Dysferlin deficient muscular dystrophy is a devastating disease that leads to loss of mobility and quality of life in patients. Dysferlin is a 230 kD protein primarily expressed in skeletal muscle that functions in membrane resealing. Dysferlin loss of function leads to a decrease in the membrane resealing response after injury in skeletal muscle, which is thought to cause degeneration of the musculature over time. Dysferlin cDNA is 7.4 kb and exceeds AAV packaging capacity of ~ 5kb. This thesis focuses on the generation of mini dysferlin mutants that can be packaged in AAV for downstream testing of therapeutic efficacy. In addition, this thesis creates the groundwork for preclinical studies in mice that can potentially be translated to human patients. A mouse model for dysferlin deficiency was characterized and key disease phenotypes were identified. In addition, cell lines carrying a genetically encoded calcium indicator protein, gCaMP, were established to measure mini dysferlin resealing capacity and for downstream testing in vivo.

Genetic discoveries have highlighted the role of gene expression dysregulation in both rare and common diseases. In particular, a large number of chromatin modifiers, transcription factors, and RNA-binding proteins have been implicated in neurodevelopmental diseases, including epilepsy, autism spectrum disorder, schizophrenia, and intellectual disability. Elucidating the disease mechanisms for these genes is challenging, as the encoded proteins often regulate thousands of downstream targets. In Chapter 2 of this thesis, we describe the use of single-cell RNA-sequencing (scRNA-seq) to characterize a mouse model of HNRNPU-mediated epileptic encephalopathy. This gene encodes a ubiquitously expressed RNA-binding protein, yet we demonstrate that reduction in its expression leads to cell type-specific transcriptomic defects. Specifically, excitatory neurons in a region of the hippocampus called the subiculum carried the strongest burden of differential gene expression. In Chapter 3, we use scRNA-seq to identify convergent molecular and transcriptomic features in four different organoid models of a cortical malformation called periventricular nodular heterotopia. In Chapter 4, we build on these successes to propose a high-throughput drug screening program for neurodevelopmental genes that encode regulators of gene expression. This approach—termed transcriptomic reversal—attempts to identify compounds that reverse disease-causing gene expression changes back to a normal state. Finally, in Chapter 5, we focus on the role of synonymous codon usage in human disease. Codon usage can affect mRNA stability, yet its role in human physiology has been historically overlooked. We use population genetics approaches to demonstrate that natural selection shapes codon content in the human genome, and we find that dosage sensitive genes are intolerant to reductions in codon optimality. We propose that synonymous mutations could modify the penetrance of Mendelian diseases through altering the expression of disease-causing mutations. In summary, the work in this thesis broadly focuses on the role of gene expression dysregulation in disease. We provide novel frameworks for interrogating disease gene expression signatures, prioritizing mutations that may alter expression, and identifying targeted therapeutics.

MDD is a severe and debilitating disorder that is associated with a growing global economic burden due to reduced workplace productivity along with increased healthcare resource utilization. Furthermore, depression markedly enhances the risk for suicide, mortality that is especially worrisome given that 30% of depressed individuals have an inadequate response to current antidepressants. This inadequacy of antidepressants necessitates the discovery of a better understanding of the pathobiology of MDD. Most current antidepressants work through monoamine neurotransmitters, and their relative efficacy in depression led to the now dated monoamine-deficiency hypothesis. The limited usefulness of antidepressants has led to a reinvigorated search for other pathologies in depression that might yield clues for the development of better drug treatments. In this regard, a strong association has been found between oxidative stress and MDD. Our lab recently found increased DNA oxidation and elevated poly(ADP)ribose polymerase (PARP1) gene expression in the brain from donors that had MDD at the time of death. Besides DNA damage repair, PARP1 mediates several downstream inflammatory effects that may contribute to pathology in MDD. In fact, our lab has demonstrated that PARP-1 inhibition produces antidepressant-like effects in rodents, suggesting that PARP-1 inhibitors hold promise as a novel antidepressant drug. While our lab had previously demonstrated elevated PARP1 gene expression in the frontal cortex in MDD, whether PARP1 protein levels were also increased in depression had not been verified. My thesis research was performed to determine whether PARP1 protein expression was also elevated in the brain in MDD. I studied primarily the hippocampus because it is part of the limbic (mediating emotion) system of the brain and because previous research has shown numerous other pathologies in the hippocampus. My study was carried out simultaneously as others in our lab were measuring PARP1 protein levels in frontal cortex in MDD. This latter work was important since the lab’s previous work had observed elevated PARP1 gene expression in the frontal cortex, rather than in the hippocampus which was not previously studied. Hippocampal and frontal cortical brain sections were cut from frozen blocks of both MDD and psychiatrically normal control brain donors for these studies. PARP1 protein levels were estimated by assisted-imaging software. The findings herein demonstrate that levels of PARP1 immunoreactivity are significantly elevated in the frontal cortex of MDD donors as compared to control donors. However, there was no change in PARP1 immunoreactivity in the hippocampus in MDD.

High-voltage activated calcium channels underlie many critical functions in excitable cells and their dysfunction has been implicated in a myriad of cardiovascular and neurological diseases. These channels are multimeric protein complexes composed of α1, β, and α2δ subunits; currently, all calcium channel blockers target either the pore-forming α1 or extracellular-facing α2δ auxiliary subunit. These pharmacological agents have been invaluable in delineating the individual function of each subunit within excitable cells that express multiple calcium channels. Yet, no current tool allows similar pharmacological dissection of individual cytosolic β subunits, preventing our understanding of how distinct β subunits affect the function of calcium channel complexes. Further, small-molecule calcium channel blockers are highly-valued therapeutics for certain conditions, yet their propensity for off-target effects precludes their use in other diseases. In certain applications, genetically-encoded calcium channel blockers may enable channel inhibition with greater tissue-precision and versatility than is achievable with small molecules. Previous work that found the family of RGK proteins powerfully inhibits high-voltage activated calcium channels in part via an association with the β subunit. However, the myriad functions of RGK proteins limit the utility of this approach. In this work, we circumvent this issue by isolating single-domain antibodies (nanobodies) that target the auxiliary CaVβ subunit. We then paired these nanobodies with the powerful enzymatic activity of the HECT domain E3 ubiquitin ligase Nedd4L, to selectively target the calcium channel for ubiquitination. We found this strategy effectively eliminated functional calcium channels from the surface of HEK293 cells, myocytes, and DRG neurons. This modular design permitted us to characterize a pan-β inhibitor (CaV-aβlator) in chapter 2 while refining the approach with a β1-selective channel inhibitor in chapter 3. In chapter 4 I demonstrate that it is possible to hijack the endogenous ubiquitin machinery of the cell by creating Divas: divalent nanobodies that are capable of recruiting endogenous Nedd4L to regulate the calcium channel. Finally, we demonstrate the potential for these genetically-encoded calcium inhibitors to be employed as therapeutic agents by targeting CaV-aβlator to sensory neurons in order to reduce the onset of neuropathic pain. Altogether, this work lays the foundation for nanobody-based genetically-encoded calcium channel inhibitors that have the potential to achieve superior precision in regards to molecular and tissue specificity.

Indiana University-Purdue University Indianapolis (IUPUI) / Damage Associated Molecular Patterns (DAMPs) act largely as endogenous ligands to initiate and maintain the signaling of both inflammatory processes and the acquired immune response. Prolonged action of these endogenous signals are thought to play a significant role sterile inflammation which may be integral to the development of chronic inflammation pathology. HMGB1 (High Mobility Group Box 1) is a highly conserved non-acetylated protein which is among the most important chromatin proteins and serves to organize DNA and regulate transcription. Following stress or injury to the cell, hyperacetylation of lysine residues causes translocation of HMGB1 and eventual release into the extracellular environment where it can take the form of a DAMP and interact with cell types bearing either the Receptor for Advanced Glycation End-products (RAGE) or Toll-Like Receptor 4 (TLR4). Activation of these surface receptors contribute directly to both acute and chronic inflammation. This project investigated the role of HMGB1 through its receptors Receptor for Advanced Glycation End-products (RAGE) and Toll-Like Receptor 4 (TLR4) as it pertained to the development of chronic inflammation and pathology in small diameter, nociceptive sensory neurons. It was demonstrated that the neuronal signaling associated with exposure to HMGB1 is dependent upon the ligands conformational states, as the state dictates its affinity and types of neuronal response. Neuronal activation by bacterial endotoxin or the disulfide state of HMGB1 is dependent on TLR4 and the associated signaling adapter protein, Myeloid differentiation primary response gene 88 (MYD88). Interruption of the receptor-mediated signaling cascade associated with MyD88 was shown to be sufficient to mitigate ligand-dependent neuronal activation and demonstrated significant behavioral findings. Further downstream signaling of HMGB1 in the neuron has yet to be identified, however important steps have been taken to elucidate the role of chronic neuroinflammation with hopes of eventual translational adaptation for clinical therapeutic modalities.

Ferroptosis is a regulated junction between cell death, metabolism, and disease, and it hasbeen implicated in many pathologies. The assorted ferroptosis pharmacology modulators offer valuable means to modulate ferroptosis in multiple diseases, to explore disease etiology, and to develop potential therapeutics. In the first part, the work focuses on inhibiting ferroptosis in a Huntington’s disease model. Ferrostatin-1 (Fer-1) is a potent small-molecule ferroptosis inhibitor that has been adopted to investigate the role of ferroptosis in many disease models. However, its further application is limited by its low potency, poor stability, possible toxicity, and lack of brain penetration. We developed the fourth and fifth generations of ferrostatins and investigated the in vitro and in vivo pharmacokinetics of lead compounds. We identified PHB4082 preferentially accumulating in the kidney as a potential candidate for kidney disease-relevant contexts. Moreover, TH-4-55-2 displayed an excellent brain penetration, preferentially accumulating in the brain at concentrations of magnitude higher than the in vitro IC50 values. In the in vivo toxicity study, it was well-tolerated over 30 days in wild-type and R6/2 mice and exhibited a protective effect against weight loss in a Huntington’s disease model, suggesting it is a strong candidate for application in HD and more neurodegenerative disease models. The second part describes the efforts to explore the therapeutic potential of inducing ferroptosis in a tumor model. Imidazole ketone erastin (IKE) induced ferroptosis by specifically inhibiting system xc– in a subcutaneous xenograft model of Diffuse Large B Cell Lymphoma (DLBCL), suggesting the potential of IKE as a therapeutic strategy for cancer. A biodegradable polyethylene glycol-poly (lactic-co-glycolic acid) nanoparticle formulation was used to aid in delivering IKE to cancer cells in vivo, exhibiting improved tumor accumulation and therapeutic index relative to free IKE, indicating its potential for treating DLBCL. In summary, this work explored the possibility to modulate ferroptosis using small molecule modulators in multiple disease models and identified some potential drug candidates and useful chemical probes.

Glioblastoma is the most common malignant brain tumor, accounting for 17% of all primary brain tumors in the United States. Despite the available surgical, radiation, and chemical therapeutic options, the invasive and infiltrative nature of the tumor render current treatment options minimally effective. Recent reports have identified multiple regulators of glioblastoma progression and invasiveness. It has been demonstrated that ADAM12, A Disintegrin And Metalloproteinase encoded by ADAM12 gene, is over-expressed in glioblastoma and directly correlated with tumor proliferation. Additionally, dysregulation of the Notch signaling pathway has been implicated in the pathogenesis of many gliomas. Lastly, an evolving role of microRNAs, small noncoding RNAs, in carcinogenesis is progressively growing. A recent study has identified ADAM12 as a notch-related gene, and another demonstrated that inhibition of notch signaling decreased glioblastoma recurrence. However the mechanisms of regulation are still unknown. In this study, we hypothesize that direct downregulation of microRNA-29, downstream of over-expression of notch enhances glioblastoma malignancy through upregulation of ADAM12. Although our data demonstrate upregulation of Notch1, its downstream target HES1, and ADAM12 in U87MG glioblastoma cell line. Expression of the cleaved intracellular Notch1 was not detected. Furthermore, we were unable to demonstrate an inhibitory effect of ɣ-secretase inhibitor on Notch signaling, likely reflecting the requirement for modifying culturing conditions or detection in our assays. Furthermore, miR-29 was detected in glioblastoma cells. The expression of miR-29 was further elevated by ɣ-secretase inhibitor treatment, suggesting a role for Notch1 inhibition on miR-29 expression. Although no conclusive results are shown in our work, a role of Notch1 through miR-29 is implicated in the pathogenesis of glioblastoma pathogenesis warranting further investigation into the role downstream target genes in the Notch signaling pathway.

Traumatic brain injury (TBI) is a prevalent condition worldwide with 1.7 million incidences in the U.S. alone. A range of clinical outcomes have been reported post TBI, including dementia, memory loss, and impaired balance and coordination. The lack FDA approved treatments for TBI drives the need for improved prevention and therapeutic strategies. Finite element (FE) models of brain injury mechanics can be used to advance these efforts. These computational models require appropriate constitutive properties in order to predict accurate brain tissue response to injury loading. Suitable experimental models need to be implemented to match the resolution and computational power of FE models. The first aim of this thesis was to characterize the mechanical properties of brain tissue. Here, human, porcine, and rat brain tissue mechanical responses to multistep indentation of increasing strains up to 30% strain were recorded. We tested whether the quasilinear theory of viscoelasticity (QLV) was required to capture the mechanical behavior of brain tissue, but observed that linear viscoelasticity was sufficient under the loading condition applied. Using this fitting model, brain tissue stiffness was found to be dependent on anatomical region, loading direction, age, sex and species to varying degrees. This analysis elucidated factors that affect brain tissue injury mechanics and can be used to improve the accuracy of FE models of brain tissue deformation to predict a biofidelic response to TBI. There is growing evidence linking TBI to pathologies leading to increased risk of neurodegeneration, like tauopathies. However better understanding of these underlying mechanisms is still needed. In our study, we utilized a custom shock tube design to induce blast TBI (bTBI). To isolate the effect of bTBI-induced tau pathology, tau was extracted from sham and shockwave exposed mice 24 hours post injury, referred to as sham and blast tau respectively. We showed that bTBI increased phosphorylation of tau and its propensity to oligomerize. Treatment with blast tau resulted in impaired behavior in mice as well as reduced long term potentiation (LTP) in acute hippocampal slices. Treatment with brain isolate from shockwave exposed tau knockout mice did not exhibit altered behavior or LTP response, eliminating the possibility that any confounding factor in the blast tau preparation was responsible for the impaired outcome. Administration of de-oligomerized blast tau prevented these cognitive impairments, suggesting that toxic effect of blast tau was attributed to its oligomeric form. Here we showed that blast injury can initiate cascades in tau pathology and exposure to this progression results in worsened neurological outcome. Tau phosphorylation is mainly regulated by protein phosphatase 2A (PP2A), whose activity can be altered by leucine carboxyl methyltransferase 1 (LCMT-1) and protein phosphatase methylesterase 1 (PME-1). We sought to leverage this mechanism by infusing LCMT-1 and PME-1 transgenic mice with sham and blast tau. LCMT-1 overexpression prevented behavior and LTP deficits induced by oligomeric blast tau. Furthermore, PME-1 overexpression worsened behavior and LTP response at subthreshold doses of oligomeric blast tau. Together, this illustrated the ability of these two enzymes to regulate the response to exposure of bTBI-induced pathogenic forms of tau. This study indicates the potential of targeting PP2A activity as a viable strategy for therapeutic intervention. In conclusion, this research expands our understanding of the complexity of brain tissue injury mechanics to inform computational models of TBI, illustrates the deleterious effect of pathogenic forms of tau induced by blast injury on cognitive function, and presents a potential target mechanism for the investigation of therapeutic strategies.

Amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD) represents a spectrum of neurodegenerative disease with clinical presentations ranging from progressive paralysis to cognitive impairment. Approximately 15% of ALS-FTD patients initially presenting with motor symptoms also receive a diagnosis of dementia, but a majority of these patients demonstrate some level of cognitive impairment over the course of disease. Identifying molecular pathways that contribute to the development of cognitive deficits in ALS-FTD has thus far been limited by the quality of clinical information and postmortem tissue preservation as well as available technologies. This thesis aims to investigate early stages of cognitive involvement in ALS-FTD using postmortem tissues from a cohort of non-demented ALS patients who have had cognitive and pathological phenotyping. Spatially resolved transcriptome profiling of prefrontal cortex tissues from this cohort identifies dysregulated pathways in non-motor regions, contributing to our understanding of molecular perturbations underlying cognitive impairment in ALS-FTD.

Double-stranded RNA (dsRNA) is a key molecule that initiates the immune response to viral infection, but increasingly endogenous (self) dsRNA has been found to be central to the pathology of diverse non-infectious diseases, from neurodegenerative disease to autoimmunity to cancers. Therefore, it is critical to understand the mechanisms that regulate endogenous dsRNA and the pattern recognition receptors that sense dsRNA. In this dissertation, I address three main questions pertaining to this. First, why is the brain so prone to dsRNA-mediated non-infectious disease, especially considering that dsRNA sensors are expressed in almost all tissues. Using stem cell differentiation, gene expression manipulation, and microscopy, I determined that neurons are a special cell type that express high levels of endogenous dsRNA. This high dsRNA burden in neurons is driven by global lengthening of 3`untranslated regions (3`UTRs) and induces tonic inflammation. Second, I examined the mechanism through which the dsRNA regulator ADAR1 controls endogenous dsRNA levels. I employed heavy use of tissue culture and visualization of dsRNA by confocal microscopy to determine that both the dsRNA-binding and dsRNA-editing activities of ADAR1 are required to suppress global endogenous dsRNA levels. Third, after identifying the existence of transcript isoforms of the key dsRNA sensor PKR, I explored their regulatory potential on the PKR protein itself. By genetically altering human cells, I identify that 3`UTR isoforms of PKR regulate transcript localization, translation efficiency, and PKR protein activatability. Overall, the studies described herein demonstrate novel regulatory roles of endogenous dsRNA and underscore the importance of dsRNA in neurological disease.