Elizabeth Simpson

Aniridia is a rare eye disorder with no cure and is caused by pathogenic variants in the paired box 6 (PAX6) gene. Patients have low vision at birth due to retinal foveal hypoplasia, which typically progresses to blindness by early adulthood due to corneal clouding and glaucoma. Since aniridia is caused by PAX6 haploinsufficiency, one potential approach to treating it is targeted CRISPR-based gene editing. Preclinical studies in an appropriate animal model are important first steps towards the translation of the research into a clinical trial. Thus, in Chapter 2, we inserted a 3xFLAG tag on the Pax6 small eye (Sey) allele, creating a novel mouse model for aniridia that is ideal for testing CRISPR strategies. Next, we developed a CRISPR strategy in vitro and subsequently evaluated its efficacy in vivo in the germline of our new mouse. We showed that our CRISPR strategy corrected the Sey variant in the mouse germline, resulting in the full rescue of the eye phenotype.Next, we worked towards developing a somatic therapy, the success of which relies on effective delivery of CRISPR components to therapeutically significant cells. In Chapter 3, we tested a novel lipid nanoparticle-based platform, and successfully edited cultured mouse cortical neurons. We then directly injected LNP-CRISPR into the mouse cornea to evaluate in vivo delivery. We demonstrated wide-spread gene editing of corneal stromal and endothelial cells but not the PAX6-expressing epithelial or limbal stem cells (LSCs). Hence, in Chapter 4, we shifted our focus to recombinant adeno-associated viruses (rAAVs), a more conventional delivery vector for CRISPR. We carried out a series of experiments to test viral capsid, dose, and route of administration. We also investigated if functional LSCs are present in the already cloudy aniridic mouse corneas and whether rAAV can transduce them. We reported unexpected ataxia and lethality in mice after intraocular rAAV-PHP.B injections. We also showed that intrastromal and intravitreal delivery of rAAV9 transduced functional LSCs, as well as all PAX6-expressing retinal cell types in aniridic eye, respectively, with no observed adverse events, making rAAV9 the capsid of choice for the future gene therapy development for aniridia.

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Aniridia is a rare, congenital, blinding disorder, caused by mutations in the paired box 6 (PAX6) gene. People with aniridia are born with poor vision, which deteriorates towards blindness in early adulthood due to glaucoma and aniridia associated keratopathy. Glaucoma can be managed by conventional treatments, however interventions for keratopathy fail to provide lasting vision. Aniridia is caused by haploinsufficiency, where the underlying cause of the phenotype is insufficient production of PAX6. Therefore, PAX6 augmentation is a possible approach to treating aniridia. Gene therapy, defined as the manipulation of gene expression, or repair of abnormal genes, has recently demonstrated clinical success, providing therapeutics for genetic disorders such as lipoprotein lipase, Leber's congenital amaurosis, spinal muscular atrophy, and hemophilia B. All of these gene therapies use recombinant adeno associated viruses (rAAV) as a vector to transfer genes to patient cells, augmenting protein production. However, PAX6 is a potent morphogen, and using gene transfer technologies to express PAX6 ectopically risks detrimental effects in off target cells. Therefore, towards developing a PAX6 gene therapy for aniridia, I tested PAX6 minimal promoters (MiniPromoters) to restrict gene expression from rAAV to cells that endogenously express PAX6. Using regulatory regions from the PAX6 gene, seven MiniPromoters were tested, and four were found to restrict expression to the four cell types that express PAX6 in the adult retina. Most gene therapies begin in a mouse model before they are tested clinically. Therefore, before I began testing PAX6 gene transfer, I studied the Small eye (Sey) mouse model of aniridia to define therapeutic targets for PAX6 gene transfer, and to quantify phenotypic features of clinical interest. These studies identified the cornea as a target with a clinically relevant phenotype, epithelial thinning, which I could target for gene transfer. Finally, I tested PAX6 gene transfer to the Sey mouse cornea by injecting rAAV encoding a PAX6 open reading frame (ORF) directly into the cornea. These tests revealed that PAX6 gene transfer to the cornea transiently reverses corneal epithelial thinning in Sey mice, and lays the foundation for the development of a gene therapy for aniridia.

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No abstract available.

Three challenges exist for human neurobiology, specifically in the areas of genomics and geneticmedicine: understanding of genome regulation, understanding of central nervous system (CNS) development,and the lack of promoters for human gene therapy. To address these issues, we used computational biologystrategies, primarily involving phylogenetic footprinting, to identify putative regulatory elements in genes with aregionalized or cell-type specific expression pattern. We generated human MiniPromoter constructs, less than 4kilobases in size, and made genetically engineered mice by single-copy knock-in at the mouse Hprt locus.Neuroanatomical analyses were performed on brain and eye, primarily. Using this strategy, we generated 50novel MiniPromoters for use in driving gene therapy constructs. Lastly, we demonstrated retained specificity ofthree retinal ganglion cell layer MiniPromoters when these were moved from knock-ins to an adeno-associatedviral vector, exemplifying the utility of these constructs in other systems. In order to study CNS development, wechose to functionally analyze non-endogenous expression of the neural stem cell regulator NR2E1 in mice. Weemployed a DCX-based MiniPromoter from the Pleiades Promoter Project, in addition to the ubiquitous CAGpromoter, to drive ectopic and ubiquitous expression of human NR2E1. DCX-based expression of human NR2E1did not result in any overt phenotypes and was unable to rescue the brain and eye defects observed in Nr2e1frc/frcmice. In contrast, the CAG promoter resulted in embryonic death at ~E8, with failure of neural tube closure. Weshowed that expression of NR2E1 has negative effects on embryonic stem cell growth. Furthermore, weobserved altered Pax6 expression in NSCs and embryos. Future work on promoter design and NR2E1 biology willadvance our knowledge of genome regulation and CNS development.

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No abstract available.

Nuclear receptor 2E1 (Nr2e1) is expressed in the developing and adult brain and eye, and controls proliferation and differentiation of neural and retinal stem/progenitor cells by regulating genes important in these cellular processes. The Simpson laboratory discovered and characterized a spontaneous deletion of mouse Nr2e1 (the fierce allele, frc) and demonstrated the functional equivalence of human and mouse NR2E1 when the behavioural and neuroanatomical phenotypes of Nr2e1frc/frc mutants were rescued by introducing human NR2E1. NR2E1 has recently been implicated in human psychiatric disorders and variants in NR2E1 were identified in patients with brain and behavioural abnormalities, including bipolar I disorder (BPI). Although NR2E1 had been implicated in BPI, the validity of Nr2e1frc/frc mice to model BPI has not yet been tested. In anticipation of subtle behavioural phenotypes, the hypothesis that dark-phase testing affects the outcome of high-throughput behavioural tests was tested. We demonstrated that dark-phase testing improved discrimination between genetically distinct inbred mouse strains. This result was integrated into the experimental design for evaluating Nr2e1frc/frc mice as a model for BPI by behavioural measures and lithium treatment. Nr2e1frc/frc mice exhibited behavioural traits used to model BPI in rodents, including hyperactivity and learning deficits; however, adult Nr2e1frc/frc mice were resistant to the effects of lithium treatment, and therefore our results did not provide support for Nr2e1frc/frc mice as an appropriate pharmacological model for BPI. Since the nature of patient variants in NR2E1 is likely regulatory, resulting in transcriptional alterations, and the effects of variable levels of Nr2e1 are currently unknown, I tested the hypothesis that variable Nr2e1 levels will affect gene expression and neurological and ocular development. Mice overexpressing Nr2e1 showed alterations in transcription levels of key target genes in both the brain and the eye, significant increase in neural stem/progenitor cell proliferation in the subventricular zone of the adult brain, and severe eye abnormalities. Gene expression changes in Gfap, Gsk3β, Pax6, and Nr2e3 suggest a role for Nr2e1 in genetic pathways important in psychiatric and eye disorders, including BP, Alzheimer Disease, cancer, Aniridia, and enhanced S-cone syndrome. Collectively, these results justify the further investigation of NR2E1 in these human disorders.

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