technical proficiency of P0 intracerebroventricular (ICV) AAV injection by assessing brain-wide human synapsin promoter-driven eGFP expression in 10 week old AAV9-eGFP-Cre mice.    2.3.4 In vitro transduction HEK293 cells were transduced for 5 days with 2 mL volumes of media containing increasing concentrations of AAV-GRN-R493X-V5 expression vector (8.8E8, 8.8E9, and 8.8E10 PFU/mL) and 8 µg/mL polybrene for increased transduction efficiency. 48 h after transduction, each transduced well was treated with G418 (100 µg/mL). Following 72 h G418 treatment, supernatant was collected and cells were lysed. Cell lysates and supernatant were both subjected to automated capillary electrophoresis western analysis.     71  2.4 Antibodies Table 1-1 Primary antibodies Antibody Dilution Source Identifier Polyclonal Rabbit Anti-Human ACTIN Antibody  1:10000 (WB / Wes) Novus Biologicals NB600-532, RRID: AB_10002039 Monoclonal Rabbit Anti-Mouse C1q Antibody  1:500 (IF) Abcam ab182451, RRID: AB_2732849 Polyclonal Goat Anti-Human CTSD Antibody  1:1000 (WB) R&D Systems AF1014, RRID: AB_2087218 Polyclonal Goat Anti-Mouse Ctsd Antibody  1:500 (WB) R&D Systems AF1029, RRID: AB_2087094 Polyclonal Rabbit Anti-Human DESMIN Antibody  1:500 (IF) Invitrogen PA5-16705, RRID: AB_10977258 Polyclonal Goat Anti-Mouse DppII Antibody  1:500 (IF) R&D Systems AF3436, RRID: AB_2093882 Polyclonal Rabbit Anti-Human FOXG1 Antibody  1:500 (IF) Abcam ab18259, RRID: AB_732415 Polyclonal Rabbit Anti-Mouse Foxp2 Antibody  1:500 (IF) Abcam ab16046, RRID: AB_2107107 Polyclonal Rabbit Anti-Human GAD65/67 Antibody  1:500 (IF) Sigma-Aldrich G5163, RRID: AB_477019 Polyclonal Rabbit Anti-Human GFAP Antibody  1:500 (IF) STEMCELL Technologies 60128, RRID: AB_215513 Monoclonal Rat Anti-Mouse Lamp1 Antibody  1:500 (IF/WB) BD Biosciences 553792, RRID: AB_2134499 Polyclonal Rabbit Anti-Mouse LC3-I/II Antibody   1:1000 (WB) Cell Signaling Technology 2775, RRID: AB_915950 Polycloncal Rabbit Anti-Human MAP2 Antibody  1:500 (IF) Proteintech 17490-1-AP, RRID: AB_2137880 72  Antibody Dilution Source Identifier Polycloncal Goat Anti-Human NANOG Antibody  1:1000 (IF) R&D Systems AF1997, RRID: AB_355097 Monoclonal Mouse Anti-Human OCT3/4 Antibody  1:1000 (IF) STEMCELL Technologies 60093, RRID: AB_2801346 Polyclonal Goat Anti-Human PGRN Antibody  1:1000 (IF) R&D Systems AF2420, RRID: AB_2845434 Polyclonal Rabbit Anti-Human PGRN Antibody  1:1000 (WB) Sigma-Aldrich HPA008763, RRID: AB_1850339 Polyclonal Rabbit Anti-Mouse Pgrn Antibody  1:1000 (WB) Yu/Herz lab (82) Mouse Linker 1 Peptide (C)TLLKKF PAQKTNRAVSI Polyclonal Sheep Anti-Mouse Pgrn Antibody  1:100 (WB) R&D Systems AF2557, RRID: AB_2114504 Monoclonal Rabbit Anti-Human SOX1 Antibody  1:1000 (IF) STEMCELL Technologies 60095, RRID: AB_2801347 Polyclonal Goat Anti-Human SOX17 Antibody  1:500 (IF) R&D Systems AF1924, RRID: AB_355060 Polyclonal Rabbit Anti-Human SYNAPSIN Antibody  1:500 (IF) EMD Millipore 5747777, RRID: AB_212517 Polyclonal Rabbit Anti-Human TBR1 Antibody  1:500 (IF) Abcam ab31940, RRID: AB_2200219 Polyclonal Rabbit Anti-Mouse N-terminal TDP-43 Antibody  1:1000 (WB), 1:500 (IF) Proteintech 10782-2-AP, RRID: AB_615042 Polyclonal Rabbit Anti-Human phospho-Ser409 TDP-43 Antibody   1:500 (WB) Cosmo Bio USA CAC-TIP-PTD-P03, RRID: AB_1961901  Polyclonal Chicken Anti-Human TUJ1 Antibody  1:500 (IF) Neuromics CH23005, RRID: AB_2210684 73  Antibody Dilution Source Identifier Monoclonal Mouse Anti-V5 Antibody  1:500 (Wes) Abcam ab27671, RRID: AB_471093 Monoclonal Mouse Anti-Mouse Vgat Antibody  1:300 (IF) Synaptic Systems 131011, RRID: AB_887872 Monoclonal Mouse Anti-Human VGLUT1 Antibody  1:200 (IF) Synaptic Systems 135311, RRID: AB_887880  2.5 Drug treatments 2.5.1 In vitro G418 sulfate powder was reconstituted in sterile PBS to 50 mg/mL and CDX-series compounds in dimethyl sulfoxide (DMSO) to 50 mM. These stock solutions were stored at -20C.  Upon addition of CDX compounds to cell culture media, gentle vortexing was applied for 2 min to ensure complete solubilization. Vehicle solutions were prepared by adding an equivalent volume of PBS and/or DMSO. Rec. PGRN (Adipogen, AG-40A-0068Y-C010) was reconstituted to 0.1 mg/mL in sterile water. CTSL inhibitor (Z-Phe-Phe-FMK, Abcam, ab141386) 10 mM stock in DMSO was first diluted to 100 and 300 µM, prior to 1:10 dilution in cell culture medium.  2.5.2 AAV mouse model In vivo treatment solutions of vehicle (1.6% solutol), 16.6 mg/mL G418 (1.6% solutol), 0.5 mM CDX5-288 (1.6% solutol), and 16.6 mg/mL G418 + 0.5 mM CDX5-288 (1.6% solutol) were prepared in sterile saline. A 50 mM solution of CDX5-288 in DMSO was first diluted to 3 mM in 10% solutol (diluted in sterile saline) and further diluted 1:6 in 74  treatment solutions.  2.5.3 GrnR493X/R493X mouse model In vivo treatment solutions of either vehicle (saline) and G418 reconstituted in saline (25 and 100 mg/mL) were used to treat Grn+/+ and GrnR493X/R493X mice. A range of G418 concentrations and injection volumes were used to achieve different doses of G418 in the brain.   2.6 Western blot 2.6.1 Conventional western blot Cortical neuron, astrocyte, and MEF supernatant were collected, and cell monolayers were rinsed with 1 mL ice-cold PBS. Cells were lysed in 50 µL lysis buffer (20 mM Tris–HCl pH 7.5, 150 mM NaCl, 1mM EDTA, 1 mM EGTA, 1% (v/v) Triton X-100, 2.5 mM sodium pyrophosphate, 1 mM β-glycerophosphate) supplemented with fresh 1 mM Na3VO4, and 1X complete protease inhibitor cocktail (Roche Molecular Biochemicals). Lysates and supernatants were pre-cleared by centrifugation at 19,500 x g for 10 min at 4 °C. Neuronal, astrocyte, and MEF lysate protein concentrations were quantitated using the Bradford assay and diluted in 4X SDS-PAGE loading buffer + 100 mM DTT. Hemi-brain RIPA-soluble and -insoluble lysates were prepared and quantified according to section 2.16.2 and were diluted in 4X SDS-PAGE loading buffer + 100 mM DTT. In brief, 10-30 µg protein from each boiled (5 min at 95 °C) SDS lysate was separated on 4-15% gradient precast polyacrylamide gel (Bio-Rad), electroblotted onto a 0.45 µm nitrocellulose membrane (Thermo Fisher Scientific) and blocked for 1 hour in 5% (w/v) 75  non-fat milk in TBS + 0.1% (v/v) Tween-20 (TBST). Samples from GrnR493X/R493X and wildtype control mice (Grn+/+) were run on the same precast gel to allow for direct comparison. Membranes were incubated with primary antibodies diluted in 5% non-fat milk TBST blocking buffer overnight at 4 °C, washed 3X 5 min with TBST, incubated with 1:10,000 HRP-conjugated secondary antibody diluted in 5% non-fat milk TBST blocking buffer, washed again 3X 5 min with TBST, and incubated with enhanced chemiluminescence substrate (EMD Millipore). Films were developed, scanned, and analyzed using the Fiji processing package for ImageJ (National Institute of Health) for densitometry analysis. To reprobe blots with the same species of primary antibody, membranes were stripped with 0.1 N NaOH for 5 min, washed twice with deionized H2O, and incubated for 30 min in 5% non-fat milk TBST blocking buffer before incubation with an additional primary antibody.  2.6.2 ProteinSimple Wes Automated capillary electrophoresis western analysis was carried out with manufacturer’s reagents according to the user manual (Wes, ProteinSimple). HEK293 cell lysates were prepared and quantified following the methods used for neurons/astrocytes/MEFs (see section 2.6.1), and AAV-GRN-R493X-V5 whole-brain RIPA-soluble lysates were prepared and quantified as in section 2.16.1. Briefly, 5.6 µL of 1 mg/mL HEK293 cell or whole-brain lysate was mixed with 1.4 µL fluorescent master mix and heated at 95 °C for 5 min. The samples, blocking reagent, wash buffer, primary antibody, secondary antibody, and chemiluminescent substrate were dispensed into the 76  microplate provided by the manufacturer, and the microplate was centrifuged at 1000 x g for 5 min. The electrophoretic separation and immunodetection were performed automatically using default settings. The data were analyzed with inbuilt Compass software (ProteinSimple). The truncated and full-length V5 (PGRN) peak intensities (area under the curve) were normalized to that of the actin peak, used as a loading control. In Figure 3-1, Figure 3-2, Figure 3-4, and Figure 3-7, electropherograms are represented as pseudo-blots, generated from the quantification of chemiluminescence by the Compass software.  2.7 hiPSC models 2.7.1 hiPSC reprogramming Erythroid progenitor (EP) cells were isolated from peripheral blood obtained from a healthy control subject (WT) and a GRN p.R418X mutation carrier (R418X+/-) (350) using the erythroid progenitor reprogramming kit (STEMCELL Technologies). Expanded EPs were reprogrammed into hiPSCs with Epi5TM episomal reprogramming kit plasmids (Invitrogen, Thermo Fisher Scientific) delivered in AmaxaTM Human CD34+ Cell nucleofection buffer (Lonza) using the AmaxaTM Nucleofector II (Lonza) electroporation device according to the erythroid progenitor reprogramming kit manufacturer’s instructions.  2.7.2 hiPSC culture hiPSCs were cultured in a feeder-independent manner on Matrigel (BD Biosciences) coated plates and fed daily with mTeSR1 medium (STEMCELL Technologies). Every 4-77  5 days, 70-80% confluence cultures were passaged as aggregates using ReLeSR (STEMCELL Technologies) at ~1:5 split ratio. During the first 24 h post-plating, mTeSR1 medium was supplemented with 10 µM rho-associated protein kinase inhibitor (Y-27632, EMD Millipore). S116X+/- hiPSCs were obtained from existing stock and previously described (60).  2.7.3 hiPSC trilineage differentiation hiPSCs were differentiated into the three germ layers using the StemDiff™ trilineage differentiation kit (STEMCELL Technologies) according to manufacturer's instructions. After differentiation, cells were fixed in 4% PFA for 15 min for immunofluorescence analysis with anti-SOX1 (ectoderm), anti-SOX17 (endoderm), and anti-DESMIN (mesoderm) antibodies (see section 2.13.1).  2.7.4 hiPSC CNS lineage differentiation WT and FTLD-GRN mutant hiPSCs were differentiated into neuronal progenitor cells (NPCs) using the dual SMAD inhibition protocol (351). These NPCs were frozen and thawed as needed onto Matrigel-coated plates in neural stem cell medium for week-long expansion. Expanded NPCs were then plated onto poly-L-ornithine / laminin (PLO/L) coated plates and further differentiated into cortical neurons using complete BrainPhysTM media system (352) supplemented with 1X CultureOneTM (Gibco, Thermo Fisher Scientific) for the first two weeks of neuron maturation. cAMP and ascorbic acid were withdrawn from BrainPhysTM media after 3 weeks (from hiPSC stage, DIV 50) for continued neuronal maturation until DIV 80 to allow lysosomal phenotypes to develop. 78  Astrocytes were differentiated from expanded cryopreserved NPCs according to the STEMDiffTM astrocyte differentiation and maturation kit (STEMCELL Technologies) protocol to produce DIV 60+ frozen stocks to be thawed and passaged as needed onto Matrigel-coated plates in STEMDiffTM astrocyte maturation medium.  2.7.5 Karyotyping analysis Karyotyping was performed on WT, R418X+/-, & R493X-/- KI by WiCell Cytogenetics, Inc. (Madison, WI). The S116X+/- line was previously karyotyped by Cell Line Genetics (Madison, WI) following the initial production of this line (60).  2.8 CRISPR/Cas9 gene editing  An isogenic hiPSC line homozygous for GRN R493X knock-in (R493X-/- KI) was generated from WT using aspects of a previously established CRISPR/Cas9 gene editing protocol (353). Briefly, guide RNA (gRNA) sequences were designed according to the online Optimized CRISPR Design tool (http://crispr.mit.edu) to target a region for double-strand breakage slightly upstream of the GRN R493 codon. A mutagenizing single-stranded oligonucleotide (ssODN, Integrated DNA Technologies) was designed to knock-in the R493X mutation and silently introduce a HindIII restriction enzyme site. hiPSCs were co-transfected (Lipofectamine Stem Transfection Reagent, Invitrogen) with knock-in ssODN and gRNA/Cas9 ribonucleoprotein (Integrated DNA Technologies) complexes for 72 h. CRISPR/Cas9 edited hiPSCs were seeded at clonal density (25 cells/cm2). Individual colonies of adequate size and morphology, were picked and plated for expansion. Genomic DNA was isolated using QuickExtractTM DNA Extraction 79  Solution (Lucigen) and PCR products containing the R493X target site were digested with HindIII (New England Biolabs). Clones with positive digestion signal were selected for Sanger sequencing to confirm the clean homozygous introduction of the R493X KI mutation. Sanger sequencing was performed by the UBC Sequencing + Bioinformatics Consortium.  2.9 Multielectrode array electrophysiology  WT and mutant hiPSC-derived NPCs (DIV 30) were co-cultured with hiPSC-derived WT astrocytes (DIV 60+) at a 1:1 ratio and plated onto 48-well multielectrode array (MEA) plates (Axion Biosystems) coated with PLO/L. For the 2 month time course MEA experiment WT NPCs, WT astrocytes, and co-cultures of WT NPCs and WT astrocytes were compared to evaluate the electrophysiological benefits of astrocyte inclusion. Cells were plated using the drop seed method, where 15 µL of mixed cell suspension (60,000 cells in total) in a 10% dilution of Matrigel in BrainPhysTM media was pipetted onto the electrode array in the center of each well. Cultures were fed by partial media replacement every 3 days according to our cortical neuron differentiation protocol described in section 2.7.4. Spontaneous electrophysiological activity of neuron-astrocyte co-cultures was recorded for either 10 min at cortical neuron DIV 50 (WT/mutant NPC + WT astrocyte co-cultures) or 5 min weekly for 2 month time course experiment using the Axion Biosystems Maestro MEA at 37 °C and 5% CO2. Data analysis was performed using AxIs software (Axion BioSystems) to extract the number of spikes and bursts from the recording file. Quality criteria for the assays were defined as follows: an electrode having an average of more than 5 spikes/min and wells with 80  less than 30% of the total electrodes active were considered inactive and excluded from the analysis. To assess synchronous network activity, at least 25% of the total 16 electrodes in each well were required to participate in a network event to be designated as a network burst.  2.10 ELISA PGRN levels in hiPSC-derived cortical neuronal and astrocyte whole cell lysates (prepared according to section 2.5.1) and concentrated supernatants (Amicon Ultra 0.5 mL, 50 kDa, 25X concentrated) were determined by ELISA (Adipogen, human) using the manufacturer’s protocol. Cultures were treated with an equal volume of media, and an equal volume of supernatant was concentrated for each sample. Cortical neuron and astrocyte lysates (1 mg/mL) and concentrated supernatant were diluted in ELISA buffer at optimized dilutions. Pgrn levels in MEF whole cell lysates (prepared according to section 2.5.1) and RIPA-soluble Grn+/+ and GrnR493X/R493X hemi-brain lysates (prepared according to 2.16.2) were determined by ELISA (Adipogen, mouse) using the manufacturer’s protocol. MEF lysates (1 mg/mL, Grn+/+ 1:20 and GrnR493X/R493X 1:5) and RIPA-soluble hemi-brain lysates (10 mg/mL, Grn+/+ 1.5:10 and GrnR493X/R493X 1:5) were diluted in ELISA buffer. G418 concentration levels in whole-brain lysates (prepared according to 2.16.3) were determined by Gentamicin ELISA (Creative Diagnostics) according to the manufacturer’s protocol using a G418 standard curve of 0.1, 0.3, 1, 3, 10, 30, and 100 ng/mL.  81  2.11 qPCR Total RNA was extracted from hiPSCs using RNeasy Plus Mini Kit (Qiagen). cDNA was produced by reverse transcription using the High-Capacity RNA-to-cDNA Kit (Applied Biosystems, Thermo Fisher Scientific). To measure the endogenous gene expression of pluripotency factors, qPCR analysis was performed using the 7900HT Fast Real-Time PCR System (Applied Biosystems, Thermo Fisher Scientific). mRNA was detected with TaqmanTM probes (Thermo Fisher Scientific, OCT4 Hs01895061_u1, LIN28 Hs00702808_s1, NANOG Hs02387400_g1, SOX2 Hs00602736_s1, GRN Hs00963707_g1, GAPDH Hs03929097_g1, and HPRT1 Hs02800695_m1) in combination with the TaqmanTM Universal PCR Master Mix (Applied Biosystems, Thermo Fisher Scientific). Gene expression of hiPSC markers was normalized to GAPDH housekeeping gene and compared to human fibroblast expression using the ΔΔCt-method. GRN gene expression in cortical neurons and astrocytes was normalized to the mean of GAPDH and HPRT1 housekeeping genes and compared to vehicle-treated WT expression using the ΔΔCt-method.  2.12 Mouse genotyping Mouse ear notch DNA was isolated in Chelex® 100. Briefly, 100 µL Chelex® 100 was added to ear notch, vortexed for 10 sec, and pulse spun to ensure tissue was submerged in the solution. Samples were then incubated at 95 C for 20 min. After 10 min, sample tubes were opened to release pressure and agitated to enhance tissue digestion before completing the remaining 10 min of incubation. Samples were then further agitated by running the bottom of the tubes across a metal tube storage rack and 82  centrifuged at 21,000 x g for 1.5 min. The PCR was run according to specifications outlined on the Jackson Laboratories B6.129S4(SJL)-Grntm2.1Far/J strain data sheet with 2 µL of the resulting DNA-containing supernatant from each sample loaded into a 23 µL PCR master mix solution. The resulting PCR products were resolved on a 2% agarose gel and detected using SafeView Classic (Applied Biological Materials).  2.13 Histology 2.13.1 Immunocytochemical staining and quantification Cells were fixed with 4% paraformaldehyde (PFA) for 15 min and washed three times with Dulbecco PBS (D-PBS, Gibco, Thermo Fisher Scientific). Cells were blocked and permeabilized with 10% donkey or goat serum (Sigma-Aldrich) in D-PBS containing 0.1% Triton X-100 (Abcam) for 1 h at room temperature (RT). Primary antibodies were then diluted (Table 1-1) in 10% donkey or goat serum in D-PBS and applied to cells overnight at 4 °C. All Alexa Fluor®-tagged secondary antibodies (Molecular Probes, Thermo Fisher Scientific) were applied at a dilution of 1:500 at RT for 2 h. The coverslips were then mounted in DAPI mounting medium (Vector Laboratories). Images were captured with ZEN 2 software using a Zeiss 880 scanning laser confocal microscope. Image quantification was performed using Fiji. The % of neurons expressing FOXG1/TBR1 was determined by applying uniform thresholds and converting images to binary using the watershed segmentation tool and quantifying the number of individual DAPI+/neuronal marker+ cells with the analyze particles function. The % neurons+ for MAP2 and % astrocytes+ for GFAP was determined by manually counting nuclei of MAP2- and GFAP+ cells. Subtracting the number of MAP2- cells from 83  the total number of DAPI+ nuclei and dividing it by the total number of DAPI+ nuclei yielded % MAP2+ and dividing the number of GFAP+ cells by the number of DAPI+ nuclei yielded % GFAP+. Cytotoxicity was assayed by staining fixed 96-well plate neuronal cultures with Hoechst dye (1.5 µg/mL, Invitrogen). These plates were imaged using a Cellomics ArrayScanTM plate scanner, and the number of cells/field were automatically counted with acQuisitionTM software.  2.13.2 Brain immunofluorescence microscopy and quantification Free-floating sagittal brain sections were blocked and permeabilized with 10% donkey or goat serum (Sigma-Aldrich) in D-PBS containing 0.1% Triton X-100 (Abcam) for 2 h at RT. Primary antibodies were then diluted (Table 1-1) in 10% donkey or goat serum in D-PBS and applied to sections overnight at 4 °C with gentle agitation. All Alexa Fluor®-tagged secondary antibodies were used at a dilution of 1:500 at RT for 2 h. The sections were then mounted in DAPI mounting medium (Vector Laboratories). AAV9-eGFP-Cre mouse brain sections were simply mounted in DAPI mounting medium to assess eGFP expression. Z-stacks and tilescans were captured with ZEN 2 software using a Zeiss 880 scanning laser confocal microscope using 20X and 40X objective lenses. AAV9-eGFP-Cre whole mouse brain tilescans were captured with a 20X objective lens, while all other brain section imaging was done with a 40X objective lens. High magnification (100X, 2.5X digital zoom with 40X objective) Tuj1-TDP-43-DAPI co-stained images were captured as single Z-plane images. All other images were obtained through single field 30 µm thick (1 image / 5 µm step) z-stack and z-stack tilescan acquisitions and were processed into maximum intensity projections using ZEN 84  2 software prior to image quantification performed using the Fiji processing package for ImageJ (National Institutes of Health).  The total area (µm2) of lysosomal marker (Lamp1 and DppII) staining per CA3 or VPM/VPL field was quantified using Fiji by applying a uniform threshold to all images and watershed segmentation to distinguish individual lysosomal vesicles. The analyze particle function was used to quantify areas ranging from 0.05-infinity µm2, providing both total Lamp1+/DppII+ area and average lysosomal vesicle size. Total Pgrn staining area was quantified by applying a uniform threshold across all images and analyzing particle areas 0-infinity µm2. Microgliosis was quantified by assessing both total Iba1+ area and the number of Iba1+ cells; this was determined by applying a uniform threshold and analyzing particles with an area of 0.25-infinity µm2 and 20-infinity µm2, respectively. Astrogliosis was similarly quantified by measuring total Gfap+ area in uniformly thresholded images using the analyze particles tool (0.25-infinity µm2). Thalamic VPM/VPL total C1qa complement staining area was quantified by applying a uniform threshold across all images and analyzing particle areas 0-infinity µm2. Ventral thalamic density of Vgat+ synapses was determined by quantifying both the total Vgat+ area and the number of Vgat+ puncta. Vgat images were uniformly thresholded and segmented using the watershed function, and particles limited to a 0.3-5 µm2 area were analyzed. The % of Vgat+ synaptic area co-stained for C1qa was determined by generating regions of interest (ROIs) of Vgat+ synapses using the above image processing and analyze particle specifications. These Vgat ROIs were then applied to corresponding co-stained C1qa images, and any C1qa+ staining outside of ROIs was 85  cleared using the clear outside function. The remaining intra-ROI C1qa staining was uniformly thresholded and quantified by analyzing particle areas 0-infinity µm2. The total C1qa area within Vgat ROIs was divided by total Vgat area and multiplied by 100 to obtain % of Vgat+ synaptic area co-stained for C1qa. For data normalized on a per cell basis, the number of DAPI+ nuclei were quantified per field by applying a uniform threshold to all images and watershed segmentation to distinguish individual nuclei. The analyze particle function was used to quantify areas ranging from 25-infinity µm2 to determine the total number of cells per field.  Foxp2+ excitatory neuron and Vgat+ synaptic total thalamic density were obtained from MIPs generated from z-stack tilescans containing both the hippocampal and thalamic brain structures (40X magnification, 0.6 zoom, 8 x 12 tilescan). The polygon selection tool was used to draw a boundary surrounding the thalamus to measure the total thalamic area (mm2). Any Foxp2+ or Vgat+ staining outside of the thalamic boundary was eliminated using the clear outside function, and a uniform threshold was applied to each tilescan image. Following watershed segmentation to allow for clear detection of individual Foxp2+ nuclei and Vgat+ synaptic puncta, the number of particles 50-200 µm2 (Foxp2) or 7.75-25 µm2 (Vgat) in size were analyzed and normalized to total thalamic area.  Microglial skeletal analysis was conducted using the Fiji Analyze Skeleton (2D/3D) plugin using a modified version of a previously described protocol (354). Pre-analysis Iba1 image processing required adjusting image brightness maximum (-40 to 215), 86  applying unsharp mask (radius 3 and mask weight 0.6), and reducing background noise using the despeckle tool. These processed images were then uniformly thresholded, further despeckled, processed using the binary Close- tool, and background noise was reduced further using the remove outliers function. The analyze particles function was then used to generate ROIs masking Iba1+ staining of a 10-infinity µm2 area and add them to the ROI manager. The original image was then reopened, and the initial Iba1 image processing steps were reapplied (brightness, unsharp mask, and despeckled). All ROIs were then selected in the ROI manager and applied to this image using the OR (combine) function. Any Iba1+ staining outside of the applied ROIs was eliminated using the clear outside function, and a threshold of 1-255 was applied to completely fill in the ROIs generating a clean binary image of microglial cell shapes. This image was then skeletonized using the binary processing tool and analyzed with the Analyze Skeleton (2D/3D) plugin (prune cycle: none, checked boxes = ‘show detailed info’ and ‘display labelled skeletons’) to determine the total number of microglial branches per field. To quantify microglial Pgrn fluorescent intensity (integrated density) from Iba1-Pgrn co-staining microglial ROIs were generated from Iba1 images according to the above skeletal analysis method. These ROIs were applied to their corresponding Pgrn co-stained image, and any Pgrn+ staining outside of the applied microglial ROIs was removed using the clear outside function. Pgrn integrated density in each microglial ROI was then measured from the ROI manager. The calculated integrated densities for all microglial ROIs per image were averaged, providing the Pgrn microglial fluorescent intensity per field.     87  2.13.3 Brightfield microscopy Live cultures were photographed with a digital camera mounted to a tissue culture microscope (40X obj. lens) throughout the differentiation process from hiPSCs to cortical neurons.  2.14 Surgical procedures 2.14.1 Intracerebroventricular injection of AAV particles P0 C57BL/6J neonates were anesthetized using isoflurane and bilaterally injected ICV with 0.5 µL of viral vector (AAV-GRN-R493X-V5, 8E13 PFU/mL and AAV9-eGFP-Cre, 1E13 PFU/mL) through a finely drawn glass micropipette as described previously (355). PTC readthrough treatments were performed when AAV-GRN-R493X-V5 mice were 6 weeks old.  2.14.2 Bolus intracerebroventricular injection of drugs 2.14.2.1 AAV-GRN-R493X-V5 mice A single bolus ICV injection of vehicle, CDX5-288, or G418 ± CDX5-288 was performed in 6 week old AAV-GRN-R493X-V5 mice according to previously published works with some modifications (356). First, to establish ICV targeting technical proficiency, a healthy C57BL/6J control mouse right lateral ventricle was injected stereotactically through a borehole (coordinates: -1.0 mm lateral/-0.3 mm posterior/-3.0 mm depth to bregma) by loading a glass micropipette needle attached via tubing to a 5 µL glass syringe (Hamilton, 600 series, model 65) with 5 µL 0.1% Fast Green FCF dye (Sigmal-Aldrich) driven by microinjection syringe-pump (UMP3T-1, World Precision Instruments) 88  to deliver the dosage at a flow rate of 1 µL/min. The dye-injected mouse was immediately euthanized, and its brain was collected to evaluate the pattern of CNS delivery. Following similarly conducted 3 µL drug injections in AAV-GRN-R493X-V5 mice, the needle was left in place for 3 minutes and then removed at a rate of 1 mm/second while holding a cotton swab against the skull at the base of the needle. The incision was then sutured with monocryl sutures (Ethicon, J303H) to close the skin, and the mice were placed on the heating pad warmed half of a cage to ensure the mice were kept at 36-38 °C for the first 1.5 h while they recovered from the anesthesia, with the option for them to move away from the heat source. After treated AAV-GRN-R493X-V5 mice had recovered fully from surgery, they were singly housed for 72 h. 5 mg/kg of meloxicam was injected subcutaneously once per day for the first 2 days post-operation.  2.14.2.2 Grn+/+ and GrnR493X/R493X mice Bolus ICV injections of both vehicle and G418 were performed in Grn+/+ and Grn493X/R493X mice to validate in vivo PTC readthrough in this model and optimize G418 dosing for a proposed recurrent injection model according to previously published works with some modifications (122). Briefly, both 1X (100 µg, 72 h treatment) and 2X (50 µg repeated 48 h treatments) ICV injections of G418 were tested. Mice lateral ventricles were injected stereotactically (1-3 µL volume, coordinates: -1.0 mm lateral/-0.3 mm posterior/-3.0 mm depth to bregma) with microinjection syringe-pump driven 10 µL glass syringe (Hamilton, 701 LT) connected to a 51 mm Luer-locking needle (Hamilton, 31G, 89  K-Fel) loaded with either saline or G418 solutions delivered at a flow rate of 0.5 µL/min. The incision was sutured, and post-surgical care was provided as in 2.14.2.1.   2.14.3 Intracerebroventricular iPRECIO® pump implantation in Grn+/+ and GrnR493X/R493X mice To establish iPRECIO® pump ICV targeting technical proficiency, a SMP-310R iPRECIO® Programmable Infusion Pump (AZLET) was loaded with 0.1% Fast Green FCF dye, programmed to immediately deliver dye the max rate of 8 µL/hour for 1 hour, and implanted subcutaneously in a Grn+/+ mouse under isoflurane anesthesia. Pumps were connected to a 30G 3 mm long Brain Infusion Kit 3 (AZLET) cannula. The base of the cannula was coated in Loctite 454 (AZLET) glue and was stereotactically driven through a borehole in mice right lateral ventricles (coordinates: -1.0 mm lateral/-0.3 mm posterior/-3.0 mm depth to bregma). The physical pump and excess tubing were then sterilely inserted into a subcutaneous pocket created caudally from the incision using a blunt dissection tool. Following completion of iPRECIO® pump dye ICV perfusion, the mouse was immediately euthanized, and its brain was collected to evaluate the pattern of CNS delivery. iPRECIO® pumps loaded with saline or 25 mg/mL G418 were similarly implanted, and the brain infusion cannula was inserted into the right lateral ventricles of Grn+/+ and Grn493X/R493X mice. Saline/G418 loaded pumps were programmed to allow mice to recover for 48-72 h and then dispense recurring bolus ICV doses of 1-2 µL volumes (saline or 25/50 µg G418) at the max flow rate (8 µL/hr) every 48-72 h for the experimental duration (see Figure 5-20 for more details). The incision was sutured, and 90  post-surgical care was provided as in 2.14.2.1.   2.15 Open-field behavioural assay The open-field test was performed to evaluate anxiety in the GrnR493X/R493X mouse model of frontotemporal dementia. The test consisted of a single 10 min trial in a white opaque 40 cm x 40 cm x 30 cm arena (Maze Engineers). The center zone was defined as a square covering 16% of the total area (16 cm x 16 cm central square). The mice were moved to the experimental room at least 1 hour before starting the tests. To begin each test, a mouse was introduced to the center of the square, and its behaviour was captured on video for 10 min. On recording days, males were tested before any females, and the area was cleaned with 50% ethanol and allowed to dry completely between each test. The duration that each mouse stayed in either the peripheral or central regions was quantified using JWatcher software (UCLA).  2.16 Brain collection and processing 2.16.1 AAV mouse model 72 h following ICV vehicle/drug injection, mice were anesthetized using isoflurane and transcardially perfused with PBS before brain collection. Brains were immediately flash frozen on dry ice and stored at -80 °C until lysate preparation. Whole-brains were later thawed, homogenized in 500 µL TBS lysis buffer (150 mM NaCl, 1 mM EDTA, 1 mM sodium orthovanadate, 1 mM NaF, 1 mM β-glycerophosphate, 2.5 mM sodium pyrophosphate, 1 mM PMSF, PhosSTOP, cOmplete mini protease inhibitor), sonicated for 10 sec at 20% amplitude and ultracentrifuged at 100,000 x g for 20 min at 4 °C. The 91  supernatants were collected as TBS-soluble extract, and the pellets were homogenized in RIPA buffer (TBS lysis buffer + 1% NP-40), sonicated, and again ultracentrifuged at 100,000 x g for 20 min at 4 °C. The supernatants were collected as RIPA-soluble extract. The protein concentration of RIPA-soluble fractions was measured by Bradford, diluted to 1 mg/mL for automated capillary electrophoresis western analysis. 10-week old AAV9-eGFP-Cre mice were perfused with PBS prior to brain collection. Brains were immediately incubated in 4% PFA overnight and transferred to PBS + 0.05% azide at 4 °C for long term storage. 40 µm thick sagittal brain sections were prepared using a vibratome (Leica, VT1000 S) and stored in PBS + 0.05% azide at 4 °C.  2.16.2 GrnR493X/R493X baseline characterization 80 week old Grn+/+ and GrnR493X/R493X mice were anesthetized using isoflurane and transcardially perfused with PBS before brain collection. Brains were hemisected down the midsagittal plane, one half was immediately flash frozen on dry ice, and the other fixed overnight in 4% PFA. Frozen halves were stored at -80 °C until lysate preparation, and fixed halves were transferred to PBS + 0.05% azide for long term storage. Floating sections were prepared and stored according to section 2.16.1. Frozen brain halves were thawed, homogenized in 250 µL RIPA buffer sonicated for 10 sec at 20% amplitude and ultracentrifuged at 100,000 x g for 20 min at 4 °C. The supernatants were collected as RIPA-soluble extract, and the insoluble protein pellet was further extracted with urea buffer (30 mM Tris-HCl pH 8, 7 M urea, 2 M thiourea, 4% CHAPS, PhosSTOP, cOmplete mini protease inhibitor) and centrifuged at 150,000 x g for 45 min at 4 °C. The protein concentration of RIPA-soluble fractions was measured by Bradford, 92  diluted to 1 mg/mL for ELISA and western blots. The insoluble urea fractions were diluted according to the protein concentration of corresponding RIPA-soluble fractions.  2.16.3 Vehicle/G418 treated Grn+/+ and GrnR493X/R493X mice ICV injected (bolus/iPRECIO® pump) vehicle/G418 treated Grn+/+ and GrnR493X/R493X -mice were anesthetized using isoflurane and transcardially perfused with PBS prior to brain collection. The majority of brains were hemisected down the midsagittal plane, one half was immediately flash frozen on dry ice, and the other fixed overnight in 4% PFA, though a subset of experiments were conducted on whole flash frozen brains. Frozen brain tissue was stored at -80 °C until lysate preparation, and fixed halves were transferred to PBS + 0.05% azide for long term storage. Floating sections were prepared and stored according to section 2.16.1. In a minority of cases, whole-brains were dissected, flash frozen, and stored at -80 °C until lysate preparation. Frozen hemi-brains were thawed, homogenized in 250 µL (500 µL for whole-brains) RIPA buffer sonicated for 10 sec at 20% amplitude and ultracentrifuged at 100,000 x g for 20 min at 4 °C. The protein concentration of RIPA-soluble fractions was measured by Bradford, diluted to 1 mg/mL for Pgrn and G418 quantification by ELISA/western blot.   2.17 Statistical analysis All values are expressed as the mean ± standard error of mean (SEM). In experiments where two groups were compared a standard unpaired two-tailed Student’s t-test was performed. For comparisons of more than two groups, one-way analysis of variance (ANOVA) was used followed by Tukey’s post hoc test. For comparisons of two or more 93  groups with multiple time points, two-way ANOVA was used followed by Bonferroni post hoc test comparing each column to all other columns. For comparing the frequency of lesion development and whisker barbering in our cohorts of Grn+/+ and GrnR493X/R493X mice, Chi Square test was used. p-values less than 0.05 were considered significant. Statistical analysis was performed using GraphPad Prism Software, Version 5.0.          94  Chapter 3: Exogenous PTC readthrough of nonsense mutant GRN expression constructs   3.1 Introduction Despite 23% of known causal FTLD-GRN variants introducing nonsense mutations, PTC readthrough of GRN nonsense mutations had not yet been experimentally demonstrated when this research project was initiated. Exogenous nonsense mutant gene expression is a common approach used to validate whether a particular mutation and surrounding sequence context are susceptible to PTC readthrough. Transfection is a process that enables exogenous delivery of extracellular material (DNA expression plasmids, mRNA, protein) into animal cells through a variety of methods. Typically, transfection methods gain entry into the cell by creating transient pores in the plasma to enable uptake of exogenous materials. Two of the most common transfection methods, lipofection, and electroporation were employed in this chapter. Lipofection gains entry into the cell through liposomal-membrane fusion, which releases encapsulated target material into the cytoplasm. Electroporation involves a brief application of an electric field to the cells, which temporarily increases the permeability of cell membranes allowing for the introduction of foreign material. The highly transfectable HEK293 cell line is believed to have originated from an embryonic adrenal precursor cell transformed by incorporation of an ~4.5 kb segment of adenovirus 5 DNA into chromosome 19 (357,358). HEK293 cells are used widely for transfection experiments due to their short doubling time, propensity to highly express exogenously delivered genes, and routine culture methods.  95  AAVs are single-stranded DNA viruses commonly used as expression vectors in mammalian systems. These viruses are particularly well-suited for transduction due to their apparent lack of pathogenicity and ability to stably integrate into the host cell genome at a specific AAVS1 locus in chromosome 19. These properties have generated significant interest in utilizing AAVs for gene therapy applications. As previously mentioned in section 1.2.7, an AAV GRN gene therapy-based approach has been shown to restore GRN expression in preclinical models (218,221), leading to the development of the AAV9 GRN expression vector, PR006, which is currently undergoing phase I/II clinical validation in FTLD-GRN patients.   Generating complex genetic knock-in mouse models generally requires time-consuming and expensive germ-line manipulations. ICV AAV injection into the murine neonatal brain represents an alternative, more cost-effective way to manipulate mouse CNS gene expression (359). When AAV are injected ICV on P0, mice develop stable long-term brain-wide neuronal transgene expression (355). In this chapter, we sought to determine whether we could induce PTC readthrough in HEK293 cells exogenously expressing nonsense mutant GRN with the aminoglycoside G418. We also set out to determine whether any of the recently generated CDX-series readthrough enhancer compounds could synergistically increase GRN nonsense mutation readthrough. Finally, we assessed whether we could induce in vivo brain PTC readthrough of exogenously expressed nonsense mutant GRN in our AAV-GRN-R493X-V5 mice.  96  3.2 Results   3.2.1 PTC readthrough in transiently transfected HEK293 cells PTC readthrough efficiency is affected by the specific nonsense codon sequence and the flanking nucleotide sequences (234,240). Therefore, to survey the responsiveness of GRN nonsense mutations to PTC readthrough, we designed several clinical GRN nonsense mutation expression constructs. We first transiently transfected HEK293 cells with S116X (UAA), R418X (UGA), and R493X (UGA) C-terminally V5-tagged human PGRN expression constructs (Figure 3-1, A) and treated them for 72 h with the aminoglycoside G418. Mock transfected HEK293 cells showed no detectable V5 signal (Figure 3-2). Since the V5 tag was inserted at the C-terminus, any V5 detected represented full-length PGRN generated by PTC readthrough. G418 induced GRN PTC readthrough in cells with the R418X and R493X mutations, with V5 (full-length PGRN) detected in both the cell lysate (intracellular) and supernatant (extracellular) fractions (Figure 3-2). The accumulation of full-length PGRN in both the intra- and extracellular fractions of transiently transfected HEK293 cells suggests that the PGRN readthrough product retains its ability to be post-translationally processed via the secretory pathway. The S116X mutant did not respond to G418 treatment (Figure 3-2), and this may be because aminoglycoside-induced PTC readthrough is most efficient at UGA nonsense codons and least efficient at UAA nonsense codons (UGA > UAG > UAA) (234).   97     98  Figure 3-1 Induction of PTC readthrough by G418 and CDX5 enhancers in cells stably expressing nonsense mutant GRN-V5. (A) Schematic of full-length PGRN highlighting the position of the S116X (UAA), R418X (UGA), and R493X (UGA) nonsense mutations in relation to the position of individual GRNs and the C-terminal V5 tag. (B) HEK293 cells transiently transfected with GRN-V5 expression constructs bearing the indicated nonsense mutations were treated with G418 for 72 h. (C) HEK293 cell lines stably expressing GRN-V5 with the indicated nonsense mutations were treated with G418 and the indicated concentrations of CDX5-1, CDX5-196, and CDX5-288 for 72 h. Cell culture supernatants (extracellular) and cell lysates (intracellular) were subjected to automated capillary electrophoresis western analysis. Full-length PGRN was detected with a V5 antibody. Actin was measured in cell lysates as a loading control. The readthrough enhancement ratios (normalized to G418 alone) are indicated under the lanes. The proportion loaded was 15-20X lower for the extracellular samples than for the intracellular samples.   99              Figure 3-2 Induction of PTC readthrough by G418 in transiently transfected cells expressing nonsense mutant GRN-V5. HEK293 cells transiently transfected with GRN-V5 expression constructs bearing the indicated nonsense mutations were treated with G418 for 72 h. Cell culture supernatants (extracellular) and cell lysates (intracellular) were subjected to automated capillary electrophoresis western analysis. Full-length PGRN was detected with a V5 antibody. Actin was measured in cell lysates as a loading control. The proportion loaded was 15-20X lower for the extracellular samples than for the intracellular samples.  100  3.2.2 PTC readthrough in stably transfected HEK293 cells To further screen and validate the GRN PTC readthrough observed in transiently transfected cells, we generated HEK293 lines stably expressing GRN-V5 nonsense mutant constructs.  When treated with G418, these cell lines exhibited a similar GRN PTC readthrough response to that observed in transiently transfected cells (Figure 3-1, B). Stable GRN-V5 expressing HEK293 lines provided an ideal screening platform to test which CDX-series compounds could most effectively enhance G418-induced GRN PTC readthrough. We treated HEK293 cell lines expressing nonsense mutant GRN-V5 with G418 alone or in combination with readthrough enhancers CDX5-1 (337), CDX5-196 (Figure 3-3, A), or CDX5-288 (Figure 3-3, B) for 72 h, and measured intra- and extracellular V5 levels. CDX5 compounds may enhance G418-induced PTC readthrough activity in both the R418X and R493X mutant lines, and full-length PGRN was detected in both the intra- and extracellular fractions (Figure 3-1, B). Given that the data presented in Figure 3-1 is n=1, we did not conduct statistical analysis and therefore viewed this data as a preliminary low confidence observation. Since CDX5-288 may possess the highest enhancement of readthrough activity (Figure 3-1, B), we selected co-treatment with G418 and CDX5-288 for further validation in patient hiPSC-derived cortical neurons and astrocytes and AAV-GRN-R493X-V5 mouse model.   101                               Figure 3-3 Chemical structures of CDX5-196 and CDX5-288. N-substituted phthalimide derivatives CDX5-196 (A) and CDX5-288 (B).    102  3.2.3 PTC readthrough in HEK293 cells transduced with AAV-GRN-R493X-V5 viral particles Upon generating AAV-GRN-R493X-V5 viral particles, we wanted to assess whether transduced cells expressing the GRN-R493X-V5 construct were responsive G418-induced PTC readthrough before proceeding with in vivo studies. To this end, we transduced HEK293 cells for a total of 5 days with increasing concentrations of AAV-GRN-R493X-V5 and co-treated them with G418 for 72 h. G418-induced GRN-R493X-V5 PTC readthrough was only observed in HEK293 cells transduced with the highest viral titer of 8.8E10 PFU/mL, as indicated by both intra- and extracellular V5 detection (Figure 3-4).       103                          Figure 3-4 Induction of PTC readthrough in cells transduced with increasing titers of AAV-GRN-R493X-V5.  HEK293 cells transduced for 5 days with increasing titers of AAV-GRN-R493X-V5 viral vector were treated with G418 48 h post-transduction for an additional 72 h. Cell culture supernatants (extracellular) and cell lysates (intracellular) were subjected to automated capillary electrophoresis western analysis. Full-length PGRN was detected with a V5 antibody. The proportion loaded was 15-20X lower for the extracellular samples than for the intracellular samples.   104  3.2.4 Technical demonstration of CNS P0 delivery of AAV particles and bolus ICV injection in adult mice Since the AAV-GRN-R493X-V5 plasmid does not contain a reporter gene, we first wanted to establish that our AAV injection technique achieved an adequate percentage of neuronal transduction. Before testing the AAV-GRN-R493X-V5 virus, we first conducted P0 pup ICV injections of a serotype matched AAV9-eGFP-Cre expression vector. We observed diffuse eGFP expression in the brains of 10 week old AAV9-eGFP-Cre mice (Figure 3-5), thus validating that our AAV injection technique should be capable of achieving robust CNS expression of GRN-R493X-V5. To confirm whether the stereotactic coordinates (-1.0 mm lateral/-0.3 mm posterior/-3.0 mm depth to bregma) we planned to use for targeted infusion of mice right lateral ventricles resulted in successful ICV delivery; we conducted a test ICV injection of 0.1% Fast Green FCF dye in a healthy control C57BL/6J mouse. Photographic observation of freshly harvested dye-injected brain tissue demonstrated the expected ventricular distribution of Fast Green FCF dye (Figure 3-6).   105          Figure 3-5 Technical demonstration of AAV P0 ICV injection method. P0 ICV injection using an AAV9-eGFP-Cre viral vector with expression driven by the human SYN1 promoter. Diffuse brain-wide eGFP (green) expression apparent 10 weeks after bilateral P0 ICV injection. Cell nuclei were counterstained with DAPI (blue). Scale bar, 1 mm.   106               Figure 3-6 Technical demonstration of bolus ICV injection method in adult mice. A C57BL/6J mouse was stereotactically injected with 5 µL 0.1% Fast Green FCF dye at coordinates: -1.0 mm lateral/-0.3 mm posterior/-3.0 mm depth to bregma. Immediately following dye injection, the brain was collected and photographed, demonstrating ventricular delivery.   107  3.2.5 PTC readthrough in AAV-GRN-R493X-V5 mice Having demonstrated PTC readthrough in exogenous GRN nonsense mutant expression models in vitro, we sought to demonstrate initial proof-of-concept for this approach in vivo. Brain PTC readthrough induced by ICV G418 has been previously demonstrated in mice harboring an inducible gene-targeting system driven by the full-length expression of a nonsense mutant Cre recombinase and in R294X Mecp2 knock-in mice (360,361). Newborn pups (P0) were bilaterally injected ICV with virus solution and aged to at least 6 weeks to allow for sufficient blood-brain-barrier (BBB) maturation before treatment (362). RIPA-soluble brain lysates from each ICV treated AAV-GRN-R493X-V5 mouse were probed for V5 expression to assess the extent of GRN R493X PTC readthrough in vivo. No V5 signal was detected in either the vehicle (n=6) or CDX5-288 (n=4) AAV-GRN-R493X-V5 brains 72 h after ICV injection (Figure 3-7, A-B). By contrast, ICV injections with G418 alone (n=5) or G418 and CDX5-288 (n=4) induced clear GRN-R493X-V5 PTC readthrough, as shown by the detection of V5 signal at the expected molecular weight of PGRN, using automated capillary electrophoresis western analysis (Figure 3-7, A-B). G418 significantly induced readthrough in AAV-GRN-R493X-V5 mice compared to treatment with vehicle solution (Figure 3-7, A-B). Though robust V5 levels were detected, co-treatment of AAV-GRN-R493X-V5 mice with CDX5-288 did not increase full-length PGRN levels compared to G418 alone (Figure 3-7, A-B). Our data indicate that short term administration of the aminoglycoside G418 can induce GRN PTC readthrough in vivo when delivered intraventricularly in an exogenous AAV transgene expression model.   108                           Figure 3-7 Induction of PTC readthrough in AAV-R493X-GRN-V5 mice. (A) 6-week-old AAV-GRN-R493X-V5 mice were stereotactically injected ICV with either vehicle solution, G418, CDX5-288, or a combination of G418 + CDX5-288 ICV and sacrificed after 72 h. Whole-brain RIPA-soluble protein extracts were subjected to automated capillary electrophoresis western analysis. Full-length PGRN was detected with a V5 antibody, and actin was measured in brain lysates as a loading control. (B) Chemiluminescence quantification of automated capillary electrophoresis western analysis V5 detection normalized to actin. Values are shown as mean ± SEM; * p < 0.05, one-way ANOVA with Tukey’s multiple comparison test.   109  3.3 Discussion We generated several human expression constructs with known clinical GRN nonsense mutations and observed a more robust PTC readthrough response to G418 and CDX5-288 enhancer treatment in R418X and R493X mutant HEK293 cells compared to G418 alone or co-treatment with other enhancer compounds. To avoid confounding measures of endogenous PGRN in HEK293 cells and ensure the measured PGRN was reflective of full-length protein produced by readthrough, the GRN expression constructs bore a C-terminal V5 tag. The readthrough enhancer compounds are N-substituted phthalimide derivatives identified in a high-throughput screen in combination with sub-active concentrations of the aminoglycoside paromomycin and further systematically functionalized to increase their potency (337). These results provide a clear demonstration that GRN UGA PTCs are most susceptible to readthrough, in alignment with previously published reports evaluating the impact of nonsense codon sequence on readthrough efficiency (234).   The production of AAV-GRN-R493X-V5 viral particles enabled us to validate whether PTC readthrough could be achieved from exogenously delivered CNS nonsense mutant GRN. Bilaterally injecting this virus into the developing P0 murine lateral ventricles induced widespread CNS neuronal expression of V5-tagged R493X GRN. Since G418 and other aminoglycosides do not readily cross the BBB, we sought to determine whether ICV administration of compounds could be a viable strategy for widespread brain exposure and readthrough. Indeed, our results provide proof-of-concept that a single ICV injection of G418 can induce PTC readthrough in an AAV-GRN-R493X-V5 110  mouse model in only 72 h. However, given the likely massive overexpression of the GRN-R493X-V5 construct driven by the strong hybrid chicken β-actin promoter, it is difficult to make meaningful conclusions regarding the optimal dosage of either G418 or CDX5-288 enhancer compound. The recently generated GrnR493X/R493X nonsense mutant knock-in mouse (165) is a superior model for further exploration of the optimal in vivo doses of both G418 and enhancer compounds (see chapter 5).     111  Chapter 4: Generation of FTLD-GRN hiPSC lines and endogenous PTC readthrough of GRN nonsense mutant hiPSC-derived CNS cell types  4.1 Introduction For decades ethical controversy and limited availability of human embryonic stem cells limited their basic science research applications. As discussed in section 1.2.5, over a decade ago, Dr. Shinya Yamanaka published an elegant study demonstrating the first instance of adult somatic cell reprogramming into hiPSCs (195). This masterful work has since sparked a revolution in our understanding of human developmental biology and our ability to model human genetic disorders that originate in previously unattainable tissues. The reprogramming of human somatic cells into hiPSCs is now routine in labs worldwide, enabling rapid developments in personalized medicine and improved investigation of pathological mechanisms driving complex disease processes. Several methodologies have been established enabling somatic cell to hiPSC reprogramming through the exogenous delivery of Yamanaka factors (OCT3/4, SOX2, KLF4, MYC, and LIN28); the most common being Sendai viral transduction, non-integrating episomal transfection, mRNA transfection, and protein transduction (reviewed here (363,364)).   These technological advances have been particularly relevant to the fields of neurology and neurodegeneration, as a multitude of hiPSC differentiation methods have been 112  developed that enable the derivation of distinct neuronal subtypes and glial cell types (196-198). Decades of embryonic neurodevelopmental biology research provided the foundational knowledge of growth factor patterning gradients required to guide the establishment of hiPSC to neuroectoderm differentiation protocols. Chemical inhibition of the anaplastic lymphoma kinase family has been shown to disrupt BMP4/TGF-β signaling through the TGFβR-1 receptor and downstream activation of SMAD signal transducers, promoting expression of the neuroectoderm lineage SOX1 transcription factor while suppressing endoderm/mesoderm pathways (196). This approach, known as dual-SMAD-inhibition, is widely used to derive pure populations NPCs for further downstream differentiation/maturation into various CNS cell types.   hiPSC-derived NPCs neurodevelopmentally mirror the neuroepithelial cells that line the apical surface of the ventricular zone and asymmetrically divide to produce radial glial stem cells, which give rise to the majority of neuronal and glial cell types (365). Extrinsic patterning cues in the form of recombinant protein growth factors (e.g., BDNF/GDNF) are often provided to mature NPCs into the desired neuronal cell type. In 2015, Bardy et al. generated a novel neuronal culture medium (BrainPhysTM) that more accurately reflected neurophysiological ion concentrations and enhanced hiPSC-derived neuronal electrophysiological maturation (352). Since obtaining human CNS neurologic tissue primary cell cultures is severely limited by the risks and potential complications associated with brain biopsies, the use of hiPSC-derived CNS tissue modelling has accelerated research into human neurobiology.   113  The field of molecular biology was radically transformed following the landmark 2012 publication by Dr. Doudna and Dr. Charpentier, demonstrating that the bacterial adaptive immune system (CRISPR/Cas9) could be co-opted for targeted genetic engineering (366). Briefly, gRNA (dual complex of crRNA and tracrRNA) forms a ribonucleoprotein complex with the Cas9 endonuclease, and the crRNA-guide sequence localizes the complex to a complementary sequence of the genome triggering double-strand break formation. Utilization of CRISPR/Cas9 gene editing is ubiquitous throughout molecular biology research, with hiPSC modelling efforts being a major benefactor. Dissecting precise phenotypic contributions of disease-associated SNPs has been hampered by inadequate control hiPSC lines often derived from healthy and/or genetically related individuals, which introduces background genetic variation that may either silence or amplify observed phenotypes. CRISPR/Cas9 gene editing solves this dilemma, enabling the generation of isogenic control/mutant hiPSC lines with identical genetic backgrounds.   To expand on the results presented in chapter 3, we sought to determine whether PTC readthrough treatments could restore endogenous nonsense mutant GRN expression in hiPSC-derived cortical neurons and astrocytes. To evaluate readthrough efficiency in GRN nonsense mutant hiPSC-derived brain cells, we measured both GRN mRNA and intracellular/extracellular PGRN protein levels using qPCR and immunoassays. We also assessed whether restoring PGRN expression in mutant neurons could rescue mutant lysosomal dysfunction.  114  4.2 Results   4.2.1 Generation of WT and FTLD-GRN patient-derived hiPSC lines We generated hiPSC lines from erythroid progenitors isolated from peripheral blood obtained from a healthy control (WT) and an FTLD-GRN patient carrying the g.2923 C > T (p.R418X) GRN nonsense mutation (R418X+/-) (350). Additionally, our collaborators provided a stock of a previously published hiPSC line produced from an FTLD-GRN patient bearing the g.585 C > A (p.S116X) GRN nonsense mutation (S116X+/-) (60). These pluripotent cell lines enabled us to produce disease-relevant CNS cell types to assess whether the compounds identified in chapter 3 could also restore endogenous nonsense mutant GRN expression.  4.2.2 Generation of an isogenic GRN R493X homozygous knock-in hiPSC line using CRISPR/Cas9 gene editing The development of isogenic hiPSC lines limits non-specific phenotypic differences from background genetic variability when comparing two distinct hiPSC lines derived from healthy control and mutation carriers. We utilized the CRISPR/Cas9 gene editing tool to homozygously introduce the most common FTLD-GRN mutation, p.R493X, into our WT hiPSC line (Figure 4-1, A-C). Clones positive for the successful introduction of the HindIII restriction enzyme digest site (Figure, 4-1, B) were Sanger sequenced to confirm seamless homologous recombination of the knock-in ssODN (Figure 4-1, C). The resulting isogenic mutant clone, R493X-/- KI, is the first hiPSC model of the rare form of NCL, CLN11. As expected, R493X-/- KI hiPSC-derived cortical neuronal cultures 115  immunofluorescently stained for PGRN exhibit limited expression levels compared to the parental isogenic WT neurons (Figure 4-2).  4.2.3 Characterization of hiPSC line pluripotency To characterize the hiPSC lines, we assessed their expression of pluripotent markers at the protein and mRNA level, and their ability to differentiate into all three germ layers (Figure 4-3, A-B). Colonies from the WT, S116X+/-, R418X+/-, and R493X-/- KI hiPSC lines exhibited strong nuclear staining for the pluripotent transcription factors NANOG and OCT4 (Figure 4-3, A). Moreover, these hiPSC lines possessed elevated expression of pluripotent markers, LIN28, OCT3/4, SOX2, and NANOG mRNA transcripts (Figure 4-3, B). To functionally validate these hiPSC lines’ pluripotential, we conducted in vitro differentiation into the primary germ layers. All four hiPSC lines could differentiate into ectodermal, mesodermal, and endodermal tissue as indicated by SOX1, DESMIN, and SOX17 expression, respectively (Figure 4-3, A). Since chromosome abnormalities are known to occur during hiPSC reprogramming, we had the hiPSC lines that we generated (WT, R418X+/-, and R493X-/- KI) karyotyped, confirming that they were karyotypically normal (Figure 4-3, A). Karyotyping analysis of the S116X+/- hiPSC line was normal as previously described (60).     116                       117  Figure 4-1 Generation of isogenic CRISPR/Cas9 gene edited R493X-/- KI hiPSC line from WT. (A) Schematic representation of the gene editing strategy using the CRISPR/Cas9 system. (B) Clonal screening for the silent introduction of the AAGCTT HindIII restriction enzyme site to identify potential R493X knock-in clones. (C) Simultaneous Sanger sequencing of the R493 codon region in both GRN alleles in WT and isogenic R493X-/- KI clone confirming homozygous introduction of the UGA nonsense codon at codon 493 (red highlight) and silent deletion of the PAM site.    118    Figure 4-2 PGRN immunofluorescence in WT and R493X-/- KI hiPSC-derived cortical neurons. R493X-/- KI hiPSC-derived cortical neurons (DIV 50) possess greatly reduced and more diffuse PGRN expression (green) than the WT parental line. Cell nuclei were counterstained with DAPI (blue). Scale bar, 10 µm.  119       Figure 4-3 Characterization of WT and GRN-deficient hiPSC lines. (A) Immunofluorescence analysis of pluripotent markers in WT, S116X+/-, R418X+/-, and R493X-/- KI hiPSC lines, and their respective normal karyotypes. In vitro trilineage differentiation of WT, S116X+/-, R418X+/-, and R493X-/- KI hiPSC lines, cells were immunostained for SOX1 (ectoderm), DESMIN (mesoderm), SOX17 (endoderm). Cell nuclei were counterstained with DAPI (blue) except for SOX17. Scale bar, 50 µm. (B) 120  mRNA expression of pluripotent reprogramming factors in WT, S116X+/-, R418X+/-, and R493X-/- KI hiPSC lines relative to the values in WT fibroblasts, as assessed by qPCR. Values are shown as mean ± SEM.     121  4.2.4 Differentiation of WT and GRN-deficient hiPSC lines into cortical neurons and astrocytes  We then differentiated the hiPSC lines into cortical neurons using a recently reported  version of the dual SMAD inhibition neuroectoderm induction protocol (351) in  combination with BrainPhysTM medium NPC neuronal maturation (352) (Figure 4-4, A).  The resulting neuronal cultures possessed high levels of purity, as indicated by the high  percentage of MAP2 positive (> 95%) and low percentage of GFAP positive cells (< 4%)  (Figure 4-4, B-D). This high degree of purity is likely attributable to the early addition of  the proprietary CultureOneTM supplement known to limit NPC proliferation during neuronal maturation. Additionally, greater than 75% of cells expressed both FOXG1 and  TBR1, confirming these neurons express cortical layer VI markers (Figure 4-4, B, E,  and F). Synaptogenesis was demonstrated in these cultures by staining to analyze the  expression of synapsin and excitatory/inhibitory synaptic markers (Figure 4-5, A-B).  Interestingly, GRN mutant hiPSC-derived cortical neurons all exhibited significantly  lower VGLUT1+ excitatory synapse levels than WT (Figure 4-5, A-B). Astrocytes were  also differentiated from NPCs using an astrocyte differentiation/maturation kit protocol.  Mature astrocyte cultures (DIV 60+) derived from both WT and R493X-/- KI hiPSC lines  both expressed high levels (80%) of GFAP (Figure 4-4, G-H). Co-culturing cortical  neurons with WT astrocytes on MEA plates induced accelerated their electrophysiological maturation and the formation of neural networks with frequent and  robust spontaneous action potentials measured by MEA (Figure 4-5, C and Figure 4-6,  A-B).   122    123  Figure 4-4 Differentiation and characterization of cortical neurons and astrocytes derived from WT and GRN-deficient hiPSCs. (A) Brightfield images of the cells at different stages of cortical neuronal differentiation. SB = SB 431542, LDN = LDN 193189, RI = Y-27632, BP = BrainPhysTM, N2 = N-2 supplement, B27 = B-27 supplement. (B) Representative immunofluorescence images of DIV 50 WT, S116X+/-, R418X+/-, and R493X-/- KI hiPSC-derived cortical neurons stained for MAP2, GFAP, TUJ1, FOXG1 (forebrain), and TBR1 (cortical layer VI). Cell nuclei were counterstained with DAPI (blue). Scale bar, 50 µm. (C-F) Cells positive for MAP2, GFAP, FOXG1, and TBR1 (neuronal, astrocytes, forebrain, and cortical layer VI markers, respectively) as a percentage of DAPI+ cells. On average, ~900 cells were analyzed per replicate, in (C-F) n = 3 independent cultures, 3 images per biological replicate; values are shown as mean ± SEM. (G) Representative immunofluorescence images of DIV 60+ WT and R493X-/- KI hiPSC-derived astrocytes stained for GFAP. Cell nuclei were counterstained with DAPI (blue). Scale bar, 50 µm. (H) Cells positive for GFAP as a percentage of DAPI+ cells. On average, ~400 cells were analyzed per replicate, n = 3 independent cultures, 3 images per biological replicate; values are shown as mean ± SEM.    124     125  Figure 4-5 Characterization of hiPSC-derived cortical neuron synaptic development and neural network formation. (A) Representative immunofluorescence images of DIV 50 WT, S116X+/-, R418X+/-, and R493X-/- KI hiPSC-derived cortical neurons stained for synapsin, VGLUT1 (excitatory), and GAD65 (inhibitory). Cell nuclei were counterstained with DAPI (blue). Scale bar, 20 µm. (B) Quantification of the synaptic density (excitatory/inhibitory) per 100 µm2 area of TUJ1+ staining in DIV 50 WT, S116X+/-, R418X+/-, and R493X-/- KI hiPSC-derived cortical neuron cultures. n = 3 independent cultures, 3 images per biological replicate; values are shown as mean ± SEM; *** p < 0.0001, one-way ANOVA with Tukey’s multiple comparison test. (C) Electrophysiological properties of DIV 50 WT, S116X+/-, R418X+/-, and R493X-/- KI hiPSC-derived cortical neurons co-cultured with WT human astrocytes were recorded via MEA to quantify the number of spikes and bursts detected over a 10 min interval. n = 4 independent cultures; values are shown as mean ± SEM.   126                  Figure 4-6 Co-culturing hiPSC-derived cortical neurons with hiPSC-derived astrocytes accelerates electrophysiological maturation and neural network formation. Weekly electrophysiological recordings were performed on WT astrocytes, WT cortical neurons, and WT cortical neurons + WT astrocytes MEA plate cultures. Recordings were obtained via MEA to quantify the number of spikes (A) and network bursts (B) detected over a 5 min interval. WT astrocytes alone were excluded from network burst analysis due to lack of electrical activity detected in (A). n = 4 127  independent cultures; values are shown as mean ± SEM, *** p < 0.001, ** p < 0.01, p * < 0.05, two-way ANOVA with Bonferroni post-tests.   128  4.2.5 PTC readthrough in GRN-deficient hiPSC-derived cortical neurons hiPSC-derived cortical neurons were matured to DIV 50 and exposed to PTC readthrough compounds for 72 h. The levels of WT neuronal full-length PGRN expression were not sufficiently high for detection by western blotting with available anti-PGRN antibodies (Figure 4-7, A-B and Figure 4-8). As an alternative, intracellular and concentrated extracellular fractions were assayed by ELISA using a PGRN polyclonal antibody to multiple epitopes (GRN 1/3/5/7 peptides) that detects not only full-length PGRN but also truncated PGRN as well as granulin (GRN) peptides, collectively referred to here as PGRN/GRNs. Vehicle-treated S116X+/-, R418X+/-, and R493X-/- KI neurons expressed 33.1% ± 1.5%, 49.9% ± 1.3%, and 74.5% ± 1.2% less intracellular PGRN/GRNs than vehicle-treated WT neurons, as expected (Figure 4-9, A-D). In general, treatment of FTLD-GRN mutant neurons with G418 without or with CDX5-288 produced a similar pattern of PGRN/GRNs expression to that observed in the stably transfected HEK293 cell lines bearing the same mutations. Again, the S116X+/- neurons exhibited little to no intra- or extracellular increase in the levels of PGRN/GRNs in response to PTC readthrough treatment (Figure 4-9, A, E). R418X+/- neurons exposed to G418 alone or to G418 and CDX5-288 showed significantly increased intracellular PGRN/GRNs levels to 67.5% ± 1.2% and 75.8% ± 5.8% of vehicle-treated WT levels, respectively (Figure 4-9, B). Treatment of R493X-/- KI neurons with G418 alone significantly increased intracellular PGRN/GRNs levels, to 54.0% ± 5.5% of vehicle-treated WT levels, and exposure to G418 and CDX5-288 further significantly increased intracellular PGRN/GRNs levels compared G418 alone, to 83.9% ± 1.3% of vehicle-treated WT (Figure 4-9, C). For both R418X+/- neurons and R493X-/- KI neurons, 129  extracellular PGRN/GRNs levels were not significantly increased in response to treatment, although a trend toward a minor increase was observed (Figure 4-9, F-G). Since R493X-/- KI neurons have no intact GRN allele, the observed increase in intracellular PGRN/GRNs is derived from the mutant alleles. G418 did not show significant cellular toxicity in iPSC-derived neurons (Figure 4-10).    130                Figure 4-7 Baseline expression and secretion of PGRN in WT hiPSC-derived cortical neurons and astrocytes. PGRN expression is significantly greater in the intra- (A) and extracellular (B) fractions of WT hiPSC-derived astrocytes compared to cortical neurons. WT and R493X-/- KI hiPSC-derived cortical neurons and astrocytes were cultured in fresh medium for 72 h. Intracellular (1 mg/mL lysate) and extracellular (25X concentrated supernatant) samples were subjected to PGRN ELISA. Values are shown as mean ± SEM; *** p < 0.0001, Student’s t-test.        131                        Figure 4-8 Detecting PGRN in WT and R493X-/- KI hiPSC-derived cortical neurons  by western blot. Expression of intracellular PGRN was assessed in DIV 80 WT and  R493X-/- KI hiPSC-derived cortical neuron cultures treated with G418, combination with  CDX5-288, or rec. human PGRN. Expression of intracellular ~70 kDa PGRN was only  detected in WT and R493X-/- KI neurons treated with 1 µg/mL rec. human PGRN. GRN- 2,3 peptides were only detected in WT neurons treated with rec. human PGRN.  Neuronal lysates were analyzed by western blotting, using actin as the loading control.  ns = nonspecific. 132    133  Figure 4-9 Induction of PTC readthrough by G418 and enhancers in hiPSC-derived cortical neurons bearing FTLD-GRN nonsense mutations. DIV 50 S116X+/-, R418X+/-, R493X-/- KI, and WT hiPSC-derived cortical neurons were treated with G418 and CDX5-288 at the indicated concentrations for 72 h. Intracellular (A-D, 1 mg/mL lysate) and extracellular (E-H, 25X concentrated supernatants) samples were subjected to PGRN ELISA using a polyclonal anti-PGRN antibody that targets multiple epitopes (GRN 1/3/5/7 peptides) and cannot differentiate between PGRN/GRNs. n = 3 independent cultures; values are shown as mean ± SEM; * p < 0.05, ** p < 0.01, *** p < 0.0001, one-way ANOVA with Tukey’s multiple comparison test.   134                            Figure 4-10 Quantification of G418-induced neuronal cytotoxicity. R418X+/- hiPSC-derived neurons treated with escalating doses of G418 for 120 h with fresh media/drug solutions replaced after 72 h. Cultures were stained with Hoechst dye and counted using a Cellomics ArrayScanTM device. n = 3 independent cultures, 12 images per biological replicate; values are shown as mean ± SEM.   0200040006000Avg. # of cells / fieldG418 (g/mL) - 10 30 100135  qPCR analysis revealed that readthrough compounds significantly increased GRN mRNA levels in R493X-/- KI neurons. This observation was anticipated as mRNAs bearing nonsense mutations are targeted for degradation by nonsense-mediated mRNA decay (NMD) (233), and PTC readthrough enables escape of nonsense mutant mRNA from degradation by NMD. Vehicle-treated R493X-/- KI neurons expressed 5.1-fold less GRN mRNA relative to vehicle-treated WT neurons (Figure 4-11), indicating downregulation of mutant mRNA by NMD. When treated with G418 or combination, R493X-/- KI neurons express increased GRN mRNA levels (Figure 4-11). The selective stabilization of PTC-bearing GRN mRNA over WT GRN mRNA strongly supports inhibition of NMD consequent to readthrough in R493X-/- KI neurons. Taken together, these results show that the G418 - CDX5-288 combination induces PTC readthrough and effectively restores intracellular levels of PGRN in both heterozygous and homozygous GRN nonsense mutant neurons to levels approaching that of healthy control cells.      136                         Figure 4-11 Selective increase of nonsense mutant GRN mRNA in R493X-/- KI hiPSC-derived cortical neurons in response to PTC readthrough treatments. qPCR analysis of human GRN mRNA levels in DIV 50 WT and R493X-/- KI hiPSC-derived cortical neurons treated with G418 and CDX5-288 at the indicated concentrations for 72 h. Relative mRNA levels were normalized to the mean of GAPDH and HPRT1 housekeeping genes and compared to vehicle-treated (VT) WT. n = 3 independent cultures; values are shown as mean ± SEM; * p < 0.05, ** p < 0.01, *** p < 0.0001, one-way ANOVA with Tukey’s multiple comparison test.   137  4.2.6 PTC readthrough rescues lysosomal dysfunction in R493X-/- KI hiPSC-derived cortical neurons The specific nonsense mutant codon (e.g., R493X-/- KI, Arg-CGA to X-UGA) restricts which near-cognate aminoacyl-tRNA molecules (Trp UGG, Cys UGC, Arg CGA, etc.) pair with the PTC in the ribosome A site and contribute their amino acid to the growing polypeptide during a readthrough event. Previous studies have demonstrated that the amino acids most commonly incorporated at UGA nonsense mutations during readthrough were Trp, followed by Cys and Arg (367). Thus, it is likely that a proportion of full-length PGRN derived from GRN R493X-/- KI PTC readthrough would possess a missense mutation at codon 493. Therefore, it was important to assess the functionality of PGRN produced by PTC readthrough through its ability to rescue known cellular FTLD-GRN and NCL phenotypes.   As discussed in sections 1.2.4 and 1.2.6, lysosomal defects are among the earliest disease phenotypes in Grn-/- mice. Grn-/- brains upregulate the expression, maturation rate, and catalytic activity of cathepsin lysosomal proteases (cathepsin D, B, and L) in an age-dependent manner (119), and this aberrant lysosomal phenotype has been previously rescued in vivo by treating aged Grn-/- mice with AAV-mediated Grn gene therapy (218). Moreover, hiPSC-derived neurons with heterozygous GRN mutations have been shown to exhibit an increased CTSD maturation phenotype (200). We quantified the CTSD levels in aged (DIV 80) WT and R493X-/- KI hiPSC-derived cortical neurons and observed significantly increased expression of the mature form of CTSD in vehicle-treated R493X-/- KI neurons compared with WT neurons (Figure 4-12, A-B). 138  Treating WT neurons with G418, G418 + CDX5-288, or rec. PGRN did not affect mature CTSD expression levels (Figure 4-12, A-B). However, treating R493X-/- KI neurons with G418 and CDX5-288 significantly reduced mature CTSD levels, thus rescuing their dysregulated lysosomal enzyme phenotype. Importantly, this effect was also observed in R493X-/- KI neurons treated with extracellular rec. PGRN with a trend towards reduced mature CTSD levels (Figure 4-12, A-B). These findings provide evidence that PGRN expression restored by PTC-readthrough in R493X-/- KI cortical neurons (Figure 4-8, C) is biologically active and functional in vitro.   139                                 Figure 4-12 GRN PTC readthrough rescues FTLD-GRN/CLN11 lysosomal pathological CTSD maturation phenotype in R493X-/- KI hiPSC-derived cortical neurons. (A) DIV 80 WT and R493X-/- KI hiPSC-derived cortical neurons were treated with vehicle solution, G418 alone, G418 in combination with CDX5-288, and rec. human PGRN at the indicated concentrations for 72 h. Expression of mature CTSD in treated WT and R493X-/- KI cortical neuron lysates analyzed by western blotting, using actin as 140  the loading control. (B) Densitometric quantification of CTSD expression in the aforementioned cortical neuron lysates normalized to vehicle-treated WT levels. n = 3-6 independent cultures; values are shown as mean ± SEM; * p < 0.05, ** p < 0.01, one-way ANOVA with Tukey’s multiple comparison test.        141  4.2.7 PTC readthrough in R493X-/- KI hiPSC-derived astrocytes Next, WT and R493X-/- KI hiPSC-derived astrocytes were matured to DIV 60+ to extend testing of readthrough compounds to another relevant CNS cell type with endogenous nonsense mutant GRN expression. WT hiPSC-derived astrocytes produced 17.9-fold more intracellular PGRN/GRNs, secreted 25.0-fold more PGRN/GRNs, and expressed 3.7-fold higher GRN mRNA than WT hiPSC-derived neurons as measured by ELISA and qPCR (Figure 4-6 and 4-13). This considerably higher expression level enabled analysis of intracellular PGRN levels by western blotting in hiPSC-derived astrocyte cultures (Figure 4-14). The PGRN antibody used in this western blot analysis has previously been shown to detect full-length PGRN and GRNs (GRN-2,3) (118). Both PGRN and GRN-2,3 peptides were detected in WT astrocytes, though the GRN-2,3 peptides were more abundant than full-length PGRN (Figure 4-14, A). R493X-/- KI astrocytes expressed small amounts of a band at ~70 kDa that may be PGRN truncated at R493, and no detectable GRN-2,3 peptides (Figure 4-14, A).   Treating R493X-/- KI astrocytes with either G418 alone or G418 and CDX5-288 significantly increased intracellular ~70 kDa PGRN by 3.3- and 4.6-fold, respectively (Figure 4-14, A, B.i). This increase in intracellular ~70 kDa PGRN was accompanied by a small increase in GRN-2,3 peptide signal, which indicates that at least some of the protein entered lysosomes and was cleaved into individual GRNs (Figure 4-14, A, B.ii). Exposing R493X-/- KI astrocytes to extracellular rec. PGRN showed that these cells could take up and process PGRN, as the vast majority of endocytosed full-length PGRN was converted into GRNs (Figure 4-14, A-B). Since the conversion rate of full-length 142  PGRN to GRN-2,3 peptides is so efficient in astrocytes, we hypothesized that full-length PGRN generated by readthrough would be rapidly processed into GRNs, perhaps explaining why we observe limited full-length PGRN in G418 and CDX5-288 combination-treated R493X-/- KI astrocytes. The lysosomal cysteine protease CTSL cleaves PGRN into GRNs (150). Therefore, we tested whether inhibiting CTSL during G418 and CDX5-288 induced PTC readthrough in R493X-/- KI astrocytes could enable clear visualization of full-length PGRN by western blot. Co-treating R493X-/- KI astrocytes with 30 µM Z-Phe-Phe-FMK (CTSL inhibitor), G418, and CDX5-288 led to accumulation of PTC readthrough derived full-length PGRN (Figure 4-14, C-D), consistent with our hypothesis.   143                           Figure 4-13 qPCR analysis of GRN mRNA levels in WT hiPSC-derived cortical neurons and astrocytes. Relative GRN mRNA levels were measured in vehicle-treated (VT) DIV 50 WT hiPSC-derived cortical neurons and DIV 60+ WT hiPSC-derived astrocytes and were normalized to the mean of GAPDH and HPRT1 housekeeping genes and compared to VT cortical neurons. n = 3 independent cultures; values are shown as mean ± SEM; *** p < 0.0001, Student’s t-test.   144    145  Figure 4-14 Induction of PTC readthrough by G418 and enhancers in R493X-/- KI hiPSC-derived astrocytes demonstrated by western blot. (A) R493X-/- KI hiPSC-derived astrocytes were treated with vehicle solution, G418 alone, G418 in combination with CDX5-288, and rec. human PGRN at the indicated concentrations for 72 h. Expression of PGRN and GRN-2,3 peptides in treated WT and R493X-/- KI astrocyte samples were analyzed by western blotting, using actin as the loading control. (B) Densitometric quantification of ~70 kDa PGRN (i) and GRN-2,3 peptide (ii) in astrocyte lysates (A) normalized to vehicle-treated WT levels. (C) R493X-/- KI hiPSC-derived astrocytes were treated with vehicle solution, G418 in combination with CDX5-288, and G418 CDX5-288 combination with either 10 or 30 µM of Z-Phe-Phe-FMK for 72 h. Again, expression of PGRN in WT and R493X-/- KI astrocyte lysates was also analyzed by western blotting, using actin as the loading control. n = 3 independent cultures; values are shown as mean ± SEM; p < 0.05, ** p < 0.01, *** p < 0.0001, one-way ANOVA with Tukey’s multiple comparison test.   146  We next used ELISA to measure intra- and extracellular PGRN/GRNs levels in astrocytes. Vehicle-treated R493X-/- KI astrocytes expressed 81.8% ± 1.6% less intracellular PGRN/GRNs than vehicle-treated WT astrocytes (Figure 4-15, A-B). R493X-/- KI astrocytes exposed to G418 alone or G418 and CDX5-288 showed significantly increased intracellular PGRN/GRNs levels, to 75.7% ± 6.5% and 75.8% ± 3.2%, respectively, of vehicle-treated WT levels, only slightly less than PGRN/GRNs restoration achieved through the application of exogenous rec. PGRN (Figure 4-15, B). Vehicle-treated R493X-/- KI astrocytes secreted 94.9% ± 0.3% less PGRN/GRNs than vehicle-treated WT astrocytes (Figure 4-15, C-D). Exposure to G418 alone or G418 and CDX5-288 caused a considerable increase in secreted PGRN/GRNs, to 30.4% ± 1.7% and 32.5% ± 1.2%, respectively, of vehicle-treated WT levels (Figure 4-15, C-D), unlike R493X-/- KI cortical neurons, where treatment increased intracellular PGRN/GRNs but only subtly increased PGRN/GRNs secretion.   As observed in cortical neurons, qPCR analysis found that PTC readthrough compounds also significantly increased in GRN mRNA levels in R493X-/- KI astrocytes. Vehicle-treated R493X-/- KI astrocytes expressed 3.3-fold less GRN mRNA than vehicle-treated WT astrocytes (Figure 4-16). When treated with G418 or combination with CDX5-288, R493X-/- KI astrocytes showed significantly increased GRN mRNA levels compared to vehicle-treated control (Figure 4-16). These findings support of inhibition of NMD consequent to PTC readthrough in R493X-/- KI astrocytes.   147         Figure 4-15 Induction of PTC readthrough by G418 and enhancers in R493X-/- KI hiPSC-derived astrocytes demonstrated by ELISA. DIV 60+ WT and R493X-/- KI hiPSC-derived astrocytes were treated with G418, CDX5-288, and rec. human PGRN at the indicated concentrations for 72 h. Intracellular (A-B, 1 mg/mL lysate) and extracellular (C-D, 25X concentrated supernatant) samples were subjected to PGRN ELISA using a polyclonal anti-PGRN antibody that targets multiple epitopes (GRN 1/3/5/7 peptides). Therefore, the antibody cannot differentiate between PGRN/GRNs. n = 3 independent cultures; values are shown as mean ± SEM; * p < 0.05, ** p < 0.01, *** p < 0.0001, one-way ANOVA with Tukey’s multiple comparison test.   148                          Figure 4-16 Selective increase of nonsense mutant GRN mRNA in R493X-/- KI hiPSC-derived astrocytes in response to PTC readthrough treatments. qPCR analysis of human GRN mRNA levels in DIV60+ WT and R493X-/- KI hiPSC-derived astrocytes treated with G418 and CDX5-288 at the indicated concentrations for 72 h. Relative GRN mRNA levels were normalized to the mean of GAPDH and HPRT1 housekeeping genes and compared to vehicle-treated (VT) WT. n = 3 independent cultures; values are shown as mean ± SEM; * p < 0.05, ** p < 0.01, *** p < 0.0001, one-way ANOVA with Tukey’s multiple comparison test.  149  4.2.8 Impact of G418 on PGRN expression in WT hiPSC-derived cortical neurons and astrocytes Contrary to expectation, we observed that WT cortical neurons treated with G418 alone and in combination with CDX5-288 showed significantly increased intracellular PGRN/GRNs levels relative to vehicle-treated cells, by 37.9% ± 3.2% and 42.9% ± 3.7, respectively (Figure 4-8, D). This intracellular increase in WT neuronal PGRN/GRNs levels was not due to PTC readthrough as both GRN alleles are WT. CDX5-288 alone did not increase intracellular WT neuronal PGRN/GRNs, and its combination with G418 did not increase PGRN/GRNs over G418 treatment alone, indicating the observed increase is mediated by G418 (Figure 4-8, D). The G418-mediated increase in intracellular WT neuronal PGRN/GRNs expression was not accompanied by a corresponding increase in PGRN/GRNs secretion (Figure 4-8, H). These findings in WT neurons suggest that G418 may disrupt PGRN exocytosis. The potential mechanisms driving this phenomenon are addressed in more detail in the context of WT astrocytes (Figure 4-15 and Figure 4-16).  G418 increased intracellular PGRN/GRNs in WT astrocytes by 31.7% ± 5.6%, without a corresponding increase in secreted PGRN/GRNs (Figure 4-15, A, C), as was observed with WT cortical neurons. Western blotting revealed that G418 significantly increased the intracellular levels of PGRN while decreasing the levels of GRN-2,3 peptides in WT astrocytes (Figure 4-17). Therefore, G418 may disrupt the normally highly efficient lysosomal processing of full-length PGRN to GRNs in astrocytes. To further probe the mechanism of this unanticipated readthrough-independent increase in WT intracellular 150  PGRN, we conducted GRN qPCR analysis in WT hiPSC-derived neurons and astrocytes. Treating WT neurons or astrocytes with G418 alone or in combination with CDX5-288 did not significantly increase GRN mRNA levels (Figure 4-10 and Figure 4-16). We speculate that G418 affects PGRN homeostasis at the protein level resulting in reduced lysosomal processing of full-length PGRN into individual GRNs.   151                                 Figure 4-17 G418-mediated disruption of PGRN homeostasis in WT hiPSC-derived astrocytes. G418 disrupts PGRN homeostasis in WT hiPSC-derived DIV 60+ astrocyte cultures. (A) Expression of intracellular full-length PGRN and GRN-2,3 peptides in G418, combination, and rec. human PGRN treated WT astrocyte lysates analyzed by western blotting, using actin as the loading control. Densitometric quantification of PGRN (B) and the ratio of PGRN:GRN-2,3 peptide (C) expression in the 152  aforementioned astrocyte lysates normalized to vehicle-treated WT levels. n = 3 independent cultures; values are shown as mean ± SEM; * p < 0.05, ** p < 0.01, one-way ANOVA with Tukey’s multiple comparison test.  153  4.3 Discussion As the founding graduate student researcher in the Nygaard laboratory, it was my responsibility to establish novel cellular models for the study of FTLD-GRN. A critical aim of my thesis was to assess the potential of PTC readthrough drugs to restore endogenous nonsense mutant GRN expression in disease-relevant CNS cell types; therefore, it was essential to generate and characterize healthy control- and FTLD-GRN patient-derived hiPSC lines. WT and R418X+/- hiPSC lines were produced from healthy control and a presymptomatic member of a Canadian family of GRN haploinsufficient mutation carriers (UBC15), respectively. Our lab resource publication of the R418X+/- hiPSC line in the journal of Stem Cell Research represents the contribution of a novel research tool to the field of FTLD (350). Since the phenotypes reported in past studies of GRN+/- hiPSC-derived neurons are not particularly robust (see section 1.2.5), we used CRISPR/Cas9 to generate a WT hiPSC-derived isogenic homozygous GRN R493X hiPSC line (R493X-/- KI). Additionally, the isogenicity of the WT and R493X-/- KI hiPSCs provides greater confidence in attributing phenotypic differences to a lack of GRN expression. Moreover, the homozygous nature of this knock-in hiPSC line ensured that any increase in full-length PGRN expression detected in response to PTC readthrough treatment was derived from a nonsense allele and not the intact allele present in heterozygous hiPSC lines (S116X+/- or R418X+/-).  Considerable efforts were undertaken to optimize and identify an hiPSC neuroectoderm induction method that reproducibly generated high-quality homogenous NPC cultures from various hiPSC lines derived from either fibroblasts or erythroid progenitor cells. 154  This specific variant of dual-SMAD inhibition was adapted from a 2018 Rose et al. study (351) and has been validated on at least eight different hiPSC lines in our lab. This protocol’s key benefit was its ability to rapidly (3.5 weeks) produce 1E8+ NPCs starting from a single 6-well plate well of confluent hiPSCs that could be frozen down for long-term storage and thawed for future experiments requiring neuronal/astrocyte differentiation. Thawed NPCs plated in BrainPhysTM supplemented with CultureOneTM immediately initiated neurite sprouting and neural network formation, and within just 3 weeks, cultures were positive for forebrain and cortical neuron markers FOXG1 and TBR1. Furthermore, the inclusion of CultureOneTM likely contributed to the minimal accumulation of GFAP+ cells. This may be achieved through a mechanism similar to previous differentiation efforts utilizing DAPT (γ-secretase and Notch pathway inhibitor) to inhibit NPC proliferation and increase neuronal culture purity (368). A secondary benefit of generating large quantities of frozen NPC stocks from each hiPSC line was the ability to differentiate astrocytes from the same cells used to produce cortical neurons. Astrocytes differentiated using the commercial STEMCELL Technologies differentiation/maturation kit expressed high levels of GFAP. Importantly, we also observed that the inclusion of WT astrocytes with WT cortical neurons in MEA co-cultures significantly accelerated their electrophysiological development (Figure 4-5, A-B); these hiPSC-derived astrocytes functionally support neuronal maturation as expected. The generation of these hiPSC lines and optimization of the neural lineage differentiation method was integral, enabling further assessment of their responsiveness to nonsense suppression therapy.  155  Here, we showed that PGRN insufficiency caused by GRN nonsense mutations can be ameliorated through PTC readthrough in disease-relevant cell types and that the resultant increase in PGRN reverses FTLD-GRN related lysosomal dysfunction. We used a commercially available ELISA kit that detects PGRN at multiple epitopes (GRN-1, 3, 5, & 7) to measure intra- and extracellular of cortical neuron PGRN expression levels, precluding discrimination between truncated and full-length forms of PGRN or GRNs. This is because we could not detect full-length PGRN in hiPSC-derived cortical neurons by western blot, likely due to their low levels of basal PGRN expression or rapid processing into smaller GRNs. In contrast, we showed that full-length and truncated PGRN is measurable by western blot in human astrocytes, allowing more precise measurements of PGRN protein of various sizes, including full-length, truncated forms, and GRNs. In response to G418 and CDX5-288, there was a significant increase in truncated and likely full-length PGRN in R493X-/- KI astrocytes, as well as an increase in GRN-2,3. This increase reflects a greater than 6-fold increase in GRN mRNA in response to G418 and CDX5-288 combination treatment. PTC readthrough treatment only restored R493X-/- KI neuronal GRN mRNA to WT levels, while astrocytes exhibited > 2-fold increase in R493X GRN mRNA over WT levels, perhaps reflecting their overall elevated basal GRN expression level. This increase in mRNA is characteristic of escape from NMD, in which nonsense mutant mRNA undergoes its pioneering round of full-length translation without stalling at its PTC.   This process is thought to be regulated by the degree of PTC readthrough, and only a minor increase in translation beyond a proposed 0.5% threshold would be sufficient for 156  substantial NMD inhibition and increased translation, as shown in yeast (369). G418 has been previously demonstrated to inhibit NMD through this readthrough-dependent mechanism (370). Stabilization of R493X mutant GRN mRNA leads to accumulation of truncated protein, which was evident in R493X-/- KI astrocytes treated with both G418 alone and CDX5-288 combination. Moreover, the increase in ~70 kDa PGRN signal detected in the R493X-/- KI astrocytes was accompanied by a faint, slightly higher MW band (Figure 4-14, A), which likely represents full-length PGRN. Given that both WT and R493X-/- KI astrocytes rapidly and efficiently process PGRN into individual GRNs, likely, the majority of PTC readthrough-derived full-length PGRN would also be cleaved into GRNs, thus making full-length PGRN particularly difficult to detect. This hypothesis is supported by the observed increase in full-length PGRN in R493X-/- KI astrocytes in response to readthrough treatment when the major lysosomal PGRN processing enzyme CTSL is inhibited. Thus, suggesting that the increase in intracellular PGRN/GRNs in R493X-/- KI cortical neurons likely reflects a mixture of truncated and full-length PGRN. These findings highlight the value of conducting drug screening in multiple cell types to evaluate differential drug responses, informing cell type-specific therapeutic targeting methods.  Interestingly, treating R493X-/- KI cortical neurons with G418 and CDX5-288 combination rescued aberrant lysosomal function in these cells, reducing mature CTSD levels back to WT levels. Recent studies have discovered a physical interaction between PGRNs C-terminus and CTSD (200,202,203). Despite some conflicting reports (119), the growing consensus is that PGRN binds to the pro-form of CTSD, promoting 157  its maturation, thus increasing its enzymatic activity (200,208). However, this hypothesis is contradicted by the observation that mature CTSD is upregulated in Grn-/- mice brains/microglia and can be rescued with exogenous mouse rec. Pgrn (180,218). Nevertheless, our results suggest that PGRN generated by PTC RT can perform biological functions and provides supplementary validation for at least a portion of the readthrough derived neuronal PGRN being full-length. It has also been recently demonstrated that the truncated PGRN R493X protein retains some of its biological properties, such as lysosomal localization and an ability to suppress a proinflammatory immune response in Grn-/- mice bone marrow-derived macrophage cultures (165). Therefore, we cannot rule out a contribution of truncated PGRN in the correction of this excess mature CTSD phenotype.  Unexpectedly, G418 induced accumulation of WT endogenous intracellular PGRN in all of our in vitro models. Given that G418 increases WT PGRN levels, it was difficult to prove that PTC readthrough was responsible for the elevated PGRN expression detected in heterozygous R418X+/- cortical neurons, as any increase in PGRN could be attributable to either increased expression from the WT allele or PTC-readthrough of the nonsense mutant allele. This provided the rationale for developing a homozygous R493X-/- KI line to address this issue and establish that at least a portion of the increased PGRN expression we observed in R418X+/- neurons were likely reflective of PTC readthrough. GRN expression analysis in WT cortical neurons and astrocytes treated with G418 confirmed that the increase in intracellular PGRN is not due to an accumulation of GRN mRNA, suggesting the mechanism is post-translational in nature. 158  The G418-mediated intracellular PGRN increase in WT neurons and astrocytes does not result in corresponding accumulation of PGRN in culture media, implying that G418 may interfere with the PGRN secretory pathway. Further studies are needed to better understand the possible post-translational role of G418 in PGRN processing.     159  Chapter 5: Phenotypic characterization of the GrnR493X/R493X mouse model and dose-limiting in vivo toxicity of G418  5.1 Introduction The neuropathology observed in patients bearing GRN LOF mutations is dictated by a gene dosage-dependent effect, with haploinsufficient individuals developing FTLD-GRN (35,36) and those lacking intact GRN alleles suffering from a rare form of NCL, CLN11 (95,96). The discovery that GRN-null individuals develop a lysosomal storage disease has encouraged investigation into the role of PGRN and GRNs in regulating lysosomal function (see section 1.2.4.2). The majority of the known neurobiological functions of PGRN have been uncovered using Grn-/- mouse models, partially because models of Grn haploinsufficiency do not replicate many of the neuropathological hallmarks observed in either FTLD-GRN or CLN11. Microglial lysosomal dysfunction and neuronal lipofuscin accumulation are the earliest pathological phenotypes observed in the Grn-/- mouse brain (119,179), preceding well-established neuroinflammatory and neurodegenerative phenotypes (see sections 1.2.4.1 and 1.2.4.4).  Previous in vivo FTLD-GRN therapeutic intervention studies have aimed to identify drugs capable of upregulating the intact allele and thus had to be performed in Grn+/- mice (135). The GrnR493X mouse model was recently generated to more accurately model FTLD-GRN by introducing one of the most frequent GRN mutation (R493X) at the analogous mouse Grn codon (R504X), providing an ideal model for preclinical 160  validation of novel PTC readthrough therapies. Characterization of this nonsense mutant Grn model identified several previously observed Grn-/- disease phenotypes, including microgliosis, lipofuscin accumulation, synaptic loss, and TDP-43 pathology (165). We sought to comprehensively characterize behavioural and neuropathological phenotypes in aged GrnR493X/R493X mice and attempt to restore CNS Pgrn expression through PTC readthrough treatment. These findings provide additional phenotypic markers of pathogenesis in aged GrnR493X/R493X mice that will contribute to better defining mechanisms underlying FTLD-GRN, and offer relevant outcome measures for preclinical efficacy testing of novel therapeutics that target nonsense mutations leading to this devastating disease.  5.2 Results   5.2.1 Pgrn expression in the brains of aged GrnR493X/R493X mice  We obtained the previously generated FTLD-GRN/CLN11 mouse model bearing homozygous Grn R504X mutations analogous to the human GRN R493X mutation for further neuropathological and behavioural characterization (165). Homozygous introduction of the GrnR493X PTC in these mice was confirmed by PCR (Figure 5-1). Brain Pgrn expression in 18 month old Grn+/+ and GrnR493X/R493X mice was assayed using multiple immunological detection methods, including western blot (Figure 5-2, A), ELISA (Figure 5-2, B), and immunofluorescence microscopy (Figure 5-2, C-D). These results demonstrate that nonsense mutant Pgrn expression is significantly reduced, detecting GrnR493X/R493X global Pgrn brain expression levels of 14.7% ± 1.7% (ELISA) and 21.7% ± 161  2.5% (western blot) relative to Grn+/+ expression levels. Immunofluorescent quantification of Pgrn expression in hippocampal CA3 and thalamic VPM/VPL GrnR493X/R493X pathological hotspots identified even lower levels of Pgrn, with total Pgrn area per cell of 4.3% ± 0.7% (CA3) and 4.6% ± 0.7% (VPM/VPL) of Grn+/+ tissue levels.     162               Figure 5-1 GrnR493X/R493X genotyping. PCR genotyping results confirm the presence of the homozygous GrnR493X knock-in alleles in GrnR493X/R493X mice. nt = no template, bp = base pair.          163                  Figure 5-2 Pgrn expression in the brains of aged GrnR493X/R493X mice. 18 month old Grn+/+ and GrnR493X/R493X hemibrain RIPA-soluble lysate samples were subjected to both Pgrn western blot (A) and Pgrn ELISA (B). Densitometric quantification of Pgrn western blot signal was normalized to actin loading control. (C) Pgrn expression was also detected in the hippocampal CA3 and thalamic VPM/VPL regions by 164  immunofluorescence staining of 18 month old Grn+/+ and GrnR493X/R493X brain sections (scale bar, 20 µm). (D) Total Pgrn+ area in CA3 (i) and VPM/VPL (ii) was quantified and normalized to the total number of cells (DAPI, blue). For western blot/ELISA n = 6 mice were used per sex/genotype; for immunofluorescence staining n=10 mice were used per sex/genotype (except male GrnR493X/R493X n=8); values are shown as mean ± SEM; *** p < 0.0001, Student’s t-test.              165  5.2.2 Lysosomal dysfunction in the brains of aged GrnR493X/R493X mice  NCL pathophysiology is generally driven by disrupted lysosomal catabolic functions resulting from lysosomal enzyme deficiencies. As discussed in section 1.2.4, a growing consensus in the literature suggests that loss of PGRN directly and indirectly disrupts both protein and lipid recycling pathways. Studies of Grn-deficient mouse models have helped identify PGRN’s roles in maintaining autophagic homeostasis in the CNS (107,119,120,178). To assess the potential efficacy of therapeutic interventions in our GrnR493X/R493X mice, it was critical to first characterize the various disease phenotypes that develop in this model. Additionally, since GrnR493X/R493X mice express low levels of a semi-functional truncated form of Pgrn (Pgrn-R493X) (165), it was also important to assess whether these mice pathologically mirror Grn-/- mice disease progression. Previous studies in Grn-/- mice have found CNS lipofuscin accumulation occurs as early as 2-3 months of age (179). We replicated the thalamic/hippocampal autofluorescent lipofuscin phenotype reported in the seminal GrnR493X/R493X model characterization paper (165), observing extensive lipofuscin in 18 month old mice in both the CA3 hippocampal region and thalamus (Figure 5-3, A). Further, aged R493X knock-in mice exhibit increased expression of lysosomal proteins Lamp1 and DppII, which were also shown to accumulate in these brain regions (Figure 5-3, B-C). We quantified Lamp1+ and DppII+ areas in the thalamus and hippocampus of aged GrnR493X/R493X mice and observed a significant increase in the expression of these lysosomal markers in the CA3 and VPM/VPL brain regions (Figure 5-3, D-G). Increased lysosomal vesicle size has been previously reported in several models of Grn-deficiency, including both Grn-/- mouse hippocampal neurons (107) and in GrnR493X/+ primary cortical neurons (136). We 166  also found that GrnR493X/R493X CA3 and VPM/VPL regions accumulate significantly larger Lamp1+ lysosomal vesicles than Grn+/+ control mice (Figure 5-4, A-B).    167     168   Figure 5-3 Lysosomal dysfunction in the ventral thalamus and CA3 hippocampal region of aged GrnR493X/R493X mice. Representative hippocampal/thalamic tilescans highlighting autofluorescent lipofuscin (A, green channel), Lamp1 (B), and DppII (C) accumulation in the CNS of 18 month old GrnR493X/R493X mice (scale bar, 500 µm). (D-E) Representative Lamp1 and DppII immunofluorescence images of hippocampal CA3 and thalamic VPM/VPL regions in 18 month old Grn+/+ and GrnR493X/R493X brain sections (scale bar, 20 µm). (F-G), Total Lamp1+ and DppII+ area/cell in CA3 (i) and VPM/VPL (ii) images were quantified and normalized to the total number of cells (DAPI, blue). For immunofluorescence staining n=10 mice were used per sex/genotype (except male GrnR493X/R493X n=8); values are shown as mean ± SEM; ** p < 0.01, *** p < 0.0001 was determined by Student’s t-test.   169           Figure 5-4 Enlarged lysosomes in the ventral thalamus and CA3 hippocampal region of aged GrnR493X/R493X mice. Average Lamp1+ vesicle size was quantified in images of Grn+/+ and GrnR493X/R493X CA3 (A) and VPM/VPL (B). For immunofluorescence staining n=10 mice were used per sex/genotype (except male GrnR493X/R493X n=8); values are shown as mean ± SEM; *** p < 0.0001 was determined by Student’s t-test.   170  Aged Grn-/- mice develop global CNS lysosomal dysfunction, including disrupted autophagosome clearance (106), overexpression of lysosomal enzymes (119), and cytoplasmic accumulation of insoluble TDP-43 (93). To evaluate CNS-wide lysosomal dysfunction in this model, we conducted a series of western blot assays on RIPA-soluble and -insoluble hemi-brain lysates. Unlike previous findings in Grn-/- mice (218), Lamp1 protein levels were not found to be significantly increased in the GrnR493X/R493X brain, although the data trended toward elevated Lamp1 expression (Figure 5-5, A-B). Increased expression and enzymatic maturation of the lysosomal protease Ctsd has been reproducibly observed in whole Grn-/- brain tissue (119). Expression of both the pro- and mature forms of Ctsd were significantly increased in GrnR493X/R493X brain compared to Grn+/+ (Figure 5-5, A, C). Lysosomal dysfunction can lead to functional impairments in autophagy, an essential process in maintaining cellular health. Chang et al. identified impaired ALP signaling in whole cortical tissue obtained from 18 month old Grn-/- mice, including an approximate 35% increase in the LC3-II:LC3-I ratio, which indicates autophagosome accumulation (106). Our similarly aged GrnR493X/R493X mice exhibited a nearly 2-fold increase in LC3-II:LC3-I over Grn+/+ (Figure 5-5, A, D), suggesting a dysregulated autophagy phenotype persists despite the low levels of lysosomal accumulation of partially functional Pgrn-R493X that may occur in these mice (165).     171          Figure 5-5 Global lysosomal dysfunction in the brains of aged GrnR493X/R493X mice.  Representative western blots of hemibrain RIPA-soluble lysates from 18 month old Grn+/+ and GrnR493X/R493X mice probed with the indicated antibodies (A). Expression of Lamp1, total/pro/mat-Ctsd, and LC3-I/II in Grn+/+ and GrnR493X/R493X hemibrains lysates was analyzed by western blotting, using actin as the loading control. Densitometric quantification of brain-wide Lamp1 (B) and Ctsd (C) expression was normalized to actin and Grn+/+ levels. The LC3-II:LC3-I densitometric expression ratio (D) was normalized to Grn+/+ levels. n=6 mice were used per sex/genotype; values are shown as mean ± SEM; ns = not significant, ** p < 0.01, *** p < 0.0001, Student’s t-test. 172  Impaired autophagy has been linked to increases in pathological forms of TDP-43, a pathologic hallmark of FTLD-GRN. Although Grn-/- mice develop a limited form cytoplasmic/nuclear TDP-43 aggregation slightly resembling histopathology observed in FTLD-GRN patients (371), biochemical analyses have identified increased full-length and phosphorylated TDP-43 (p-TDP-43) expression in whole-brain RIPA-insoluble fractions (93,371). Full-length TDP-43 can be cleaved into aggregation-prone CTFs that form the major protein component of TDP-43+ inclusions (23,24). 12 month old GrnR493X/R493X brains were found to contain diffuse cytoplasmic TDP-43/p-TDP-43 positivity similar to Grn-/- mice, that was absent in Grn+/+ mice (165). We reasoned that older mice might display a more robust TDP-43 phenotype. Using a polyclonal N-terminal TDP-43 antibody known to detect multiple forms of TDP-43, including full-length and several truncated CTFs (372), we probed RIPA-soluble and -insoluble hemi-brain lysates for TDP-43 expression. Full-length TDP-43 expression in the soluble fraction was significantly decreased in GrnR493X/R493X mice (Figure 5-6, A-B), with a similar trend observed for CTFs (Figure 5-6, A, arrows). Surprisingly, decreased soluble TDP-43 expression did not correspond with an increase in insoluble TDP-43 levels (Figure 5-6, A, C). We further probed these lysate fractions for Ser409 p-TDP-43 expression and observed a similar phenotype to that observed with TDP-43 total (Figure 5-7, A-C). As previously observed in Grn+/+ and Grn-/- brains (371), the insoluble fractions of both Grn+/+ and GrnR493X/R493X exhibited higher levels of full-length p-TDP-43 compared to the soluble fraction (Figure 5-6, A and Figure 5-7, A). Since TDP-43 pathology in this model has previously been demonstrated using TDP-43 immunofluorescent staining (165,373), we co-stained Grn+/+ and GrnR493X/R493X brain 173  sections for Tuj1 and TDP-43 to assess neuronal TDP-43 cellular localization (Figure 5-6, D-E). Tuj1-TDP-43 GrnR493X/R493X hippocampal/thalamic tilescans showed a major increase in neuronal TDP-43 expression localized to the thalamic VPM/VPL regions compared to Grn+/+. Similar to previous reports, high magnification micrographs of the GrnR493X/R493X VPM/VPL revealed considerable cytoplasmic TDP-43 accumulation in ventral thalamic neurons (Figure 5-6, E).   174                   175  Figure 5-6 Neuronal TDP-43 proteinopathy is localized to the ventral thalamus of aged GrnR493X/R493X mice. Representative western blots of hemibrain RIPA-soluble and -insoluble lysates from 18 month old Grn+/+ and GrnR493X/R493X mice probed for TDP-43 expression. (A) Expression of full-length TDP-43 in Grn+/+ and GrnR493X/R493X hemibrains in soluble and insoluble lysates was analyzed by western blotting, using RIPA-soluble actin as the loading control (no actin detected in insoluble urea fraction). Arrows indicate TDP-43 CTFs, and the * demarks a remnant TDP-43 signal observed upon reprobing stripped RIPA-soluble TDP-43 blot with actin antibody. Densitometric quantification of brain-wide full-length TDP-43 expression in soluble (B) and insoluble (C) lysate fractions were normalized to RIPA-soluble actin and Grn+/+ levels. (D) Representative hippocampal/thalamic tilescans highlighting the neuronal (TUJ1, green) TDP-43 (red) proteinopathy phenotype in the ventral thalamus of 18 month old GrnR493X/R493X mice (scale bar, 500 µm). (E) High magnification images from the thalamic VPM/VPL regions demonstrating neuronal cytoplasmic accumulation of TDP-43 in 18 month old GrnR493X/R493X mice (DAPI, blue; scale bar, 10 µm). For western analysis n=6 mice were used per sex/genotype; values are shown as mean ± SEM; ns = not significant, ** p < 0.01, Student’s t-test.   176             Figure 5-7 Absence of global p-TDP-43 proteinopathy in the brains of aged GrnR493X/R493X mice. Representative western blots of hemibrain RIPA-soluble and -insoluble lysates from 18 month old Grn+/+ and GrnR493X/R493X mice probed for TDP-43 expression. (A) Expression of full-length p-TDP-43 in Grn+/+ and GrnR493X/R493X hemibrains in soluble and insoluble lysates was analyzed by western blotting, using RIPA-soluble actin as the loading control (no actin detected in insoluble urea fraction). Arrows indicate TDP-43 CTFs, and the * demarks a remnant TDP-43 signal observed upon reprobing stripped RIPA-soluble TDP-43 blot with actin antibody. Densitometric quantification of brain-wide full-length p-TDP-43 expression in soluble (B) and insoluble (C) lysate fractions were normalized to RIPA-soluble actin and Grn+/+ levels. n=6 mice were used per sex/genotype; values are shown as mean ± SEM; ns = not significant, ** p < 0.01, Student’s t-test.  177  5.2.3 Neuroinflammation and astrogliosis in the ventral thalamus of aged GrnR493X/R493X mice  Pathologic increases of both microglia and astrocytes in the CA3 hippocampal region and ventral thalamus are well established phenotypes in Grn-deficient mice (see section 1.2.4.1). We sought to characterize neuroinflammation and astrogliosis in aged GrnR493X/R493X mice. Nguyen et al. previously described a temporal increase in thalamic microglial density in GrnR493X/R493X mice (165), and this was also observed in our aged GrnR493X/R493X mice (Figure 5-8, A). The number of microglia per thalamic VPM/VPL field was significantly greater in mutant mice (Figure 5-8, B, C.ii); however, no microgliosis was observed in the hippocampal CA3 region (Figure 5-8, B, C.i). A common feature of pro-inflammatory activated microglia is a morphological transition from a highly ramified state to an amoeboid shape with enlarged soma (374). To quantify microglia morphology, we conducted skeletal analysis to measure the number of Iba1+ branches and normalized that to the number of microglia present in a given field to obtain the average branches/microglia (Figure 5-9, A-B) (354). Decreased microglial branching was observed in both the CA3 and VPM/VPL regions of the GrnR493X/R493X brain, although the phenotype was more pronounced in the VPM/VPL, which exhibited 56.3% ± 6.6% of the branching levels observed in wildtype mice (Figure 5-8, B, C.iii-iv).   Counterintuitively, increased GRN expression has been detected in the frontal and temporal cortices of FTLD-GRN patients (94). This observation is believed to result from upregulation of the intact GRN allele in hyperactivated, proliferating microglia in 178  degenerating brain regions. In GrnR493X/R493X mice, upregulation of the mutated alleles could also result in increased basal PTC readthrough which would result in increased full length Pgrn expression. To test this hypothesis, we conducted Pgrn-Iba1 co-staining in Grn+/+ and GrnR493X/R493X mice to assess whether diseased brain regions in the knock-in mice display upregulated microglial Pgrn-R493X expression. We found that microglial Pgrn fluorescent intensity was significantly lower in the CA3 and VPM/VPL of GrnR493X/R493X mice, suggesting that microglial activation in these regions does not result in substantial basal PTC readthrough or accumulation of truncated Pgrn-R493X (Figure 5-8, B, D).   As discussed in section 1.2.4.4, the innate immune defense system has been previously implicated in the pathology of FTLD-GRN (92,120). Complement-driven synaptic pruning is a critical microglial-mediated neurodevelopmental mechanism (189) that is hyperactivated in the context of Grn-deficiency, resulting in selective depletion of thalamic inhibitory synapses in Grn-/- mice (92). Complement protein C1qa was significantly increased in the thalamic VPM/VPL of GrnR493X/R493X mice, similar to that observed in Grn-/- mice (Figure 5-8, E-F). Astrogliosis is another hallmark of FTLD-GRN pathogenesis demonstrated to develop in the same brain regions as microgliosis, as observed by Gfap staining in Grn-/- mice (163,371). We present the first characterization of GrnR493X/R493X astroglial pathology (Figure 5-10), observing that Gfap+ staining was significantly increased in the CA3 and VPM/VPL regions in GrnR493X/R493X mice (Figure 5-10, B-C). The astrogliosis phenotype was more striking than microgliosis, spanning 179  both the CA3 and VPM/VPL compared to microgliosis primarily observed in the thalamus.  180    181  Figure 5-8 Neuroinflammation in the ventral thalamus of aged GrnR493X/R493X mice. (A) Representative hippocampal/thalamic tilescans co-stained for Iba1/Pgrn show severe microgliosis in the brains of 18 month old GrnR493X/R493X mice (scale bar, 500 µm). (B) Representative Iba1/Pgrn co-stained immunofluorescence images of hippocampal CA3 and thalamic VPM/VPL regions in 18 month old Grn+/+ and GrnR493X/R493X brain sections (scale bar, 20 µm). (C) Quantification of microglial density (i-ii) and branching morphology (iii-iv) in the CA3 and thalamic VPM/VPL regions. (D) Microglial Pgrn fluorescence intensity in the CA3 (i) and VPM/VPL (ii). (E-F) Representative images and quantification of C1qa staining in the VPM/VPL. n=10 mice were used per sex/genotype (except male GrnR493X/R493X n=8 and male Grn+/+ Iba1-Pgrn staining of VPM/VPL n=9); values are shown as mean ± SEM; ns not significant, * p < 0.05, *** p < 0.0001, Student’s t-test.    182      Figure 5-9 Microglial skeletal analysis method. Iba1 immunofluorescent images were processed using Fiji as described in section 2.12.2 (A) and skeletonized using the Fiji Analyze Skeleton (2D/3D) plugin (B).       183                  Figure 5-10 Severe astrogliosis in the ventral thalamus and CA3 hippocampal region of aged GrnR493X/R493X mice. (A) Representative hippocampal/thalamic tilescans stained for Gfap show severe astrogliosis in 18 month old Grn+/+ and GrnR493X/R493X brain (scale bar, 500 µm). (B) Representative Gfap immunofluorescence images of hippocampal CA3 and thalamic VPM/VPL regions in 18 month old Grn+/+ and GrnR493X/R493X brain sections (scale bar, 20 µm). (C) Total Gfap+ area in CA3 (i) and VPM/VPL (ii) images were quantified and normalized to the total number of cells (DAPI, GfapGrnR493X/R493XGrn+/+A.Grn+/+GrnR493X/R493X020406080100Gfap Area (m2) / CellGrn+/+GrnR493X/R493X0204060Gfap Area (m2) / CellCA3VPM/VPLGrnR493X/R493XGrn+/+B.GfapC.VPM/VPLCA3i.ii.******184  blue). n=10 mice were used per sex/genotype (except male GrnR493X/R493X n=8); values are shown as mean ± SEM; ns not significant, * p < 0.05, *** p < 0.0001, Student’s t-test.   185  5.2.4 Partial preservation of inhibitory synaptic density in the thalamus of aged GrnR493X/R493X mice As discussed in sections 1.2.4.4, 1.2.6, and 5.2.3, there is growing support in the literature for a critical role of the complement innate immune signaling cascade in driving aberrant microglial synaptic pruning in FTLD-GRN and CLN11 (92,120). Given the robust increase in complement C1qa protein deposition observed in the GrnR493X/R493X ventral thalamus (Figure 5-8, E-F), we assessed whether this produced a corresponding decrease in inhibitory synaptic density as previously observed in Grn-/- mice (92). First, we characterized the whole thalamus Vgat synaptic density from hippocampal/thalamic tilescans, and observed a non-significant trend towards lower inhibitory synaptic density in GrnR493X/R493X mice (Figure 5-11, A-C). Since the Grn-/- synaptic phenotype was localized to the ventral thalamus, we further analyzed C1qa-Vgat images of Grn+/+ and GrnR493X/R493X VPM/VPL regions and found a similar non-significant trend towards lower Vgat synaptic area and number of puncta in GrnR493X/R493X mice (Figure 5-11, A’-B’, D-E). Interestingly, this weak trend towards a reduction of thalamic Vgat synaptic density was observed despite 26.9% ± 6.0% of total Vgat+ synaptic area being co-localized with C1qa in the GrnR493X/R493X VPM/VPL thalamic regions (Figure 5-11, F).           186                               187  Figure 5-11 Inhibitory synaptic density is preserved in the thalamus of aged GrnR493X/R493X mice. (A-B) Representative hippocampal/thalamic tilescans co-stained for C1qa and Vgat in 18 month old Grn+/+ and GrnR493X/R493X mice, the dashed outline depicts area quantified in (C) (scale bar, 500 µm). (A’-B’) C1qa-Vgat tilescan inset immunofluorescence images (from A-B) of thalamic VPM/VPL region in 18 month old Grn+/+ and GrnR493X/R493X brain sections (scale bar, 20 µm). (C) Quantification of thalamic Vgat+ synaptic area within hippocampal/thalamic tilescans normalized to thalamic area (white dashed outline). Vgat+ area (D), the number of Vgat+ synaptic puncta (E), and the proportion of Vgat+ synaptic area that is positive for C1qa (F) was quantified in high-resolution C1qa-Vgat VPM/VPL images (A’-B’). n=10 mice were used per sex/genotype (except male GrnR493X/R493X n=8); values are shown as mean ± SEM; ns not significant, *** p < 0.0001, Student’s t-test.   188  5.2.5 Reduced thalamic excitatory neuron density in the brains of aged GrnR493X/R493X mice  As outlined in section 1.2.4.4, a recent snRNA-seq study by Zhang et al. characterized disease progression in Grn-/- mice from 2-19 months of age discovered a selective decrease in the abundance of excitatory neuron markers from 12-19 months of age (120). They validated these findings immunohistochemically by staining for excitatory neuron markers Pkcδ and Foxp2 and identifying Grn-/- microglia surrounding Foxp2+ neurons contain Foxp2+ debris in their cytoplasm, suggestive of phagocytosis of dying excitatory neurons (120). We attempted to replicate these findings in GrnR493X/R493X mice by performing Foxp2 immunofluorescence staining and quantifying the number of Foxp2+ thalamic neurons. 18 month old GrnR493X/R493X thalami exhibited a significant reduction in the number of Foxp2+ excitatory neurons compared to Grn+/+ (21.0% ± 4.3%) mice, consistent with a possible neurodegenerative phenotype in this model (Figure 5-12, A-B).   189                  Figure 5-12 Reduced thalamic Foxp2+ excitatory neuron density in the brains of aged GrnR493X/R493X mice. (A) Representative hippocampal/thalamic tilescans from 18 month old Grn+/+ and GrnR493X/R493X mice brain sections stained for Foxp2, the dashed outline depicts area quantified in (B) (scale bar, 500 µm). (B) Quantification of total number of thalamic Foxp2+ nuclei. n=9 male Grn+/+ mice, n=7 female Grn+/+ mice, n=7 male GrnR493X/R493X, and n=10 female GrnR493X/R493X mice were used; values are shown as mean ± SEM; *** p < 0.0001, Student’s t-test.    190  5.2.6 Aged male GrnR493X/R493X mice exhibit an increased anxiety phenotype Several behavioural phenotypes have been identified in Grn+/- and Grn-/- mice, including deficits in social dominance, excessive grooming, and increased anxiety (92,124,160,163,165). The initial GrnR493X/R493X characterization found nearly identical onset and progression of OCD-like grooming behaviour in Grn-/- and GrnR493X/R493X mice resulting in severe skin lesions, which likely contributed to their 30% lower median survival rate (165). Though we did not specifically aim to quantify these phenotypes in our mice, we did observe significantly more animal facility health updates reporting lesions and grade 4 whisker barbering in GrnR493X/R493X mice (Grn+/+ 5/199 mice, mean age: 66.2 ± 1.8 weeks vs. GrnR493X/R493X 16/233 mice, mean age: 49.4 ± 1.8 weeks, Chi Square test, p = 0.0359) often requiring euthanasia likely attributable to excessive grooming behaviour.   The open-field test has been used to establish the increased male-specific anxiety phenotype in Grn-/- mice by quantifying the time mice were in the central or peripheral regions of the open-field (160,163). GrnR493X/R493X mice spent significantly less time in the central region of the open-field compared to Grn+/+ mice (Figure 5-13, A). We conducted a sex-specific analysis to further evaluate whether this anxiety phenotype was limited to male GrnR493X/R493X mice and found that male knock-in mice spent significantly less time in the central zone than Grn+/+ males while female Grn+/+/GrnR493X/R493X mice spent similar amounts of time in each region (Figure 5-13, B-C). However, there is a non-significant trend towards increased anxiety in female GrnR493X/R493X (Figure 5-13, C), suggesting that a larger sample size may have detected 191  a female-specific anxiety phenotype. The lack of significant difference observed between the amount of time male and female GrnR493X/R493X mice spent in the central zone (Figure 5-13, E), suggests that the stronger male-specific anxiety phenotype is likely reflective of the trend towards lower baseline anxiety levels in male vs. female Grn+/+ mice (Figure 5-13, D). To probe whether any of the previously presented neuropathological phenotypes show any sex-dependent effects, we conducted further sex-specific analyses of these data and failed to observe any statistically significant differences between sexes (Figure 5-14, Figure 5-15, and Figure 5-16).    192                 Figure  Figure 5-13 Aged male GrnR493X/R493X mice exhibit an increased anxiety phenotype. Proportion of time male/female (A), male (B), and female (C) Grn+/+ and GrnR493X/R493X mice spent inside the center region of an open-field arena over a 10 min trial. (D-E) 193  Comparison of intra-genotypic sex-differences in the % of time spent inside the center region of an open-field arena. Male Grn+/+ n=12, female Grn+/+ n=15, male GrnR493X/R493X n=10, and female GrnR493X/R493X n=10; values are shown as mean ± SEM; ns = not significant, * p < 0.05, Student’s t-test.   194                Figure 5-14 GrnR493X/R493X brain lysosomal dysfunction does not exhibit a sex-specific phenotype. DppII+ (A-B) and Lamp1+ (C-D) area/cell in both male and female Grn+/+ and GrnR493X/R493X CA3 and VPM/VPL images were quantified and normalized to the total number of cells (DAPI). For immunofluorescence staining n=10 mice were used per sex/genotype (except male GrnR493X/R493X n=8); values are shown as mean ± SEM, ns = not significant, one-way ANOVA with Tukey’s multiple comparison test. 195            Figure 5-15 GrnR493X/R493X microgliosis and astrogliosis does not exhibit a sex-specific phenotype. Iba1+ microglial density was quantified in both male and female Grn+/+ and GrnR493X/R493X CA3 (A) and VPM/VPL (B). Gfap+ astroglial density was quantified in both male and female Grn+/+ and GrnR493X/R493X CA3 (C) and VPM/VPL (D). n=10 mice were used per sex/genotype (except male GrnR493X/R493X n=8 male and Grn+/+ Iba1 staining of VPM/VPL n=9); values are shown as mean ± SEM, ns = not significant, one-way ANOVA with Tukey’s multiple comparison test.  196               Figure 5-16 GrnR493X/R493X decreased thalamic excitatory neuron density and inhibitory synaptic pruning does not exhibit a sex-specific phenotype. (A) Quantification of total number of thalamic Foxp2+ nuclei in male and female Grn+/+ and GrnR493X/R493X. Quantification of total thalamic (B) and VPM/VPL (C) Vgat+ inhibitory synaptic area in male and female Grn+/+ and GrnR493X/R493X. Total thalamic Foxp2 (A) n=9 male Grn+/+ mice, n=7 female Grn+/+ mice, n=7 male GrnR493X/R493X, and n=10 female GrnR493X/R493X mice, total thalamic Vgat (B) n=9 male Grn+/+ mice, n=9 female Grn+/+ mice, n=7 male GrnR493X/R493X, and n=10 female GrnR493X/R493X mice, and VPM/VPL Vgat (C) n=10 mice were used per sex/genotype (except male GrnR493X/R493X 197  n=8 male); values are shown as mean ± SEM, ns = not significant, one-way ANOVA with Tukey’s multiple comparison test.   198  5.2.7 PTC readthrough in GrnR493X/R493X MEFs Since the ultimate goal of obtaining the GrnR493X/R493X mouse model was to demonstrate in vivo PTC readthrough of endogenous nonsense mutant Grn expression, we established Grn+/+ and GrnR493X/R493X MEF lines for initial in vitro validation of treatment efficacy. GrnR493X/R493X MEFs were treated with either escalating doses of G418 alone or in combination with 5 µM CDX5-288 PTC readthrough enhancer. Western blot analysis of G418-treated GrnR493X/R493X MEF lysates using the anti-mouse Pgrn Linker-1 antibody (82) detected a dose-dependent increase in both full-length and R493X truncated Pgrn (Figure 5-17, A). Furthermore, combination treatment of GrnR493X/R493X MEF treatment with 25 µg/mL G418 and 5 µM CDX5-288 appeared to increase full-length Pgrn levels compared to 25 µg/mL G418, which may be indicative of PTC readthrough enhancement (Figure 5-17, A). 5-fold less protein was loaded in the Grn+/+ sample lane to reduce overexposure (Figure 5-17, A). A subset of these MEF samples was assessed for Pgrn levels by mouse Pgrn ELISA (Figure 5-17, B). Pgrn levels in GrnR493X/R493X MEFs treated with 200 µg/mL G418 and combination treatment of 25 µg/mL G418 and 5 µM CDX5-288 were increased by 8.3-fold and 6.8-fold, respectively (Figure 5-17, B). Given the low n-values presented in Figure 5-17, we did not conduct statistical analysis and therefore viewed this data as a preliminary low confidence observation. These results suggested that the GrnR493X loci is susceptible to PTC readthrough and prompted further in vivo preclinical investigations.     199                  Figure 5-17 Induction of PTC readthrough by G418 and enhancers in GrnR493X/R493X MEFs. Expression of intracellular Pgrn was assessed in Grn+/+ and GrnR493X/R493X MEF cultures treated with escalating concentrations of G418 alone or in combination with 5 µM CDX5-288 enhancer compound. (A) Expression of full-length Pgrn and Pgrn R493X in treated Grn+/+ (5-fold less protein loaded) and GrnR493X/R493X MEF lysates were analyzed by western blotting. (B) Quantification of Pgrn expression in a subset of these 200  Grn+/+ and GrnR493X/R493X MEF lysates by mouse Pgrn ELISA (n=1 per treatment group); values are shown as mean of 2 technical replicates.    201  5.2.8 G418-induced toxicity in GrnR493X/R493X mice limits therapeutic potential In chapter 3, we presented data demonstrating in vivo G418-induced PTC readthrough of a human GRN R493X mutant expression construct delivered to the CNS by P0 ICV AAV-GRN-R493X-V5 injection. At the time of treatment, AAV-GRN-R493X-V5 mice were beginning to exhibit minor signs of declining health commonly associated with P0 AAV injection; therefore, G418-induced toxicity was more difficult to assess. Single ICV injections with 50 µg G418 in these mice were tolerated, though, by the end of the 72 h treatment period, mice were beginning to show signs of toxicity, including increased fur piloerection, slow movement, and 10% body weight loss. Here, we aimed to translate this knowledge into CNS targeted PTC readthrough treatments of GrnR493X/R493X mice intending to delay or reverse disease progression by at least partially restoring Pgrn expression.  In vivo G418-induced neurotoxicity was expected given the established CNS ototoxicity associated with aminoglycoside treatment discussed in section 1.3.2. Although previous studies have found 2X repeated 80 µg ICV injections (at T=0 h and T=48 h) of G418 over a 96 h time point were capable of inducing CNS PTC readthrough with minimal toxicity (360,361). We first aimed to replicate the R493X GRN PTC readthrough findings we observed following short term treatment of AAV-GRN-R493X-V5 mice with 100 µg G418 in young GrnR493X/R493X mice. We conducted single ICV treatments of either saline or 100 µg G418 in Grn+/+ and GrnR493X/R493X mice for 72 h. At the time of euthanasia, two out of the three G418 treated GrnR493X/R493X mice exhibited signs of significant toxicity, including limited mobility and > 10-15% body weight loss. Measuring Pgrn expression in 202  whole-brain RIPA-soluble lysates indicated that a single 100 µg G418-treatment may have induced a 2X increase in CNS Pgrn levels (Figure 5-18), though it was unclear whether this increase was driven by PTC-readthrough or aminoglycoside-mediated toxicity. Given the low n-values presented in Figure 5-18, we did not conduct statistical analysis and therefore viewed this data as a preliminary low confidence observation.     203            Figure 5-18 A single ICV injection of G418 may induce increased Pgrn expression in the brains of GrnR493X/R493X mice. 19-21 week old Grn+/+ and GrnR493X/R493X mice were used to test the ability for a single ICV injection of G418 to induce CNS GrnR493X PTC readthrough. Control Grn+/+ and GrnR493X/R493X mice received a single ICV injection with saline, and G418 treated GrnR493X/R493X mice received a single ICV injection with 100 µg G418 dose. Whole-brains were collected after 72 h. Untreated and G418-treated whole-brain RIPA-soluble protein extracts were subjected to mouse Pgrn ELISA. n=1 mouse for saline Grn+/+, n=1 mouse for saline GrnR493X/R493X, and n=3 mice for G418 treated GrnR493X/R493X; values are shown as mean ± SEM.   02468Grn+/+ GrnR493X/R493Xn=1 n=31.001.995.73n=1G418 (100 g): - +-Pgrn (ng/mL) inwhole-brain lysates204  In 2018, Arrant et al. bilaterally infused the medial prefrontal cortices of 10-12 month old Grn-/- mice with AAV-Grn and achieved striking rescue of several neuropathological phenotypes in this model at 4-6 weeks post-transduction (218). Therefore, we hypothesized that recurrent long-term (~1 month) induction of in vivo Grn R493X PTC readthrough might be necessary to influence pathological progression in GrnR493X/R493X mice. Studies comparing daily bolus injections with sustained osmotic pump-mediated release of a related aminoglycoside, gentamicin, have identified that recurrent daily doses are more favorable for promoting aminoglycoside-induced PTC readthrough (243,375). To explore whether chronic CNS delivery of PTC readthrough-inducing doses of G418 could be tolerated in knock-in mice, we obtained implantable and programmable iPRECIO® pumps capable of automated chronic ICV dosing for up to 2 months. Before conducting PTC readthrough treatments, we first confirmed ICV targeting by implanting an iPRECIO® pump loaded with 0.1% Fast Green FCF dye programmed to deliver 10 µL of dye through the cranially implanted brain infusion cannula during the first hour post-operation. Photographic observation of freshly harvested dye-infused brain tissue demonstrated the expected ventricular distribution of Fast Green FCF dye (Figure 5-19). Additionally, we also validated G418’s thermostability up to 28 days at 37 °C, observing that it retains in vitro PTC readthrough activity after incubation in an environment thermally analogous to subcutaneous implantation (Figure 5-20).    205                       Figure 5-19 Technical demonstration of bolus iPRECIO® pump-mediated ICV injections targeting the lateral ventricles. A Grn+/+ mouse received implantation of a 0.1% Fast Green FCF dye loaded iPRECIO® pump inserted cranially at ICV coordinates: -1.0 mm lateral/-0.3 mm posterior/-3.0 mm depth to bregma. Immediately following 1 h infusion of 10 µL dye, the brain was collected and photographed, demonstrating ventricular delivery.    206            Figure 5-20 G418’s PTC readthrough activity is preserved despite prolonged incubation at physiologic temperature. R493X-/- KI hiPSC-derived astrocytes were treated with either vehicle solution or 50 µg/mL G418 for 72 h. G418 working stock solutions were incubated for either 0, 7, 14, 21, or 28 days at 37 °C. Expression of ~70 kDa PGRN in treated R493X-/- KI astrocyte samples were analyzed by western blotting, using actin as the loading control. n = 2 independent cultures per treatment condition.    207  Since single 100 µg ICV doses of G418 were poorly tolerated, we chose to assess whether recurrent doses of either 25 µg or 50 µg G418 are tolerated and capable of inducing Grn R493X PTC readthrough. Please refer to Figure 5-21 for a schematic description of iPRECIO® pump experiments #1-3. In experiment #1, we programmed pumps to constantly infuse G418 solution at the lowest flow rate (0.1 µL/h) to maintain brain infusion cannula patency and prevent clogging. This chronic low basal G418 dosing scheme resulted in rapid deterioration in the health of both 25 µg and 50 µg treated mice, likely due to major G418 accumulation in the brain to neurotoxic levels (Figure 5-22). In experiment #2, we programmed a similar G418 dosing schedule but set the flow rate to 0 µL/h during the recovery phase and between bolus 25 µg and 50 µg infusions. These mice appeared to tolerate this regimen marginally better than those in experiment #1; 4/5 mice were either found dead or required humane endpoint euthanasia by day 6. However, one extremely obese (70 g) GrnR493X/R493X mouse (blue star, Figure 5-21) tolerated five recurrent (every 48-72 h) 25 µg G418 bolus doses exhibiting initial weight loss that stabilized by day 10. Unfortunately, this experimental mouse had to be prematurely euthanized due to UBC’s COVID-19 shutdown requirements. Regardless, experiment #2 hemi-brain lysate Pgrn quantification found that 5X 25 µg G418 doses failed to increase Pgrn levels compared to untreated GrnR493X/R493X (Figure 5-23). Importantly, we did observe a modest Pgrn increase in mice treated with 2X 50 µg G418 doses. Again, given the low number of samples assessed in Figure 5-23, we did not conduct statistical analysis and therefore viewed this data as a preliminary low confidence observation.  208                   Figure 5-21 Schematic describing iPRECIO® pump experiment infusion programs and toxicity outcomes in mice. iPRECIO® pump experiments #1-3 were conducted on Grn+/+ and GrnR493X/R493X mice. Red lines indicate infusion events (25/50 µg G418 or 2 µL saline) and mice were euthanized at humane endpoints except for Exp#3 saline infused mice which were healthy at experimental endpoint and 5X 25 µg G418 treated mouse (*) which had to be euthanized due to UBC COVID-19 shutdown. 209                            Figure 5-22 Quantification of G418 concentration in the brains of Grn+/+ and GrnR493X/R493X mice treated ICV with G418. Whole-brain lysates obtained from Grn+/+ mice treated with 100 µg G418 for 2 h (n=2), GrnR493X/R493X mice treated with 100 µg G418 for 72 h (n=3), and an iPRECIO® Exp#1 50 µg G418 / 72 h treated mouse that was treated for ~100 h (blue triangle in Figure 5-20, n=1) were assayed for G418 concentration levels using a commercial Gentamicin ELISA kit; values are shown as mean ± SEM.     0204060Grn+/+ GrnR493X/R493Xn=3 n=1n=2Time-post 100 g G418 (h): 72 -2iPRECIO Exp#1 (50 g / 72 h): - +-G418 (g/mL) inwhole brain lysate210             Figure 5-23 Multiple iPRECIO® pump-mediated ICV infusions of 50 µg G418 may induce increased Pgrn expression in the brains of GrnR493X/R493X mice. 76 week old Grn+/+ and GrnR493X/R493X hemi-brain lysates derived from untreated controls and iPRECIO® pump Exp#2 treated mice were assayed for Pgrn expression to assess whether 25 µg G418 dose can induce PTC readthrough. Untreated and G418-treated hemi-brain RIPA-soluble protein extracts were subjected to mouse Pgrn ELISA. n=1 mouse for saline Grn+/+, n=1 mouse for saline GrnR493X/R493X, and n=1 mouse for 2X 25 µg G418, n=2 mice for 2X 50 µg G418, and n=1 for 5X 50 µg G418; values are shown as mean ± SEM.   051015Grn+/+ GrnR493X/R493XiPRECIO Exp#2 G418 (g): ----252502255No. of infusions:n=1 n=1 n=1 n=2 n=1Pgrn (ng/mL) inhemi-brain lysates211  Finally, for experiment #3, we implanted saline loaded pumps programmed to deliver 2 µL ICV infusions every 72 h into the brains of aged Grn+/+ mice. These mice received and tolerated 4X 2 µL saline bolus injections and were sacrificed on day 12 to assess brain Pgrn levels. We found that pump implanted mice did not exhibit increased Pgrn expression (Figure 5-24), suggesting that implanted cannula-associated neuroinflammation may not be responsible for upregulation of Pgrn expression in G418 pump implanted GrnR493X/R493X mice. This also suggests that technical surgical errors linked to pump implantation were not responsible for the severe morbidity observed in GrnR493X/R943X implanted with G418 ICV perfusing pumps. To further validate the increased Pgrn expression observed in 2X 50 µg G418 filled pump implanted mice in Exp#2 and completely rule out the possibility that pump-related non-specific phenomenon was responsible for this increase, we conducted 2X ICV syringe-pump driven 50 µg G418 injections in GrnR493X/R493X mice.   As expected, these repeated ICV injections (at t=0 h and t=48 h over 96 h) of 50 µg G418 resulted in significant toxicity, which became particularly apparent ~24 h post the 2nd G418 injection. Though all mice survived until the experimental endpoint, their weight decline and limited mobility at 96 h post-injection #1 would have soon required humane endpoint euthanasia. To definitively demonstrate GrnR493X/R493X G418-induced PTC readthrough, we pooled iPRECIO® 2X 50 µg G418 (n=2) and these syringe-pump 2X 50 µg G418 injected mice (n=3) into a single treatment group (2X 50 µg G418) and evaluated Pgrn expression compared to untreated controls. 2X 50 µg G418 injections significantly increased Pgrn expression when assayed by both western blot and Pgrn 212  ELISA (Figure 5-25). The increased levels of truncated Pgrn-R493X indicate potential in vivo G418-induced PTC readthrough of an endogenously expressed nonsense mutant Grn allele (Figure 5-25, A-B). Observing that repeated ICV treatments with 50 µg G418 increased brain Pgrn expression using two independent injection methods provides additional evidence that G418 was responsible for increased Pgrn expression.    213              Figure 5-24 Grn+/+ tolerate iPRECIO® pump ICV infusion of saline. 77-88 week old Grn+/+ hemi-brain lysates derived from untreated controls and iPRECIO® saline pump Exp#3 treated mice were assayed for Pgrn expression levels. Untreated and saline pump treated hemi-brain RIPA-soluble protein extracts were subjected to mouse Pgrn ELISA. n=7 untreated Grn+/+ mice and n=2 iPRECIO® saline pump treated Grn+/+ mice; values are shown as mean ± SEM; ns = non-significant, Student’s t-test.         214                       Figure 5-25 Increased Pgrn expression induced by 2X repeated ICV G418 injections in the brains of GrnR493X/R493X mice. 52-86 week old Grn+/+ and GrnR493X/R493X mice were used to test the ability for G418 to induce CNS GrnR493X PTC readthrough. Control Grn+/+ and GrnR493X/R493X mice were untreated or received 2X ICV saline injections t=0 h and t=48 h over 96 h. G418 treated GrnR493X/R493X mice received either 2X syringe driven bolus ICV doses of 50 µg G418 at t=0 h and t=48 h over 96 h (n=3) or ICV iPRECIO® pump injected 2X 50 µg G418 doses delivered at t=48 h and t=120 h over 124 h (n=2). Untreated and G418-treated hemi-brain RIPA-soluble protein 215  extracts were subjected to Pgrn western blot (A-B) and mouse Pgrn ELISA (C). Cropped Grn+/+ and GrnR493X/R493X western blot lanes presented were detected on the same membrane, and the loading control signal was obtained by reprobing the same membrane with actin for normalization. The first two G418-treated lanes are from ICV iPRECIO® pump injected mice, and the last three are from syringe-pump injected mice. Both Pgrn western blot and ELISA data are presented relative to untreated GrnR493X/R493X. Values are shown as mean ± SEM; * p < 0.05, *** p < 0.0001, one-way ANOVA with Tukey’s multiple comparison test.     216  5.3 Discussion In this chapter, we provide the first detailed analysis of lysosomal dysfunction and selective loss of thalamic excitatory neurons in the brains of aged GrnR493X/R493X mice. First, we established that Pgrn expression is suppressed in the brains of aged GrnR493X/R493X mice, and pathologically active brain regions do not show upregulated Pgrn expression via basal PTC readthrough. This limited expression is driven by NMD (165); therefore, the majority of Pgrn detected in the GrnR493X/R493X brain likely consist of the truncated Pgrn-R493X form. Since disrupted lysosomal homeostasis is a pathological hallmark of Grn-/- mice, we chose to evaluate several previously established brain lysosomal phenotypes in our aged GrnR493X/R493X cohort. The CA3 hippocampal and thalamic VPM/VPL brain regions of aged GrnR493X/R493X mice displayed striking expansions of their lysosomal compartments. We further evaluated aged knock-in mice for global changes in brain lysosomal function and impairments in autophagy; identifying overexpression of both the pro- and mature-forms of lysosomal protease Ctsd and impaired clearance of autophagolysosomes as indicated by an increased LC3-II:LC3-I ratio, both of which have been previously observed in aged Grn-/- mice (106,119). Notably, evidence of lysosomal dysfunction has been demonstrated in Grn-/- mice as young as 2 months of age (179). Future efforts may seek to understand whether the presence of a semi-functional, truncated Pgrn-R493X might delay the onset of this early lysosomal phenotype.  As discussed in sections 1.1.3 and 1.1.7, GRN deficiency is associated with nuclear to cytoplasmic translocation of TDP-43, ultimately resulting in the formation of insoluble 217  neuronal inclusions. The redistribution of TDP-43 from the nucleus to the cytoplasm has also been observed in Grn-/- mice, a process which may involve excessive neuroinflammation and dysfunctional autophagolysosomal and ubiquitin-proteasome systems (120,165,371,373). Similar to these findings, we found TDP-43 pathology limited to ventral thalamic neurons in GrnR493X/R493X mice, which exhibited intense nuclear to cytoplasmic TDP-43 translocation. We further observed that GrnR493X/R493X soluble hemi-brain lysates contained decreased TDP-43, potentially indicating that a proportion of the soluble TDP-43 pool had transitioned into an insoluble form. This phenomenon was observed in a mutant TDP-43 mouse model where soluble TDP-43 increased while insoluble TDP-43 decreased upon overexpression of PGRN (376). However, we failed to observe a corresponding increase in the insoluble levels of TDP-43 and were unable to detect p-TDP-43 in either soluble or insoluble lysates, both of which have been previously found in aged Grn-/- mice (93,371). The former most likely relates to our finding that TDP-43 pathology is largely limited to ventral thalamic neurons, and the phenotype may thus be lost through dilution when assessing hemi-brain lysates. Other discrepancies are less clear and may relate to inherent differences in mouse models as well as the particular age chosen for analysis.   GrnR493X/R493X mice exhibit age-dependent microgliosis that begins around 6 months of age, reaching a peak at 12 months, and is maintained until 18 months of age. We observed significant neuroinflammation in the ventral thalamus of GrnR493X/R493X mice, including astro- and microglial expansion and morphological transition into a proinflammatory state. This observation is important because we show that the 218  chronically inflamed ventral thalamic brain region also develops TDP-43 proteinopathy, providing additional support to the growing evidence demonstrating that factors secreted by Grn-deficient microglia directly induce cytoplasmic accumulation of TDP-43 (165). These inflammatory mediators include the innate immune system complement system (C1qa, C3, etc.) which have been implicated in Grn-deficient microglial mediated neurotoxicity. Although most of the literature has focused on examining microglial-driven neuropathological mechanisms, a recent study by Guttikonda et al.  conducted using hiPSC-derived neuron-astrocyte-microglia tricultures suggested that reciprocal C3 signaling between microglia and astrocytes is critical to driving excessive microglial C1qa complement protein expression and secretion (377). Therefore, future studies assessing the role of Grn-deficient astrocytes in driving disease pathophysiology may be critical to identifying novel therapeutic strategies.  As discussed in sections 1.2.4 and 1.2.6, microglial-mediated innate immune system complement pathway activation has been directly and indirectly implicated in driving thalamic neurodegeneration in Grn-/- mice through selective targeting of both inhibitory synapses and excitatory neurons for elimination (92,120). Despite observing robust C1qa tagging of Vgat+ synapses as seen in Grn-/- mice, neither GrnR493X/R493X whole thalami or the VPM/VPL region showed a significant decrease in inhibitory synaptic density. However, there was a trend towards lower levels of Vgat+ synapses in these regions. It is possible that low basal Pgrn-R493X expression in GrnR493X/R493X microglial limited their voracity for inhibitory synapses, but this is not known. A recent snRNA-seq study found that selective loss of excitatory neurons in the ventral thalamus of Grn-/- 219  mice could be rescued by simultaneous deletion of both C1qa and C3 complement genes (120). The authors proposed that elevated C1qa and C3 in this brain region result in increased MAC formation on neuronal surfaces, which permeabilizes their plasma membranes, triggering apoptosis (120). Similarly, our aged GrnR493X/R493X displayed loss of thalamic Foxp2+ excitatory neurons, perhaps suggesting that a loss of excitatory neurons precedes the synaptic pruning phenotype in this model. Nevertheless, it is still unclear how these complement-mediated neurodegenerative mechanisms selectively target inhibitory synapses and excitatory neurons.  Grn-deficient mice develop behavioural abnormalities impacting social interactions, grooming frequency, and anxiety levels (92,124,160,163,165). GrnR493X/R493X mice were no different, exhibiting an increased anxiety phenotype similar to that previously reported in Grn-/- mice, observing a stronger anxiety phenotype in males (160,163). In section 1.2.4.4, we discussed neuropathological correlates of behavioural disturbances in Grn-/-, connecting decreased inhibition of the thalamocortical circuit to their OCD-like grooming phenotype (92). Since we observed significant thalamic pathology in aged GrnR493X/R493X mice, we analyzed the major neuropathological phenotypes presented here for sexual dimorphism to assess whether increased pathology might explain the male-predominant anxiety phenotype. While we found that levels of inhibitory synaptic density in the thalamic VPM/VPL regions exhibited a strong trend towards a sex-dependent phenotype in both Grn+/+ and GrnR493X/R493X mice (Figure 5-16, C), with males displaying elevated inhibitory synaptic density compared to females, we did not observe sexually dimorphic FTLD-related pathology in GrnR493X/R493X mice. Similar efforts have 220  been made to identify the neurological basis for the increased susceptibility of male Grn-deficient mice to the development of an increased anxiety phenotype (378,379). These studies found that Grn expression is upregulated in the ventromedial hypothalamic nucleus in response to androgen and estrogen sex-hormones and that Pgrn is an essential mediator of male sexual differentiation in the developing brain. Since Grn+/+ female mice generally exhibit elevated anxiety compared to Grn+/+ males, it has been proposed that a lack of Grn expression during sexual differentiation results in at least partial fulfillment of the default female neurodevelopmental program (160). Evidence supporting this hypothesis includes the observation that Grn-/- mice lack the sexually dimorphic trait of differential locus ceruleus (LC) volume, which is normally larger in Grn+/+ females (380). Because the LC is an important regulator of stress-induced anxiety responses, it is possible that a relatively enlarged LC in male Grn-/- compared to Grn+/+ mice could predispose them to increased anxiety (381). There studies suggest profound developmental changes in the brain as a result of Grn deficiency. Improved preclinical methodology, including the use of hiPSCs, may allow future studies to probe these mechanisms which could reveal process far upstream of known FTLD pathology that may prove central to FTLD-GRN pathophysiology.   Taken together, a striking finding in both aged GrnR493X/R493X mice and other Grn-/- models is the pronounced involvement of select thalamic regions. For the clinician this might be curious as neurodegeneration in the frontal, temporal, and parietal lobes is widely recognized in driving clinical symptoms across FTLD syndromes. However, a recent study in preclinical GRN carriers found prominent hyperconnectivity between 221  cortical hub regions and the thalamus in several intrinsic connectivity networks assessed by functional magnetic resonance imaging (213). The implications of these findings are not fully clear, but abnormal thalamic physiology, which is robustly demonstrated in FTLD-GRN mouse models either through histology or electrophysiology, may have important implications for the earliest changes in human FTLD-GRN. As such, interventions to reverse these pathologic changes in mice may have important translational value.   Aminoglycoside-induced toxicity (reviewed in section 1.3.2) has been a major deterrent to the clinical translation of PTC readthrough therapy. Through the discovery of our CDX-series of PTC readthrough enhancer compounds, we aimed to lower the required concentration of G418 to a more tolerable level while still achieving readthrough. As shown in GrnR493X/R493X derived MEFs, we were able to accomplish this goal in vitro. In section 5.2.8, we chronicled our efforts to identify a dose of G418 capable of inducing PTC readthrough that would be tolerated for at least a month-long recurrent treatment regimen. These data represent the first demonstration of CNS delivery of a PTC readthrough drug using an implantable programmable pump capable of infusing bolus doses. We found that short term ICV doses of 50-100 µg G418 could induce GrnR493X PTC readthrough, though were accompanied by significant and often fatal neurotoxicity. Though not presented here, we attempted single syringe-pump ICV injections of 200 µg and 400 µg G418 doses, which resulted in rapid-onset muscular paralysis requiring euthanasia and sudden death, respectively. Given that 2/3 GrnR493X/R493X mice treated with 25 µg G418 doses for iPRECIO® Exp#2 were either found dead or required 222  humane endpoint euthanasia and that even five recurrent 25 µg G418 doses over 15 days failed to increase Pgrn expression; we conclude that there is likely no tolerated ICV dose of G418 that is capable sufficient CNS exposure to induce PTC readthrough in the GrnR493X/R493X mouse model. Unable to establish a baseline tolerated dose of G418 capable of inducing PTC readthrough, we chose to abandon efforts to attempt combination therapy with CDX5-288, as we would not have been able to assess the degree of PTC readthrough enhancement.   In conclusion, our aged cohort of GrnR493X/R493X mice displayed several pathologic phenotypes, including lysosomal dysfunction and select thalamic synaptic degeneration not previously described in this model, but in line with observations in other Grn-/- model mice. Our characterization of aged GrnR493X/R493X mice provides the field with further insight into neuropathological phenotypes that may be used to better define the mechanisms underlying FTLD-GRN, and evaluate the preclinical efficacy of novel therapeutics to target relevant nonsense mutations that cause FTLD-GRN. 223  Chapter 6: Conclusion and future directions  6.1 Contributions to the fields of FTLD-GRN and CLN11 FTLD-GRN is a devastating neurodegenerative disease, yet there are currently no disease-modifying therapies available in the clinic. The majority of drug development efforts for the treatment of FTLD-GRN have focused on restoring normal PGRN levels by increasing expression from the intact allele or exogenous delivery of PGRN to the CNS. The viability of preclinical investigation exploring novel nonsense mutation suppression therapies is dependent on the prevalence of nonsense mutations in a given genetic condition. Approximately 25% of causal FTLD-GRN mutations introduce in-frame PTCs, providing a substantial patient population that may benefit from PTC readthrough therapy. Despite the known toxicity of aminoglycosides, PTC readthrough has not been pursued as a therapy for FTLD-GRN. The work here describes proof-of-concept demonstration of PTC readthrough in several in vitro and in vivo models bearing clinical GRN nonsense mutations, and represents a major contribution to the field of FTLD-GRN incentivizing further development of this therapeutic approach.  6.1.1 In vitro and in vivo PTC readthrough of exogenously expressed nonsense mutant human GRN expression constructs Early in 2020, we showed that aminoglycoside-mediated GRN nonsense mutation readthrough in cells transfected with C-terminally tagged nonsense mutant expression GRN constructs (122). In chapter 3, we generated HEK293 cell lines stably expressing human GRN bearing several clinically relevant FTLD-GRN nonsense mutations for 224  screening our lead PTC readthrough enhancer compounds in combination with the aminoglycoside G418. These screening efforts identified that the UGA GRN R418X and R493X mutations were most susceptible to PTC readthrough and that combination treatment with CDX5-288 had the most synergistic effect on readthrough efficiency.   Based on these findings, we generated and transduced neonatal C57BL/6J mice with AAV vectors expressing tagged R493X mutant GRN. We found that a single ICV injection of G418-induced CNS wide PTC readthrough of human tagged R493X GRN expression constructs in AAV-GRN-R493X-V5 mice. CDX5-288 co-treatment with G418 in these mice did not induce PTC readthrough enhancement, suggesting that the CDX5-288 dosage we selected based on in vitro efficacy may have been too low. Complications involving poor viability of AAV-GRN-R493X-V5 mice limited our ability to conduct additional G418 and CDX5-288 combination treatment dose optimizations. Furthermore, the artificial nature of GRN-R493X-V5 overexpression precluded quantification of disease-relevant PTC readthrough efficiency in this model; therefore, we view these results as proof-of-concept demonstration of in vivo PTC readthrough.   6.1.2 In vitro and in vivo PTC readthrough in human and mouse models endogenously expressing nonsense mutant GRN To our knowledge, this is the first and only report demonstrating nonsense mutation readthrough to enhance PGRN expression in FTLD-GRN patient-derived cortical neurons and astrocytes. In chapter 4, we reviewed our efforts reprogramming healthy control and FTLD-GRN UBC15 patient somatic cells into hiPSCs and CRISPR/Cas9 225  gene editing the first isogenic hiPSC model of CLN11. These hiPSC models provided excellent sources of disease-relevant cell types bearing common pathogenic GRN nonsense mutations. We also examined the potency of our PTC readthrough combination therapy in S116X+/-, R418X+/-, and R493X-/- KI hiPSC-derived cortical neurons and astrocytes. Full-length translation of PGRN was detected in R493X-/- KI hiPSC-derived astrocytes treated with G418 and CDX5-288 by co-treatment with a CTSL inhibitor to prevent the rapid processing of readthrough-derived full-length PGRN into GRNs observed in this cell type. This is an important observation for other researchers in the field, aiming to pursue readthrough based approaches for the treatment of FTLD-GRN. We further demonstrated that increased PGRN expression induced by G418 and CDX5-288 in R493X-/- KI cortical neurons rescued an elevated mature CTSD mutant lysosomal phenotype, indicating that the combination of full-length and truncated PTC readthrough-derived PGRN had a functional benefit. These cell lines represent valuable research tools for the field of FTLD.  In chapter 5, we characterized the GrnR493X/R493X knock-in mouse model bearing a murine analog to the pathogenic R493X mutation. Our aged GrnR493X/R493X knock-in mice cohort displayed several neuropathological features previously observed in Grn-/- mice. Notably, we provide the first evidence that these mice develop striking lysosomal dysfunction and neurodegeneration in the form of selective loss of thalamic excitatory neurons. Moreover, we observed a male-specific increased anxiety phenotype in aged GrnR493X/R493X mice previously reported in Grn-/- mice. We provided preliminary results from a pilot study demonstrating in vivo PTC readthrough of endogenously expressed 226  GrnR493X through repeated ICV administrations of G418. However, the doses of G418 required to achieve readthrough caused severe neurotoxicity and were not suitable for long term therapeutic intervention. Future studies are needed to further explore whether in vivo PTC readthrough induced PGRN rescue is sufficient to surpass the therapeutic threshold required to disrupt or slow down FTLD-GRN pathogenesis.  6.2 Final conclusions In summary, we show that G418 increases PGRN through PTC readthrough in cellular and mouse models of FTLD due to pathogenic progranulin nonsense mutations. The enhancer compound CDX5-288 potentiates the readthrough effects of G418 in vitro and increases PGRN over G418 treatment alone. We further show that increased progranulin through PTC readthrough ameliorates lysosomal dysfunction in R493X-/- KI cortical neurons, showing a functional impact of raised PGRN. A single ICV administration of G418 in mice expressing tagged human GRN R493X nonsense mutation achieves proof-of-concept in vivo PTC readthrough. Our characterization of aged GrnR493X/R493X mice provides the field with insight into neuropathological phenotypes that may be used to evaluate the preclinical efficacy of novel therapeutics in this model. While G418 is not suitable for long-term human consumption, our work highlights the importance of ongoing and future efforts to find novel readthrough compounds more suitable for human use. Taken together, our findings suggest that PTC readthrough may be a potential therapeutic strategy for a subset of patients with FTLD bearing a GRN nonsense mutation, but highlight the need for better drugs with improved tolerability. 227  6.3 Future directions Our observations of severe dose-limiting G418-mediated toxicity following ICV delivery in GrnR493X/R493X mice suggest that aminoglycoside readthrough compounds are unlikely to have a therapeutic window for FTLD-GRN or CLN11 patients carrying nonsense mutant GRN alleles. As discussed in section 1.3.3, systematic examination of the chemical moieties responsible for aminoglycoside-induced toxicity and PTC readthrough by Dr. Timor Baasov’s group resulted in the synthesis of the novel eukaryotic ribosomal selective glycoside, ELX-02. Developing an academia-industry partnership with Eloxx Pharmaceuticals may enable us to conduct similar in vivo brain-targeting PTC readthrough studies in our GrnR493X/R493X mouse cohort testing ELX-02 and other synthetic aminoglycosides under their development. Additionally, we are currently in the process of conducting in vitro validation of novel PTC readthrough drugs through our collaborations with the Roberge lab, which may support further exploration of in vivo nonsense mutation readthrough therapy in GrnR493X/R493X knock-in mice.  As discussed in section 1.2.7, several ongoing clinical investigations are evaluating the efficacy of therapies aimed at restoring PGRN expression levels in FTLD-GRN patients. Alector is currently recruiting participants for a phase III clinical trial (INFRONT-3) testing the anti-SORT1 antibody AL001, which aims to disrupt SORT1-mediated extracellular uptake of PGRN to increase its extracellular bioavailability. Since brain SORT1 expression is primary localized to neurons, inhibition of SORT1-mediated PGRN endocytosis likely results in greater microglial endocytosis of extracellular PGRN through SORT1-independent transport mechanisms (described in section 1.2.3). 228  Microglia are increasingly recognized as primary drivers of FTLD-GRN pathophysiology; therefore, it is possible that recently reported improvements in CSF FTLD-GRN biomarkers following 4-week treatment with AL001 may be due to restored microglial PGRN levels. Exogenous delivery of GRN expression through gene therapy or direct delivery of intact rec. PGRN represents another promising approach to delaying or reversing pathological progression in FTLD-GRN and CLN11 patients. Prevail Therapeutics is actively recruiting symptomatic FTLD-GRN patients for a phase I/II clinical trial (PROCLAIM) to validate the safety, tolerability, and immunogenicity of a single dose (low, medium, or high) of their AAV9 GRN expression vector (PR006) delivered intraventricularly via the cisterna magna. Additionally, Passage Bio Inc. will soon begin recruiting for its own phase I/II clinical trial (upliFT-D) to test the safety, tolerability, and pharmacodynamic effects of a single dose (3.3E10 or 1.1E11 genome copies / gram of estimated brain weight) of their AAV1 GRN expression vector (PBFT02) which will also be delivered by intra-cisterna magna injection. These trials build upon several preclinical studies demonstrating viral CNS delivery of GRN expression (218,221) and may provide insight into whether restoring GRN expression in the brain can disrupt the pathogenic processes associated with FTLD-GRN. Importantly, PGRN overexpression is known to be associated with oncogenicity in multiple organ systems (382,383), therefore it will be critical to ensure GRN expression is limited to normal healthy control levels.  Drugs targeting the pathophysiological mechanisms responsible for FTLD-GRN disease pathogenesis may represent an alternative therapeutic modality for the treatment of 229  GRN deficiency. Our laboratory’s expertise and unique repository of FTLD-GRN patient- and isogenic CRISPR/Cas9-derived hiPSC models are well suited for further elucidation of disease-associated molecular pathways. Recent advances in cerebral organoid technology have enabled the production of 3D iPSC-derived spheroids that neurodevelopmentally replicate elements of the human embryonic brain (384). Although these neural constructs lack resident microglia, hiPSC-derived microglia can be co-cultured with maturing cerebral organoids, resulting in microglia chemotactic migration and integration into the mini-brains. Microglia tile the cerebral organoid tissue adopting a characteristic ramified morphology that upon neural injury become activated, undergoing classic amoeboid morphological transition (198). hiPSC-derived microglia-cerebral organoid co-cultures represent a valuable research tool for the study of FTLD-GRN and CLN11 pathology. A hypothetical experiment could involve co-culturing WT or R493X-/- KI hiPSC-derived microglia with WT or R493X-/- KI hiPSC-derived cerebral organoids to assess whether mutant microglial induce any characteristic FTLD-GRN phenotypes, such as TDP-43 cytoplasmic translocation or excessive secretion of complement (C1QA, C3, etc.) proteins. 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