RSS 1.0Upstate Graduate Student Dissertations & Theses
Recent Submissions
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Human cytomegalovirus (HCMV) exploits heat-shock transcription factor 1 (HSF1) to promote viral replication: a potential novel antiviral target to combat HCMV infection[Abstract is unavailable until after embargo date]
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Microbiota Colonization Dynamics Dictate Systemic IgAEvolution of the mammalian gut is intimately linked with the microbes that inhabit this space. Immunological development of gastrointestinal and systemic tissues is fundamentally dependent on stimulation by symbiotic microorganisms. In some cases, the same species that are critical for host immunity display pathogenic qualities when homeostasis is disrupted. Bacteroides fragilis is one such species with numerous symbiotic and pathogenic characteristics. This thesis explores the generation of B. fragilis-specific systemic IgA and the role of this response in protecting the host from B. fragilis pathogenicity. Induction of systemic IgA specific to B. fragilis requires exposure of this bacterium to small intestinal Peyer's patches and results in migration of newly generated IgA plasma cells to systemic tissues. Colonization dynamics of B. fragilis in mouse models with endogenous gut microbiota revealed that the magnitude of systemic IgA responses occurs in a dose-dependent fashion. Finally, a framework for establishing B. fragilis colonization and subsequent immune modulation within a highly diverse intestinal ecosystem was developed.
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Investigating the role of formin FHOD3 during myofibrillogenesis in embryonic chick cardiomyocytesFormins are major actin polymerizing proteins which act via the FH2 domain to promote actin nucleation and polymerization, as well as the FH1 domain to accelerate FH2 mediated actin elongation. FHOD3 is a formin that has been shown to be expressed predominantly in the heart and is critical for myofibril maturation during development in mice. FHOD3 has been shown to localize where actin filaments overlap myosin filaments within the sarcomeres of mice, rat, and human induced pluripotent stem-cell derived cardiomyocytes, flanking both sides of the M-line in the sarcomere. However, the role of FHOD3 in the myofibrillogenesis and the timing of FHOD3's activity in myofibrils has yet to be determined. Using RT-PCR, I successfully identified expression of at least two different isoforms of FHOD3 within heart tissue, matching to predicted isoforms X5 and X6. I also identified two chemically conserved regions within the FHOD3 amino acid sequence that are related to the cardiac FHOD3 isoform's localization to myofibrils. Using immunofluorescence microscopy and western blotting I found that FHOD3 is present within embryonic chick cardiomyocytes and that the localization of FHOD3 matches prior reports. FHOD3 was determined to be transiently expressed at significantly higher rates on Days 3 and 4 of culture in cardiomyocyte myofibrils. 90% of measured sarcomeres containing FHOD3 had a Z-line to Z-line length ranging from 1.4-1.9 µm, suggesting not only a length-dependent role of FHOD3, but a myofibril maturity dependent localization of FHOD3. These observations illustrate that FHOD3 likely does not have a function in the initiation of myofibrillogenesis but may instead have a role in the maturation and elongation of sarcomeres. The transient nature observed also suggests that FHOD3 may be localized within the sarcomere only as needed. Knockdowns of FHOD3 performed with shRNAs showed no indication of knockdown causing myofibrillar disruption. Knockdowns of FHOD3 using DsiRNAs were statistically inconclusive for knockdown occurring but did have an upwards nonsignificant trend in the percentage of myofibril disruption in cardiomyocytes.
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HSV-1 targets a novel antiviral response of the STING pathwayIn order to establish a successful infection, herpes simplex virus-1 (HSV-1), a ubiquitous virus with high seropositivity in the human population, must undermine a multitude of host innate and intrinsic immune defense mechanisms, including key players of the stimulator of interferon genes (STING) pathway. Recently it was discovered that not only de novo produced intracellular 2'-3'cGAMP, but also extracellular 2'-3'cGAMP can activate the STING pathway by being transported across the cell membrane via the folate transporter, SLC19A1, the first identified extracellular antiporter of this critical signaling molecule in cancer cells. We hypothesized that the import of exogenous 2'-3'cGAMP would function to establish an antiviral state similar to that seen with the paracrine antiviral activities of interferon. Further, to establish a successful infection, viruses, such as HSV-1, must undermine this induction of the STING pathway by inhibiting the biological functions of SLC19A1. Herein, we report that treatment of the monocytic cell line, THP-1 cells and SH-SY5Y neuronal cell line with exogenous 2'-3'cGAMP induces interferon production and establishes an antiviral state. Using either pharmaceutical inhibition or genetic knockout of SLC19A1 blocks the 2'-3'cGAMP-induced inhibition of viral replication. Additionally, HSV-1 infection results in the reduction of SLC19A1 transcription, translation, and importantly, the rapid removal of SLC19A1 from the cell surface of infected cells. Our data indicate SLC19A1 functions as a newly identified antiviral mediator for extracellular 2'-3'cGAMP which is undermined by HSV-1 protein ICP27. This work presents novel and important findings about how HSV-1 manipulates the host's immune environment for viral replication and discovers details about an antiviral mechanism which information could aid in the development of better antiviral drugs in the future.
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Structural insights of the histone H3 tail and its role in the mechanism of histone H3 lysine-4 methylationStructural insights of the histone H3 tail and its role in the mechanism of H3 lysine-4 methylation Gene expression relies on the proper chromatin structure to provide the necessary access to the DNA for the large transcription complexes to carry out their tasks. If the chromatin is tightly condensed, transcription is unable to occur. To regulate and initiate access to the DNA, an elaborate network of histone modifying enzymes, chromatin remodeling complexes, and other supporting proteins must coordinate the writing, reading, and erasing of histone post-translational modifications (PTMs). One such PTM, methylation of histone H3 on the lysine-4 (H3K4) residue, is critically important for maintenance of gene expression states. This is done in a spatiotemporal manner, which is influenced by the number of methyl groups that are present. However, an understanding of how the degree of H3K4 methylation is regulated remains elusive. In this dissertation, we demonstrate the remarkable conservation of length and composition in the flexible N-terminal tails of histone proteins across evolution. Recent structural studies indicate several methyltransferase complexes bind to the nucleosome core, often leaving the N-terminal tails unbound. Research from our lab has also demonstrated that non-processive buildup of lysine-4 methyl groups takes place at multiple active sites. Based on these observations, we propose a hypothesis whereby the histone H3 tail acts as a swinging arm substrate, delivering residue side chains to different active sites to facilitate the progressive establishment of these epigenetic states. To investigate this hypothesis, we employed the CRISPR/Cas9 system in Saccharomyces cerevisiae to systematically modify the length of the H3 tail. We monitored histone H3 lysine 4 (H3K4) methylation, mediated by SET1, the primary H3K4 methyltransferase in budding yeast. Our findings demonstrate that altering the length of the H3 tail has varying effects on the extent of H3K4 methylation, in accordance with the swinging arm model. We also demonstrate that three proline residues are responsible for providing a segmented, tripartite structure with hinge-like joints that likely influence the tail's range of motion. Furthermore, the results support the proposed multiple active-site model, where mono-, di-, and trimethylation occur at distinct active sites within the COMPASS or MLL Core Complexes.
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[Title is unavailable until after embargo date][Abstract is unavailable until after embargo date]
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Exploring the role of single nucleotide polymorphisms in varicella zoster virus vaccine attenuation in skinVaricella zoster virus (VZV) is a disease that can be detrimental to the health of children in its primary form, chicken pox, and later in the elderly as its reactivated form, shingles. Before the advent of the vaccine, Varivax, VZV was endemic in the United States as it is highly contagious and can be spread through both direct contact and aerosol particles. Varivax, or vOka, is a live attenuated vaccine, and while effective, has side effects ranging from rashes to possible VZV reactivation. While the vaccine has reduced the incidence and severity of VZV, there is still little known about the mechanism of its attenuation in skin. vOka is genetically heterogeneous with hundreds of single nucleotide polymorphisms (SNPs) that are a mixture of wild-type and vOka nucleotides. Previous studies have demonstrated the key to attenuation may be through five SNPs in the open reading frame (ORF) 62 region found to be fixed and stable across different licensed vOka preparations around the world. ORF62 contains the gene for IE62, a transactivator protein responsible for regulating the expression of viral genes and the host gene for KRT15, a cytokeratin protein. This project focused on if two SNPs, located in the loci positions 106262 and 107252, that are found to be almost 100% conserved across all variations of vOka are responsible for the attenuation in human skin and induction of KRT15. We evaluated four mutant viruses with SNPs found in vOka and discovered that a double SNP mutation stunted virus growth in HFF cells. In addition, we found no significant difference in the growth of our viruses in skin but variability in successful infection. Furthermore, in infected skin, we found that VZV-ORF57-Luc and single mutant virus, 68-958, upregulate KRT15 expression with VZV infection while single mutant virus, 68-62S-A, may downregulate KRT15 expression with VZV infection. This project is important because it may reveal the molecular basis of attenuation of the licensed varicella vaccine. This information could be used to make a vaccine that contains only the attenuated genotype.
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From bud scars to molecular insights: investigating V-ATPase function and assembly in yeast replicative agingAging is a complex process that involves the progressive decline of physiological functions over time. As the global population continues to age, understanding the mechanisms underlying aging has become an important area of study. Lysosomes play a crucial role in maintaining protein quality control and degrading unneeded or damaged proteins through proteolysis. Therefore, lysosomes play a prominent role in theories of aging due to their significant role in cellular homeostasis. Interestingly, many of the hallmarks of aging are conserved between yeast and humans, highlighting the relevance of yeast as a model organism to study aging processes. One key enzyme responsible for acidifying lysosomes and lysosome-like vacuoles in yeast is the vacuolar-type H+-ATPase (V-ATPase). Despite evidence showing that lysosomes alkalinize with age, compromising their proteolytic function, little is known about the regulation of V-ATPase in aging cells. Yeast cells divide asymmetrically with each division leaving a "bud scar" that can be stained to determine replicative age. In comparing cells of distinct replicative age, we find significant decreases in V-ATPase assembly, accompanied by poor vacuolar acidification, in older cells. Remarkably, partial disassembly of the V-ATPase occurs at a relatively early age, indicating its potential as a phenotypic driver in the aging process. Reversible disassembly is controlled in part by the activity of two opposing and conserved factors, the RAVE complex and Oxr1. The RAVE complex promotes V-ATPase assembly and a rav1∆ mutant has a significantly shorter lifespan than wild-type cells; Oxr1 promotes disassembly and an oxr1∆ mutation significantly extends lifespan. These data indicate that reduced V-ATPase assembly may drive the loss of lysosome acidification with age and place the balance of V-ATPase assembly factors at the center of this process. Caloric restriction, defined as reduced calories with adequate nutrition, has been shown to extend lifespan in multiple organisms including yeast. We find that caloric restriction reverses the age-related decreases in V-ATPase assembly and vacuolar acidification in yeast as well as restoring balance of assembly factors. We investigated three conserved metabolic signaling pathways that have been linked to acidification, caloric restriction, and aging: PKA, mTORC1/S6K (TORC1/Sch9 in yeast), and AMPK (Snf1 in yeast). By utilizing non-essential nutrient mutations in these signaling pathways, we determined the impact on V-ATPase assembly during replicative aging. Mutations compromising TORC1 function were known to extend lifespan and preserved V-ATPase assembly even in older cells. In contrast, a mutation that prevents recruitment of Snf1/AMPK to vacuoles prevented V-ATPase assembly even in young cells and shortened lifespan. This study provides novel insights into the importance of V-ATPase assembly and function in the aging process and suggests novel interventions to promote health aging.
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Kcnh2 Expression Profile and Continuous EEG/ECG Monitoring in a Rabbit Model of Long QT Syndrome Type 2Long QT Syndrome (LQTS) is a classically studied cardiac condition characterized by a prolonged ventricular excitation-repolarization interval (QT interval) on an electrocardiogram (ECG). LQTS is associated with an increased risk of arrhythmias and sudden cardiac death. People with LQTS, particularly those with Long QT Syndrome Type 2 (LQT2), are also at an increased risk of seizures/epilepsy. LQT2 is caused by loss of function variants in the KCNH2 gene. The dual neuro-cardiac phenotype of LQT2 can likely be explained by expression of KCNH2 in both the brain and heart. Using a rabbit model that harbors an endogenous knock-in mutation in one allele of the pore domain of the Kcnh2 gene, I characterized the molecular expression of WT vs. mutant Kcnh2 and developed a protocol for long-term subcutaneous EEG/ECG implantation. To better understand the molecular profile of WT vs. mutant rabbits, the relative expression of WT vs mutant Kcnh2 transcripts was evaluated using quantitative PCR (qPCR) with verification via Oxford Nanopore Technology (ONT) sequencing. Additionally, 44 RNA sequencing libraries were prepared and sequenced for further analysis of the molecular profile of WT vs mutant rabbits. Micro-C and high molecular weight DNA libraries were also prepared for the construction of a more thorough rabbit genome. In mutant rabbits, total Kcnh2 expression is roughly half that of WT rabbits. In mutant rabbits, the mutant Kcnh2 RNA represents 11% of the total Kcnh2. These data suggest that most mutant Kcnh2 RNA is degraded shortly after generation. To continuously monitor the rabbits’ cardiac and neuronal electrical function in vivo, a method of constant EEG/ECG recording was designed and implemented. It involves the surgical placement of subdermal electrodes and the design and manufacturing of a wiring system. The surgical placement of electrodes has been optimized to minimize time and number of incisions and improve outcomes. The wiring system enables the rabbits to have free range of motion within the housing cage and keeps all wires protected and out of reach of the rabbits. This system is functional and generates high quality continuous EEG/ECG recordings.
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The murine absolute visual threshold: behavior & retinal pathwaysConnexin 36 (Cx36) gap junctions are important for governing the sensitivity of the dark-adapted retina. Despite its importance for physiological sensitivity, the degree to which retinal Cx36 governs the psychophysical absolute threshold is not known. The purpose of this work is to study to what extent inner- and outer-retinal Cx36 governs the absolute visual threshold. In Chapter 2 we developed a one-alternative forced choice (1AFC) task for measuring murine absolute visual thresholds to full-field flash stimuli. We found that our 1AFC task, in conjunction with the theory of signal detection, gave response bias-independent absolute visual threshold estimated. Using this assay, we found that decision criteria are related to response times. In Chapter 3 we used the 1AFC task and the power of transgenic mice to assess the relative contributions of inner and outer retinal Cx36 to the absolute visual threshold. We concluded that inner, not outer, retinal Cx36 is most responsible for governing the absolute visual threshold. In parallel, by testing mice with disrupted rod vision, we determined that rod OFF pathways, and not cones, set the absolute visual threshold in the absence of Cx36. Finally, we studied the impact of Cx36 on temporal summation at absolute threshold, by obtaining thresholds for a range of flash durations. Threshold-vs-duration data was then fit with a model of temporal summation that allowed us to determine whether Cx36 influences the temporal filtering properties of scotopic vision. Our model fits suggest that photoreceptor Cx36 may play a role in temporal processing at absolute visual threshold. Overall, this work sheds new light on the behavioral dynamics and neural underpinnings of rod mediated vision.
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Battle of arms: human cytomegalovirus manipulates monocyte survival for viral dissemination.Human cytomegalovirus (HCMV) is a highly prevalent pathogen with seropositivity rates reaching upwards of 90% in the United States. Most primary infections are asymptomatic in immunocompetent individuals, but HCMV poses a significant risk in immunocompromised and immunonaїve individuals including transplant patients and developing fetuses in utero. The key to systemic dissemination of HCMV relies upon the infection of monocytes, which function as non-permissive vehicles to deliver virus to end organ tissues. These primary infected monocytes also travel to the bone marrow, infecting CD34+ stem cells, leading to the establishment of a lifelong HCMV infection. HCMV can reactivate at any point throughout the host's lifetime, leading to HCMV-infected stem cells exiting the bone marrow as monocytes, disseminating to end-organ tissue, and perpetuating HCMV disease. In circulation, monocytes have a short life span of 48 hours that can be accelerated by the cellular death pathway, apoptosis, as a cellular defense mechanism against viral infection. Our lab has shown during primary infection, HCMV circumvents intrinsic apoptotic pathways, however, the mechanism by which HCMV blocks extrinsic apoptosis is unclear. The studies in this thesis reveal that HCMV induces cFLIP expression, inhibiting extrinsic apoptosis effector caspase 8. This effective inhibition of intrinsic and extrinsic apoptosis prompts trap-door death pathway necroptosis. However, the mechanism in which this pathway is activated and how HCMV modulates this pathway to promote cell survival is unknown. In these works, we identified TLR3 as the death receptor responsible for inducing necroptosis. To circumvent this activation, HCMV upregulates autophagy, a ubiquitous cellular recycling process. We saw the inhibition of autophagy altered nucleocytoplasmic shuttling and activation of executioner kinase, MLKL, culminating in necrotic cell death. This work highlights the delicate balance between pro-survival and pro-death elements in HCMV infected monocytes. However, investigating how HCMV modulates cellular death pathways in a primary infection monocyte model does not fully encapsulate the role of monocytes in HCMV dissemination. Once HCMV latency is established in CD34+ stem cells, this allows HCMV the ability to persist in the host for their entire life span as monocytes derived from latently infected stem cells that can re-seed HCMV to peripheral organs to establish a chronic lytic infection. To investigate this understudied secondary population of HCMV-infected monocytes, we developed a model in which primary HCMV-infected monocytes and infected monocytes derived from latently infected stem cells are on the same genetic background by differentiating a CD34+ myeloblastic cell line. Though preliminary, we believe that this model, combined with investigations of mechanisms in which HCMV promotes survival in primary infected monocytes, will allow for the development of novel therapies that specifically target HCMV-infected monocytes, thus preventing viral dissemination and the establishment of disease.
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Novel signaling pathways driving experience-dependent maturation in dentate gyrus granule cells: a deep-sequencing approachThe granule cells in the dentate gyrus of the hippocampus are a cell type that is critical for learning and memory ability. Dentate gyrus granule cells exhibit the unique capacity to differentiate and mature throughout an individual's lifetime. Decades of dedicated research has revealed many transcription factors that facilitate the differentiation of granule cells from neural progenitors. The goal of this research project is to identify key molecular and transcriptional pathways that contribute to the maturation of dentate gyrus granule cells. We performed single-cell RNA sequencing and multiomic single-nuclei RNA and ATAC sequencing in an activity-dependent mouse reporter model to examine the influence of neuronal activity on the transcriptome and chromatin accessibility within individual granule cells. These experiments were performed between postnatal day 14 and postnatal day 24 due to the increased abundance of developing granule cells. We implemented an environmental enrichment paradigm where mice were reared in complex, dynamic, and socially-enriched housing. This paradigm allowed us to examine the impact of chronically increased circuit activity on granule cell maturation. This study reveals novel heterogeneity in the maturing granule cell population that is associated with previous neuronal activity and synaptic function. A follow-up investigation identifies new transcription factor candidates that appear to orchestrate the transition between maturity stages. We propose a new model where granule cell identity is established through an activity-independent transcriptional network. The subsequent experience of neuronal activity appears to drive the emergence of a distinct transcriptional network that is poised to facilitate long-lasting granule cell maturity.
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Therapeutic hydrogel for wound healing applicationsManaging chronic wounds is a complex challenge, often aggravated by the presence of inflammation and infection. Hydrogel materials stand out for their remarkable properties such as biocompatibility and drug-loading capabilities, making them ideal for applications in wound dressing and tissue regeneration. A compelling treatment strategy involves not only resolving persistent hyperinflammation but also effectively eliminating infection. The demand for an "all-in-one" hydrogel platform with dual functions, targeting both inflammation and infection in chronic wounds, is huge in clinical settings. This thesis presents two promising dual-functional hydrogel platforms specifically crafted for potent topical application in the treatment of wounds. First platform was named "pull and push" hydrogel, which is essentially micro-sized hydrogel functionalized with innovative and versatile telodendrimers (TDs). By rational design and synthesis, these conjugated TDs can strongly grab or trap inflammatory factors such as cytokines and endotoxins, as well as hold drug payload such as antibiotics and release out in a desired manner. We demonstrated the TD hydrogel's capability to scavenge proinflammatory cytokines using in vitro assays, and shown the TD hydrogel's effect in scavenging cytokines in a mouse model with skin inflammation. We also demonstrated TD hydrogel's structure dependent capabilities in encapsulating different antibiotics, and sustainable release profile. The drug maintained its efficacy with prolonged therapeutic window and reduced toxicity, as evidenced by in vitro assays and in vivo animal skin and soft tissue infection model. Second hydrogel platform was termed "kill and block", which is essentially a bulky photo-crosslinked hydrogel incorporated with telodendrimer nano-formulated antibiotics. Nanodrug released from topically applied bulky photogel can further dissociate into drug and nanocarrier telodendrimer. The released drug functions as antimicrobial to "kill" bacteria. Dead bacteria still potentially stimulate inflammation. The payload-free nanocarrier can simultaneously modulate local immune response by "blocking" inflammatory pathway. In addition, this platform address issues of wound morphology adaptiveness. We demonstrated the tunable drug release profiles, reserved drug efficacy after TD encapsulation and phtogel incorporation, and superior anti-inflammation efficacy in vitro and in vivo. Collectively, we organically combined the advantages of nanotechnology and hydrogel platform, providing promising solutions for the chronic wound treatment from immune modulation and drug delivery.
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Exploring the roles of the connecting cilium in photoreceptor healthDefects in proteins functioning at the photoreceptor connecting cilium/transition zone (CC/TZ) have been linked to retinal degenerative disorders such as retinitis pigmentosa (RP) and cone-rod dystrophy (CRD). Mutations in eyes shut homolog (EYS, RP25), a secreted ciliary protein with laminin globular (LG) domains, have been linked to RP and CRD. Previously, some LG domains have been shown to interact with O-mannosyl glycans of α-dystroglycan (α-DG). Additionally, mutations in pomgnt1, an enzyme that plays a critical role in the synthesis of these glycans, have also been linked to RP (RP76). At the CC/TZ, the tectonic protein complex functions to maintain the unique biochemical environments of the inner segments (IS) and outer segments (OS) of photoreceptors. Mutations in tectonic complex proteins have been linked to ciliopathies that often include ocular abnormalities. The pathogenic mechanism underlying these mutations are poorly understood; thus, we hypothesized that EYS is an extracellular ciliary protein that interacts with α-DG and the tectonic complex. This project investigated the role of EYS, TMEM216, a member of the tectonic complex, and O-mannosyl glycans of α-DG in photoreceptor health. We determined that the C-terminal LG domains of EYS interacted with the O-mannosyl glycan epitope of α-DG. In pomgnt1 zebrafish mutants, EYS-glycan binding was reduced, and the secretion of EYS to the CC/TZ was significantly disrupted. Furthermore, in the pomgnt1 mutant retina, a substantial accumulation of EYS protein was observed in the soma of photoreceptors. Interestingly, deletion of pomgnt1 resulted in a pattern of photoreceptor degeneration similar to that previously observed in eys zebrafish mutants. By contrast, deletion of TMEM216 did not disrupt localization of EYS or of other tectonic complex proteins, yet photoreceptor degeneration was still observed in these animals. Our study has identified a previously unknown interaction between the LG domain-containing EYS and O-mannosyl glycans. These findings provide novel insight into the functional role of EYS around the CC/TZ and suggest the importance of O-mannosyl glycosylation in the regulation of protein secretion. Furthermore, our results suggest a mechanistic link between the disruption of glycosylation and photoreceptor degeneration, providing a new perspective on the underlying mechanisms behind RP25 and RP76.
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IPSC-derived neurons as a model for studying the role of RELN in autismRELN is strongly associated with Autism Spectrum Disorder (ASD). Homozygous loss of the encoded protein REELIN is associated with severe neurodevelopmental phenotypes characterized by lissencephaly and cerebellar hypoplasia, yet the ASD linked variants are typically heterozygous and appear to require additional genetic risk to cause ASD. To functionally characterize a RELN variant in a patient with ASD, we used induced pluripotent stem cells (iPSCs) from a family of non-autistic parents and their son who had ASD (the proband). The proband has a maternally-inherited missense variant (R2457C) in the RXR motif of the REELIN protein. We differentiated the iPSCs into two types of neurons, inhibitory neurons which model the inhibitory forebrain neurons that secrete REELIN, and excitatory neurons which model the cortical pyramidal neurons that respond to REELIN. Immunoblotting revealed that the proband inhibitory neurons had a lower ratio of extracellular/intracellular REELIN compared to that of the parental neurons, suggesting a decreased REELIN secretion. Sholl analysis on the proband excitatory neurons showed reduced dendritic complexity and reduced total length compared to the parental neurons. REELIN treatment increased the dendritic length and complexity in proband neurons up to the level of parental neurons. CRISPR/Cas9-mediated RELN KO did not change the dendritic phenotype in the excitatory neurons, ruling out a cell autonomous role for REELIN in these neurons. The proband excitatory neurons also had lower mRNA expression of WNT target genes in response to WNT3a, suggesting an underactive WNT signaling, as well as higher total GSK3β protein and lower phosphorylation at the inhibitory S9 site, indicating an overactive GSK3β signaling. Inhibition of GSK3β improved the proband neurons dendritic complexity in the proximal parts of the dendritic arbor. However, inhibition of mTOR signaling, which has shown to regulate REELIN signaling, did not change the dendritic morphology. In conclusion, the pathophysiology of ASD in the proband likely consists of a reduced REELIN secretion from the inhibitory neurons and an additional vulnerability in the REELIN-responding excitatory neurons, the latter likely being an overactive GSK3β and an underactive WNT signaling, all of which result in reduced dendritic complexity.
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Monomeric DENV-reactive IgA contributes protective and non-pathologic functions during DENV infectionDengue, caused by the 4 serotypes of dengue viruses (DENVs), is a tropical and subtropical vector-borne febrile illness which causes a significant global disease burden. A particular immunological feature contributing to severe disease is antibody-dependent enhancement (ADE), in which IgG isotype antibodies raised during a primary DENV infection opsonize and enhance the infectivity of DENVs during a secondary heterotypic infection. We and colleagues have described a monomeric serum IgA response during dengue infection. Here, we report on the functional characteristics of monomeric IgA in DENV infection. We show that isotype conversion of IgG to IgA preserves neutralization capacity while abrogating enhancing capacity. We show that DENV-specific IgA competitively antagonizes both IgG-mediated infection and downstream secretion of pro-inflammatory cytokines. This effect is largely attributable to the lower avidity of IgA-DENV immune complexes for permissive cells compared to IgG-DENV complexes. These findings have implications for serodiagnosis, therapeutics, and assessing risk of severe disease.
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Finding Diamonds in the Rough: Uncovering Genetic Variants, Transcripts, and Biological Processes Associated with Resilience to Alzheimer's DiseaseLate-onset Alzheimer's disease (LOAD) is a multifactorial disease with a strong genetic component. The growing understanding of the genetic basis and molecular mechanisms underlying LOAD risk presents an opportunity to uncover the factors that counter the risk and protect individuals from developing LOAD. The phenomenon wherein individuals demonstrate adaptability to the burden of disease risk can be referred to as "resilience". In this dissertation, I presented three studies that focused on the resilience to LOAD. Because resilience depends on and interacts with risk, we employed a risk-informed strategy to uncover resilience factors. This approach leveraged the current best-estimated LOAD risk to identify resilient individuals who, despite facing the highest LOAD risk, exhibit no dementia symptoms in old age. In Chapter 1, we demonstrated that a large number of risk-independent common genetic variants could reduce the penetrance of heightened genetic risk burden in LOAD. This study provided insights into the genetic architecture of resilience to LOAD, addressing a significant knowledge gap that requires attention. In addition, this study yielded a polygenic resilience score, enabling the assessment of the relative genetic resilience levels among individuals. In Chapters 2 and 3, we explored resilience to LOAD at the transcriptomic level. The study in Chapter 2 meta-analyzed all publicly available blood and brain transcriptomic studies of AD. This study laid the groundwork for investigating the resilience-conferring genes and pathways by establishing the best-estimated transcriptomic risk features in LOAD. In Chapter 3, we capitalized on the transcriptomic risk defined in Chapter 2 and examined the risk-residual genes that might confer resilience to increased transcriptomic risk of LOAD. This study implicated a couple of interesting pathways in resilience to LOAD and suggested that resilience and risk may operate in the same biological pathways. Taken together, our findings corroborated the idea that resilience in LOAD has a polygenic basis and highlighted the need to gain a deeper understanding of the genetic components, biological mechanisms, and phenotypic characteristics of resilience to LOAD risk. The dissertation contextualized these findings with the existing literature and suggested potential future directions to help further address the gaps in understanding resilience in LOAD.
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Effort-based decision making and psychopathology in children and adultsThe Research Domain Criteria (RDoC) initiative was introduced by the National Institute of Mental Health as a new research framework aimed at addressing longstanding pitfalls within the field of psychiatric research. This framework focuses on the study of fundamental units of human psychological behavior across multiple levels of information to inform our understanding of psychopathology. These units are categorized into larger domains of similar function, such as the Positive Valence Systems domain, which encompasses aspects of human reward-related behavior. This dissertation centers on the 'effort' component of human reward behavior, defined as the moderating effect of the perceived costs of physical or cognitive requirements on the valuation of a reinforcer. Three studies are presented from a program of research spanning five years on the study of 'effort' utilizing the RDoC research framework from both a behavior and genetics perspective. The first study (Chapter 2) is an exploratory study with the first application of RDoC to the study of 'effort' in relation to psychopathology in children and adults. It finds that behavioral measures of 'effort' in children and adults were associated with specific types of psychopathologies and with differing profiles between sexes. The second study (Chapter 3) assesses the cross-generational stability, divergent validity, and replicability of 'effort' and its associations with psychopathology in children and adults. It finds that 'effort' has divergent validity from other RDoC constructs of reward behavior, and that the specific associations with psychopathology initially observed in the first study were replicated in a larger population. It also finds that 'effort' does not display cross-generational stability between children and their parents. The third study (Chapter 4) examined the genetic contributions to 'effort', and the moderating effect of 'effort genes' on psychopathology. It found that genetic loci on three different chromosomes had genome-wide significant associations with quantitative measures of 'effort', and that polygenic risk scores generated from these measures were significant predictors of parent-reported levels of psychopathology in children. Together, this program of research provides the first comprehensive application of RDoC to the study of effort-based behavior and psychopathology in children and adults and has important implications for the advancement of the RDoC framework and future research in this area.
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Neurotransmitter-mediated calcium signaling in apical dendrite initiation of cortical projection neurons and proposal for the role of Cajal-Retzius neuronsThis thesis investigates the developmental processes in the mouse cortex during embryonic days 13 to 15, corresponding to human gestational weeks 8 to 11. The primary focus is on the calcium signaling pathways in neurons, particularly as they transition from the migratory phase to the dendrite initiation and growth phase. The study places special emphasis on Cajal-Retzius neurons (CRNs), a transient population of excitatory neurons in the developing cortex. These neurons are known for their secretion of Reelin, a glycoprotein that has a role in regulating the position of glutamatergic neurons of the cortex. While the role of Reelin and its downstream effects on cortical organization have been well-documented, this work investigates a previously unexplored transient circuit between CRNs and cortical projection neurons (CPNs). The central questions addressed in this thesis include: What is the calcium signal as neurons transition from the migratory phase to dendrite initiation and growth? Is the signal important for CPN maturation and dendrite growth? How does the activity and neurotransmitter release by CRNs serve as a mechanistic substrate that informs and coordinates CPN development during the foundational phases of cortical development? What neurotransmitter systems are involved and how are they functioning? Our research employs a multidisciplinary approach, leveraging whole embryonic hemisphere explants and multiphoton microscopy to study the calcium signaling profiles of CRNs and CPNs. The findings reveal that CRNs not only secrete Reelin but also exhibit spontaneous activity and the potential for neurotransmitter release, specifically glutamate. This activity significantly influences intracellular calcium levels in CPNs, thereby affecting their dendritic growth and migration patterns. This work opens up a new avenue for understanding early cortical development by offering a novel framework that extends beyond the established role of CRNs and Reelin secretion. It provides compelling evidence that CRNs play a more multifaceted role in cortical development than previously thought, serving in a transient circuit that informs and coordinates CPN development. This thesis, therefore, not only fills a gap in our understanding of early cortical development but also sets the stage for future research into the pathophysiology of neurodevelopmental disorders.
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Bulged G-quadruplexes in the human genome: identification and characterization of a novel type of non-canonical G-quadruplexG-quadruplexes (G4s) are secondary nucleic acid structures that are abundant in the human genome and have been linked to numerous physiological and pathological conditions. The underlying DNA sequence is a major determinant of the topology and stability of folded G4s. G4s containing bulges are a subpopulation of G4-like structures, whose genome-wide localization and functions are still unknown. Our study focuses on addressing this gap. We utilized a data-driven approach to establish models for the computational genome-wide prediction of potential sites of bulge containing G4 formation (pG4-BS). We also showed that the majority of human protein coding genes contain these pG4-BS, especially in their promoters and exon-intron junctions, suggesting roles in transcription and splicing processes. Furthermore, we validated our computational models using both thermodynamic assays and datasets derived from high-throughput technologies. We also showed that bulged G4s and R-loops, another type of secondary nucleic acid structure, show strong association with each other, hinting at functional interplay between these structures.
