Filtering by
- All Subjects: Molecular Biology
- All Subjects: Alzheimer's Disease
- Creators: Newbern, Jason
Receptor-interacting serine/threonine protein kinase 1 (RIPK1) is an enzyme whose interaction with tumor necrosis factor receptor 1 (TNFR1) has been found to regulate cell death pathways, such as apoptosis and necroptosis, and neuroinflammation. Accumulating evidence in the past two decades has pointed to increased RIPK1 activity in various degenerative disorders, including Amyotrophic Lateral Sclerosis (ALS), stroke, traumatic brain injury (TBI) and Alzheimer’s Disease (AD). Given the work showing elevated RIPK1 in neurodegenerative disorders, to further understand the role of RIPK1 in disease pathogenesis, we created a conditional mouse overexpressing neuronal RIPK1 on a C57BL/6 background. These conditional transgenic mice overexpress murine RIPK1 under the CAMK2a neuronal promoter and the transgene is under the control of doxycycline. The removal of doxycycline turns on the RIPK1 transgene. Two cohorts of transgenic mice overexpressing neuronal RIPK1 (RIPK1 OE) were produced, and both had doxycycline removed at post-natal day 21. One cohort was behaviorally tested at 3-months-of-age and the second cohort was tested at 9-months-of-age. Behavioral testing included use of the RotaRod and the Morris water maze to assess motor coordination and spatial cognition, respectively. We found that the RIPK1 OE mice showed no deficits in motor coordination at either age but displayed spatial reference learning and memory deficits at 3- and 9-months-of-age. A subset of mice from two independent cohorts were utilized to assess RIPK1 levels and neuronal number. In these two cohorts of mice used for postmortem analysis, we found that at 3 months of age, ~2 months after transgene activation, RIPK1 levels are not higher in the hippocampus or cortex of the RIPK1 OE mice, however at 9 months, ~8 months after transgene activation, RIPK1 levels are significantly higher in the hippocampus and cortex of RIPK1 OE mice compared to the NonTg counterparts. A subset of tissue was stained against the neuronal marker NeuN. Using unbiased stereology to quantify hippocampal CA1 pyramidal neurons, we found no neuronal loss in the 3-month-old RIPK1 OE mice, but a 34.01% reduction in NeuN+ neuron count in 9-month-old RIPK1 OE mice. Collectively our data shows that RIPK1 overexpression impairs spatial reference learning and memory and reduces neuron number in the CA1 of the hippocampus, underlining the potential of RIPK1 as a target for ameliorating CNS pathology.
MiRNA-based gene regulation occurs in a tissue-specific manner and is implemented by an interplay of poorly understood and complex mechanisms, which control both the presence of the miRNAs and their targets. As a consequence, the precise contributions of miRNAs to gene regulation are not well known. The research presented in this thesis systematically explores the targets and effects of miRNA-based gene regulation in cell lines and tissues.
I hypothesize that miRNAs have distinct tissue-specific roles that contribute to the gene expression differences seen across tissues. To address this hypothesis and expand our understanding of miRNA-based gene regulation, 1) I developed the human 3'UTRome v1, a resource for studying post-transcriptional gene regulation. Using this resource, I explored the targets of two cancer-associated miRNAs miR-221 and let-7c. I identified novel targets of both these miRNAs, which present potential mechanisms by which they contribute to cancer. 2) Identified in vivo, tissue-specific targets in the intestine and body muscle of the model organism Caenorhabditis elegans. The results from this study revealed that miRNAs regulate tissue homeostasis, and that alternative polyadenylation and miRNA expression patterns modulate miRNA targeting at the tissue-specific level. 3) Explored the functional relevance of miRNA targeting to tissue-specific gene expression, where I found that miRNAs contribute to the biogenesis of mRNAs, through alternative splicing, by regulating tissue-specific expression of splicing factors. These results expand our understanding of the mechanisms that guide miRNA targeting and its effects on tissue-specific gene expression.
the disease by a series of motor deficits that manifest over years or decades. It is characterized by degeneration of mid-brain dopaminergic neurons with a high prevalence of dementia associated with the spread of pathology to cortical regions. Patients exhibiting symptoms have already undergone significant neuronal loss without chance for recovery. Analysis of disease specific changes in gene expression directly from human patients can uncover invaluable clues about a still unknown etiology, the potential of which grows exponentially as additional gene regulatory measures are questioned. Epigenetic mechanisms are emerging as important components of neurodegeneration, including PD; the extent to which methylation changes correlate with disease progression has not yet been reported. This collection of work aims to define multiple layers of PD that will work toward developing biomarkers that not only could improve diagnostic accuracy, but also push the boundaries of the disease detection timeline. I examined changes in gene expression, alternative splicing of those gene products, and the regulatory mechanism of DNA methylation in the Parkinson’s disease system, as well as the pathologically related Alzheimer’s disease (AD). I first used RNA sequencing (RNAseq) to evaluate differential gene expression and alternative splicing in the posterior cingulate cortex of patients with PD and PD with dementia (PDD). Next, I performed a longitudinal genome-wide methylation study surveying ~850K CpG methylation sites in whole blood from 189 PD patients and 191 control individuals obtained at both a baseline and at a follow-up visit after 2 years. I also considered how symptom management medications could affect the regulatory mechanism of DNA methylation. In the last chapter of this work, I intersected RNAseq and DNA methylation array datasets from whole blood patient samples for integrated differential analyses of both PD and AD. Changes in gene expression and DNA methylation reveal clear patterns of pathway dysregulation that can be seen across brain and blood, from one study to the next. I present a thorough survey of molecular changes occurring within the idiopathic Parkinson’s disease patient and propose candidate targets for potential molecular biomarkers.
The conservation of the dystrophin gene across metazoans suggests that both vertebrate and invertebrate model systems can provide valuable contributions to the understanding of DMD initiation and progression. Specifically, the invertebrate C. elegans possesses a dystrophin protein ortholog, dys-1, and a mild inflammatory response that is inactive in the muscle, allowing for the characterization of transcriptome rearrangements affecting disease progression independently of inflammation. Furthermore, C. elegans do not possess a satellite cell equivalent, meaning muscle regeneration does not occur. This makes C. elegans unique in that they allow for the study of dystrophin deficiencies without muscle regeneration that may obscure detection of subtle but consequential changes in gene expression.
I hypothesize that gaining a comprehensive definition of both the structural and signaling roles of dystrophin in C. elegans will improve the community’s understanding of the progression of DMD as a whole. To address this hypothesis, I have performed a phylogenetic analysis on the conservation of each member of the dystrophin associated protein complex (DAPC) across 10 species, established an in vivo system to identify muscle-specific changes in gene expression in the dystrophin-deficient C. elegans, and performed a functional analysis to test the biological significance of changes in gene expression identified in my sequencing results. The results from this study indicate that in C. elegans, dystrophin may have a signaling role early in development, and its absence may activate compensatory mechanisms that counteract disease progression. Furthermore, these findings allow for the identification of transcriptome changes that potentially serve as both independent drivers of disease and potential therapeutic targets for the treatment of DMD.