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Description
Induced pluripotent stem cells (iPSCs) are an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative

Induced pluripotent stem cells (iPSCs) are an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative diseases are commonly misdiagnosed in live human subjects. Postmortem histopathological examination of a donor's brain, combined with premortem clinical criteria, is often the most robust approach to correctly classify an individual as a disease-specific case or unaffected control. We describe the establishment of primary dermal fibroblasts cells lines from 28 autopsy donors. These fibroblasts were used to examine the proliferative effects of establishment protocol, tissue amount, biopsy site, and donor age. As proof-of-principle, iPSCs were generated from fibroblasts from a 75-year-old male, whole body donor, defined as an unaffected neurological control by both clinical and histopathological criteria. To our knowledge, this is the first study describing autopsy donor-derived somatic cells being used for iPSC generation and subsequent neural differentiation. This unique approach also enables us to compare iPSC-derived cell cultures to endogenous tissues from the same donor. We utilized RNA sequencing (RNA-Seq) to evaluate the transcriptional progression of in vitro-differentiated neural cells (over a timecourse of 0, 35, 70, 105 and 140 days), and compared this with donor-identical temporal lobe tissue. We observed in vitro progression towards the reference brain tissue, supported by (i) a significant increasing monotonic correlation between the days of our timecourse and the number of actively transcribed protein-coding genes and long intergenic non-coding RNAs (lincRNAs) (P < 0.05), consistent with the transcriptional complexity of the brain, (ii) an increase in CpG methylation after neural differentiation that resembled the epigenomic signature of the endogenous tissue, and (iii) a significant decreasing monotonic correlation between the days of our timecourse and the percent of in vitro to brain-tissue differences (P < 0.05) for tissue-specific protein-coding genes and all putative lincRNAs. These studies support the utility of autopsy donors' somatic cells for iPSC-based neurological disease models, and provide evidence that in vitro neural differentiation can result in physiologically progression.
ContributorsHjelm, Brooke E (Author) / Craig, David W. (Thesis advisor) / Wilson-Rawls, Norma J. (Thesis advisor) / Huentelman, Matthew J. (Committee member) / Mason, Hugh S. (Committee member) / Kusumi, Kenro (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Alzheimer’s disease (AD) is characterized by the aberrant accumulation and aggregation of proteins that in turn contribute to learning and memory deficits. The mammalian target of rapamycin (mTOR) plays an essential role in regulating the synthesis and degradation of proteins that contribute to cell growth and learning and memory. Hyperactivity

Alzheimer’s disease (AD) is characterized by the aberrant accumulation and aggregation of proteins that in turn contribute to learning and memory deficits. The mammalian target of rapamycin (mTOR) plays an essential role in regulating the synthesis and degradation of proteins that contribute to cell growth and learning and memory. Hyperactivity of mTOR can cause detrimental effects to protein homeostasis and has been linked to AD. The proline-rich Akt-substrate 40 kDa (PRAS40) is a negative regulator of mTOR, as it binds to mTOR directly, reducing its activity. Upon phosphorylation, PRAS40 detaches from mTOR thereby releasing its inhibitory effects. Increased phosphorylation of PRAS40, and a subsequent increase in mTOR activity has been linked to diabetes, cancer, and other conditions; however, PRAS40’s direct role in the pathogenesis of AD is still unclear. To investigate the role of PRAS40 in AD pathology, we generated a PRAS40 conditional knockout mouse model and, using a neuronal-specific Cre recombinase, selectively removed PRAS40 from APP/PS1 mice. Removing neuronal PRAS40 exacerbated Abeta levels and plaque load but paradoxically had no significant effects on mTOR signaling. Mechanistically, the increase in Abeta pathology was linked to a decrease in autophagy function. Our data highlight a primary role of PRAS40 in the pathogenesis of AD.
ContributorsSurendra, Likith (Author) / Oddo, Salvatore (Thesis director) / Velazquez, Ramon (Committee member) / Pratico, Domenico (Committee member) / School of Life Sciences (Contributor) / Dean, W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
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Description
Dementia is a collective term used to describe symptoms of cognitive impairment in learning and memory. The most prevalent form of dementia is Alzheimer’s disease (AD). In order to understand the pathological mechanisms associated with AD, animal models have been created. These various mouse models replicate the pathology found in

Dementia is a collective term used to describe symptoms of cognitive impairment in learning and memory. The most prevalent form of dementia is Alzheimer’s disease (AD). In order to understand the pathological mechanisms associated with AD, animal models have been created. These various mouse models replicate the pathology found in humans with AD. As a consequence of the fact that this disease impairs cognitive abilities in humans, testing apparatuses have been developed to measure impaired cognition in animal models. One of the most common behavioral apparatuses that has been in use for nearly 40 years is the Morris water maze (MWM). In the MWM, animals are tasked to find a hidden platform in a pool of water and thereby are subjected to stress that can unpredictably influence cognitive performance. In an attempt to circumvent such issues, the IntelliCage was designed to remove the external stress of the human experimenter and provide a social environment during task assessment which is fully automated and programable. Additionally, the motivation is water consumption, which is less stressful than escaping a pool. This study examined the difference in performance of male and female cohorts of APP/PS1 and non-transgenic (NonTg) mice in both the MWM and the IntelliCage. Initially, 12-month-old male and female APP/PS1 and NonTg mice were tested in the hippocampal-dependent MWM maze for five days. Next, animals were moved to the IntelliCage and underwent 39 days of testing to assess prefrontal cortical and hippocampal function. The results of this experiment showed significant sex differences in task performance, but inconsistency between the two testing paradigms. Notably, males performed significantly better in the MWM, which is consistent with prior research. Interestingly however, APP/PS1 females showed higher Amyloid-β plaque load and performed significantly better in the more complex tasks of the IntelliCage. This suggests that Aβ plaque load may not directly contribute to cognitive deficits, which is consistent with recent reports in humans with AD. Collectively, these results should inform scientists about the caveats of behavioral paradigms and will aid in determining translation to the human condition.
ContributorsMifflin, Marc Anthony (Author) / Velazquez, Ramon (Thesis director) / Mastroeni, Diego (Committee member) / School of Geographical Sciences and Urban Planning (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
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Description
Alzheimer’s Disease (AD) affects over 5 million individuals in the U.S. and has a direct cost estimated in excess of $200 billion per year. Broadly speaking, there are two forms of AD—early-onset, familial AD (FAD) and late-onset-sporadic AD (SAD). Animal models of AD, which rely on the overexpression of FAD-related

Alzheimer’s Disease (AD) affects over 5 million individuals in the U.S. and has a direct cost estimated in excess of $200 billion per year. Broadly speaking, there are two forms of AD—early-onset, familial AD (FAD) and late-onset-sporadic AD (SAD). Animal models of AD, which rely on the overexpression of FAD-related mutations, have provided important insights into the disease. However, these models do not display important disease-related pathologies and have been limited in their ability to model the complex genetics associated with SAD.

Advances in cellular reprogramming, have enabled the generation of in vitro disease models that can be used to dissect disease mechanisms and evaluate potential therapeutics. To that end, efforts by many groups, including the Brafman laboratory, to generated patient-specific hiPSCs have demonstrated the promise of studying AD in a simplified and accessible system. However, neurons generated from these hiPSCs have shown some, but not all, of the early molecular and cellular hallmarks associated with the disease. Additionally, phenotypes and pathological hallmarks associated with later stages of the human disease have not been observed with current hiPSC-based systems. Further, disease relevant phenotypes in neurons generated from SAD hiPSCs have been highly variable or largely absent. Finally, the reprogramming process erases phenotypes associated with cellular aging and, as a result, iPSC-derived neurons more closely resemble fetal brain rather than adult brain.

It is well-established that in vivo cells reside within a complex 3-D microenvironment that plays a significant role in regulating cell behavior. Signaling and other cellular functions, such as gene expression and differentiation potential, differ in 3-D cultures compared with 2-D substrates. Nonetheless, previous studies using AD hiPSCs have relied on 2-D neuronal culture models that do not reflect the 3-D complexity of native brain tissue, and therefore, are unable to replicate all aspects of AD pathogenesis. Further, the reprogramming process erases cellular aging phenotypes. To address these limitations, this project aimed to develop bioengineering methods for the generation of 3-D organoid-based cultures that mimic in vivo cortical tissue, and to generate an inducible gene repression system to recapitulate cellular aging hallmarks.
ContributorsBounds, Lexi Rose (Author) / Brafman, David (Thesis director) / Wang, Xiao (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
Alzheimer’s disease (AD) is one of the most prevalent neurodegenerative diseases worldwide, with no effective treatments or preventions. Evidence suggests that environmental factors, including dietary nutrients, contribute to the etiology of AD. Choline is an essential nutrient found in many common foods. Choline is produced endogenously, but not at levels

Alzheimer’s disease (AD) is one of the most prevalent neurodegenerative diseases worldwide, with no effective treatments or preventions. Evidence suggests that environmental factors, including dietary nutrients, contribute to the etiology of AD. Choline is an essential nutrient found in many common foods. Choline is produced endogenously, but not at levels sufficient for healthy metabolic function and thus requires dietary supplementation. Literature shows that ~90% of Americans do not meet the adequate intake threshold for dietary choline consumption and therefore are dietary choline-deficient. While dietary choline supplementation throughout life has been shown to have significant health benefits, such as reducing AD pathology and improving cognition in a mouse model of AD, the impacts of dietary choline deficiency are unknown. Experiments were designed to understand the effects of dietary choline deficiency in healthy, non-transgenic mice (NonTg) and in the 3xTg-AD mouse model of AD. From 3 to 12 months of age, mice received either adequate choline (ChN) in the diet or were put on a choline-deficient (Ch-) diet. A Ch- diet leads to significant weight gain throughout life in both the NonTg and 3xTg-AD mice, with AD mice showing a greater increase. Additionally, impaired glucose metabolism, which is a risk factor for AD, was induced in both NonTg Ch- and 3xTg-AD Ch- mice. Interestingly, Ch- induced cardiomegaly in 3xTg-AD mice and elevated markers of cardiac dysfunction in NonTg mice to similar levels in 3xTg-AD mice. Finally, Ch- exacerbated amyloid-β plaque pathology and tau hyperphosphorylation in the hippocampus and cortex of 3xTg-AD mice. Proteomic analyses revealed Ch- induced changes in hippocampal proteins associated with postsynaptic receptor regulation, microtubule stabilization, and neuronal development, as well as well-known AD-associated proteins (MAPT, BACE1, MECP2, CREBBP). Proteomic analyses also revealed Ch- induced changes of plasma proteins associated with secondary pathologies of AD including inflammation, immune response insulin metabolism, and mitochondrial dysfunction (SAA1, SAA2, IDE, HSPD1, VDAC-1, VDACE-2). Taken together, these data suggest that dietary choline deficiency induces system-wide cellular and molecular dysfunction associated with AD across several pathogenic axes, through proteomic changes not only in the hippocampus but also in the plasma.
ContributorsDave, Nikhil (Author) / Velazquez, Ramon (Thesis advisor) / Piras, Ignazio (Committee member) / Mastroeni, Diego (Committee member) / Arizona State University (Publisher)
Created2022
Description

Alzheimer’s Disease (AD) is the most prevalent form of dementia and is the sixth leading cause of death in the elderly. Evidence suggests that forms of stress, including prenatal maternal stress (PMS), could exacerbate AD development. To better understand the mechanism linking PMS and AD, we investigated behavior and specific

Alzheimer’s Disease (AD) is the most prevalent form of dementia and is the sixth leading cause of death in the elderly. Evidence suggests that forms of stress, including prenatal maternal stress (PMS), could exacerbate AD development. To better understand the mechanism linking PMS and AD, we investigated behavior and specific epigenetic markers of the 3xTg-AD mouse model compared to aged-controls in offspring of stressed mothers and non-stressed mothers.

ContributorsBrookhouser, Leia (Author) / Coleman, Paul (Thesis director) / Velazquez, Ramon (Committee member) / Conrad, Cheryl (Committee member) / Judd, Jessica (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor)
Created2022-12
Description
Wound healing is a complex tissue response that requires a coordinated interplay of multiple cells in orchestrated biological processes to restore the skin's barrier function post-injury. Proteolytic enzymes, in particular matrix metalloproteinases (MMPs), contribute to all phases of the healing process by regulating immune cell influx, clearing out the extracellular

Wound healing is a complex tissue response that requires a coordinated interplay of multiple cells in orchestrated biological processes to restore the skin's barrier function post-injury. Proteolytic enzymes, in particular matrix metalloproteinases (MMPs), contribute to all phases of the healing process by regulating immune cell influx, clearing out the extracellular matrix (ECM), and remodeling scar tissue. As a result of these various functions in the healing of skin wounds, uncontrolled activities of MMPs are associated with impaired wound healing. The MMP gene family consists of a highly conserved set of genes. Deleterious mutations in MMP genes cause developmental phenotypes that affect the heart, skeleton, and immune system response. The availability of contiguous draft genomes of non-model organisms enables the study of gene families through analysis of synteny and sequence identity. My project is aimed at conducting a comparative genomic analysis of the MMP gene family from the genomes of 29 tetrapod species—with an emphasis on reptiles. Results regarding the similarities and differences among MMP protein sequences can be further investigated to shed light on the causes which give rise to various adaptive mutations for specific species groups.
ContributorsYu, Alexander (Author) / Kusumi, Kenro (Thesis director) / Dolby, Greer (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2022-12
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Description

Heat shock factors (HSFs) are transcriptional regulators that play a crucial role in the cellular response to environmental stress, particularly heat stress. Understanding the evolution of HSFs can provide insights into the adaptation of organisms to their changing environments. This project explored the evolution of HSFs within tetrapods, a grou

Heat shock factors (HSFs) are transcriptional regulators that play a crucial role in the cellular response to environmental stress, particularly heat stress. Understanding the evolution of HSFs can provide insights into the adaptation of organisms to their changing environments. This project explored the evolution of HSFs within tetrapods, a group of animals that includes amphibians, reptiles, turtles, and mammals. Through an analysis of the available genomic data and subsequent genomic methodologies, HSFs have undergone significant changes throughout tetrapod evolution, as evidenced by loss events observed in protein sequences of the species under examination. Moreover, several conserved and divergent regions within HSF proteins were identified, which may reflect functional differences between HSFs in different tetrapod lineages. Our findings suggest that the evolution of HSFs has contributed to the adaptation of tetrapods to their diverse environments and that further research on the functional and regulatory differences between HSFs may provide a better understanding of how organisms cope with stress in heat-stressed environments.

ContributorsSharma, Yash (Author) / Kusumi, Kenro (Thesis director) / Benson, Derek (Committee member) / Dolby, Greer (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2023-05
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Description

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,

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.

ContributorsBoiangiu, Mara-Clarisa (Author) / Velazquez, Ramon (Thesis director) / Newbern, Jason (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution & Social Change (Contributor) / Department of Psychology (Contributor)
Created2022-05
Description
Dementia is a disease affecting many individuals worldwide resulting in neurological deficits. The most common form of dementia known as Alzheimer’s Disease (AD) is the 6th leading cause of death in the United States. The disease is defined by neuron loss, the presence of intracellular tau protein (tubulin associated unit)

Dementia is a disease affecting many individuals worldwide resulting in neurological deficits. The most common form of dementia known as Alzheimer’s Disease (AD) is the 6th leading cause of death in the United States. The disease is defined by neuron loss, the presence of intracellular tau protein (tubulin associated unit) neurofibrillary tangles (NFT), and extracellular amyloid- (Aβ) plaques. For this study, our aim was to understand the staging system used based off of the disease progression, called Braak Staging. Our hypothesis is that as disease progresses, marked by Braak stages, different brain regions will begin to show differential expressions of various biological dysregulations. Molecular dysfunctions of early disease will be precursors to later disease dysfunctions. The outcomes of our study indicated there were several molecular dysfunctions in early disease with tau pathology not present in the region yet.
ContributorsMirji, Ruchira (Author) / Huseby, Carol (Thesis director) / Velazquez, Ramon (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Human Evolution & Social Change (Contributor)
Created2024-05