Browsing by Subject "Cellular biology"
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Item Open Access A Central Role for Hypoxia-inducible Transcription Factor Signaling in the Regulation of Skeletal Lineage Cells(2022) Guo, WendiOsteoporosis and low bone density affect an estimated 54 million adults of 50 years and over in the United States, resulting in $19 billion in costs for osteoporosis-related bone breaks. Current treatments include the use of antiresorptive and anabolic drugs to decrease the rate of bone resorption and increase the rate of bone formation, respectively. However, these current treatments are unable to completely normalize skeletal integrity. As bone diseases become increasingly prevalent, there is an urgent need to identify novel therapies to improve quality of life and reduce economic burden on the healthcare system.
To identify novel therapeutic targets, we must first begin to understand the cellular complexity of the bone marrow niche and how cellular function is regulated within the bone tissue. Bone-resident cells, such as skeletal progenitors and their descendants, are critically influenced by extrinsic signals derived from the local microenvironment. Previous studies have identified hypoxia as a key microenvironment factor in bone. Thus, the ability to target the hypoxic bone marrow niche presents an attractive and untapped potential for regenerative medicine.
Much of the work investigating the role of hypoxia and HIF signaling have focused on mature osteoblast and chondrocyte populations. In contrast, studies investigating the contribution of HIF signaling on skeletal progenitors and marrow adipocyte populations are scarce. In this dissertation, I investigate the role of hypoxia and HIF signaling in skeletal lineage cells, chiefly skeletal progenitor cells and marrow adipogenic lineage cells. Using cellular, genetic, and pharmacological-based approaches, I characterize the roles of HIF-1α and HIF-2α in both homeostatic and pathological contexts in the aforementioned cell populations.
First, I propose an optimized cell-based system to investigate the function of skeletal progenitors in vitro. Here, I highlight the limitations of current in vitro isolation techniques and introduce a relatively simple method of bone marrow stromal cell purification using hypoxia. Using this system, I assess how skeletal progenitors respond to hypoxic cues and interrogate skeletal progenitor cell differentiation and functional responses in my subsequent research. Next, using genetic and pharmacological approaches, I investigate the role of HIF-2α in bone formation following radiation-injury where I identify HIF-2α as a negative regulator of bone recovery. Additionally, with the assistance of my collaborators, I develop and characterize a bone-targeting nanocarrier to ameliorate radiation-induced bone loss. Lastly, I detail early work I conducted to investigate the role of HIF signaling in marrow adipogenic lineage cells. Here, I establish and characterize animal models to determine how hypoxia and HIF signaling influences adipogenic lineage commitment and expansion in an early and mature marrow adipogenic population.
In summary, this dissertation aims to expand our limited understanding on how the hypoxic bone microenvironment and HIF signaling regulate skeletal lineage cells in vivo, with a special focus on skeletal progenitor and marrow adipogenic populations. In terms of boarder impacts, understanding the signaling networks that regulate bone homeostasis and recovery processes will not only expand our basic understanding of the molecular mechanisms underlying skeletal development, but also provide novel insights for developing therapies to treat bone loss.
Item Open Access A Genome-Wide RNAi Screen Identifies CDC-42 and GDI-1 as In Vivo Regulators of Invadopodia(2015) Lohmer, Lauren Renee LilleyBasement membrane (BM) is a sheet-like extracellular matrix that underlies most tissues and acts as a barrier to invading cells. Many cell types, including immune cells, cells migrating during development and morphogenesis, and metastatic cancer cells utilize F-actin-based structures called invadopodia to breach BM as they leave one tissue to enter another. Despite extensive study and interest in understanding invasion for its clinical importance, the molecular mechanisms regulating invadopodia and BM breach in vivo remain unclear. During uterine-vulval attachment in C. elegans, the specialized uterine anchor cell (AC) uses invadopodia to mediate breach of the underlying BM in order to contact the underlying vulval epithelium. The AC offers several advantages as a model, including experimental, visual, and genetic tractability, the presence of endogenous extracellular environment, and availability of the tissue targeted for invasion. In Chapter 2, I describe development of a novel technique for spatiotemporal-specific knockdown of proteins that will facilitate investigation of proteins, particularly those that are essential or required in other tissues, in the regulation of invadopodia and AC invasion. Using a sensitized genome-wide RNAi screen, classical genetics, and timelapse imaging of invadopodia at the AC-BM interface, Chapter 3 presents two in vivo invadopodia regulators that function by distinct mechanisms. This is the first in vivo evidence that the RhoGTPase CDC-42 regulates invadopodia formation through WSP-1. RabGTPase GDI-1 is a novel regulator of the unique membrane compartment required for invadopodia formation. CDC-42 and GDI-1 both function downstream of an unknown cue secreted by the cells targeted by the AC for invasion, illustrating that extracellular cues can play key roles in mediating cell invasion. The characterization of CDC-42 and GDI-1 as in vivo regulators of invadopodia is an important first step to understanding the mechanisms of this critical cellular process and we expect the AC will be an excellent model for future identification of novel regulators of BM breach.
Item Open Access A Genomic and Structural Study of FtsZ Function for Bacterial Cell Division(2013) Gardner, Kiani Anela Jeniah ArkusThe tubulin homolog FtsZ provides the cytoskeletal framework for bacterial cell division. FtsZ is an essential protein for bacterial cell division, and is the only protein necessary for Z-ring assembly and constriction force generation in liposomes in vitro. The work presented here utilizes structural and genomic analysis methods to investigate FtsZ function for cell division with three separate questions: (1) What is the function of the C-terminal linker peptide in FtsZ? (2) Are there interacting proteins other than those of the divisome that facilitate FtsZ function? (3) Do lateral contact sites exist between protofilaments in the Z ring, resulting in an organized Z-ring substructure?
The FtsZ protein has an ~50 aa linker between the protofilament-forming globular domain and the C-terminal (Ct) membrane-tethering peptide. This Ct linker is widely divergent across bacterial species, and has been thought to be an intrinsically disordered peptide (IDP). We have made chimeras where we have swapped the Escherichia coli IDP for Ct linkers from other bacteria, and even for an unrelated IDP from human &alpha-adducin. Most of these substitutions allowed for normal cell division, suggesting that sequence of the IDP did not matter -any IDP appears to work (with some exceptions). Length, however, was important: IDPs shorter than 39 or longer than 89 aa's had compromised function. We conclude that the Ct linker of FtsZ functions as a flexible tether between the globular domain of FtsZ in the protofilament, and its attachment to FtsA and ZipA at the membrane. As a worm-like-chain, the Ct linker will function as a stiff entropic spring linking the constricting protofilaments to the membrane.
Previous work from our laboratory found that mutant and foreign FtsZ that do not normally function for cell division can function upon acquisition of a second site suppressor mutation, somewhere in the E. coli genome. We expect that some mutant or foreign FtsZ are partially functional for division in E. coli. As such, these FtsZ require another mutation that further enables their function. These suppressing mutations may reveal proteins interacting with FtsZ and the divisome, that have previously been unknown. In the present study, we have identified, via whole genome re-sequencing, single nucleotide polymorphisms that allow 11 different foreign and mutant FtsZ proteins to function for cell division. While we see a trend toward mutations in genes related to general metabolism functions in the cell, we have also identified mutations in two genes, ispA and nlpI, that may be interacting more directly with the cell division mechanism.
Finally, we have devised a screen to identify mutations in FtsZ that may be involved in lateral bonding between protofilaments. There are presently two proposed models of FtsZ substructure: the scattered or the ribbon model. A major difference between these models is that the scattered model proposed no interaction between adjacent protofilaments in the Z ring, while the ribbon model suggests that adjacent protofilaments are bonded laterally to create an organized substructure of aligned protofilaments. Our screen was designed to identify complementary surface-exposed residues that may be involved in lateral bonding. We initially identified two lateral contact candidate residues: R174, and E250 and mutated them to abrogate FtsZ function. We also mutated L272, which is known to make contacts across the protofilament interface, to look for compensating mutations in these contact residues. Using the screen, we identified a number of secondary mutations in FtsZ that can complement these initial loss-of-function mutations. While this screen has not yielded strong candidates for lateral bonding partners, it has emerged as a high-throughput method for screening large libraries of mutant FtsZ proteins in order to identify compensating mutation pairs.
Item Open Access A mitotic DNA damage response requiring FANCD2 enables mitosis with broken DNA(2017) Bretscher, HeidiIn order to maintain genome integrity cells employ a set of well conserved DNA damage checkpoints. DNA damage checkpoints are active during interphase and serve to prevent mitosis with broken DNA. Mitosis with broken DNA is associated with DNA segregation errors, genome instability and even cell death in resulting daughter cells. It has recently has been appreciated that cells can compensate for damaged DNA during mitosis. However, little is known about this mitotic DNA damage response.
In this work, I have utilized a genetically tractable system to study mitotic DNA damage responses in Drosophila. During development, Drosophila rectal papillar cells undergo developmentally programmed inactivation of DNA damage responses. Following inactivation, papillar cells undergo two rounds of mitosis. We find that papillar cells fail to undergo cell death or high-fidelity DNA repair prior to mitosis and instead enter mitosis with DNA double stranded breaks (DSBs). Remarkably, papillar cells segregate acentric DNA fragments into daughter cells during mitosis resulting in viable daughter cells, normal organ development and function. Proper segregation and organ formation is dependent on the FANCONI Anemia gene FANCD2. Loss of FANCD2 results in unaligned acentric fragments and mis-segregation of broken DNA resulting acentric micronuclei formation. Mis-segregation of acentric DNA results in cell death and failure to form a developmentally normal and functional organ. Thus, we have uncovered a role for FANCD2 in mitotic DNA damage responses.
Additionally, we find that single-stranded DNA (ssDNA) is present during papillar cell mitosis following DNA DSB induction. ssDNA is present on both the edge of segregating and lagging DNA as well as spanning short regions between fragments of lagging DNA. The observation that ssDNA is present suggests that while papillar cells do not initiate complete repair, some level of DNA resection must occur following DNA DSB induction. In line with this reasoning, we find a role for the DNA damage sensor complex, the MRN complex, in papillar cell survival following I-Cre induction. The MRN complex consists of three components, Mre11, Rad50 and NBS1. Loss of Mre11 or NBS1 results in reduced papillar cell survival following I-Cre induction. Furthermore, Mre11 is a nuclease. Thus, we propose that MRE11 acts at sites of DNA DSBs in papillar cells to create ssDNA. We hypothesize that formation of ssDNA is sufficient to form a DNA/protein bridge between segregating and lagging DNA to enable proper DNA segregation. Interestingly, resistance to DNA damage is also observed in many cancers. We speculate that such DNA damage resistant cancer cells may utilize similar mechanisms to compensate for DNA breaks during mitosis.
Item Open Access A Role for Cytoplasmic 3'-Nucleotide Hydrolysis in Liver and Intestine Function(2012) Hudson, BenjaminBisphosphate 3'-nucleotidase (Bpnt1) is a member of a family of small molecule phosphatases whose activities depend on divalent cations and are inhibited by lithium. While the enzymes share many commonalities, they have distinct and non-overlapping substrate pools. Of the seven mammalian members, two enzymes, gPAPP and Bpnt1, hydrolyze the same small molecule 3'-phosphoadenosine 5'-phosphate (PAP) but act in separate subcellular compartments, the Golgi apparatus and cytoplasm respectively. Hydrolysis of PAP, which is a metabolite of the inorganic sulfate incorporation pathway, is highly conserved throughout evolution from bacteria to yeast to humans. Evidence in multiple species has shown that inhibiting PAP hydrolysis leads to cellular toxicity as a result of its accumulation and also that these effects can be ameliorated by modulating the rate of its production. However, despite the abundant evidence of its importance
from studies in lower eukaryotes, the role of the cytoplasmic PAP phosphatase, Bpnt1, in more complicated mammalian physiological remains poorly understood. Here we report for the first time the generation and characterization of mice deficient for Bpnt1. Bpnt1 null mice do not exhibit skeletal defects, but instead develop severe liver
pathologies and deficiencies in intestinal iron absorption. Loss of Bpnt1 leads to tissue-specific elevations of the substrate PAP. To test the hypothesis that a toxic cellular accumulation of PAP accounts for the observed phenotypes, we generated a double mutant mouse that concomitantly down regulates bisphosphorylated nucleotide synthesis in the context of Bpnt1 deficiency. Remarkably, double mutants do not display any detectable physiological defects seen in Bpnt1 null mice. In addition, we have identified and characterized a novel substrate of 3'nucleotidases, 3'-phosphoadenosine 5'-diphosphate (PAPP) that co-accumulates with PAPS and PAP and might play a role in mediating certain aspects of the physiological defects of Bpnt1 null mice. Overall, our study defines a role for Bpnt1 in mammalian physiology and provides mechanistic insights into the importance of cytoplasmic 3'-
nucleotide hydrolysis to normal cellular function.
Item Open Access A Role for Gic1 and Gic2 in Promoting Cdc42 Polarization(2018) Daniels, Christine NicoleThe Rho GTPase Cdc42 is a master regulator of cell polarity that orchestrates reorganization of the cytoskeleton. During polarity establishment, active GTP-Cdc42 accumulates at a part of the cell cortex that becomes the front of the cell. Localized GTP-Cdc42 orients the cytoskeleton through a set of “effector” proteins that bind specifically to GTP-Cdc42 and not GDP-Cdc42. A family of Cdc42 effectors, called GICs in yeast and BORGs in mammals, have been implicated in regulation of both the actin cytoskeleton and the septin cytoskeleton. Yeast cells lacking both Gic1 and Gic2 are able to polarize and grow at low temperatures, but many mutant cells fail to polarize the cytoskeleton at high temperature. This led to the conclusion that GICs communicate between Cdc42 and different cytoskeletal elements.
To better characterize the role of GIC proteins in yeast, we utilized time-lapse fluorescent microscopy to examine morphogenetic events in living single cells. Surprisingly, we found that not only the cytoskeleton but also Cdc42 itself failed to polarize in many gic1 gic2 mutant cells at high temperature. This observation indicates that GICs may act upstream of polarization rather than downstream.
Polarization of Cdc42 is triggered by cell-cycle progression, and in particular by G1 Cyclin-dependent kinase (CDK) activity. Using a live-cell reporter for G1 CDK activation, we found that cells lacking GICs were not defective in CDK activation, but showed a specific defect in polarization downstream of the CDK. Previous work had implicated the scaffold protein Bem1 in a positive feedback loop important for polarization. Cells lacking GICs failed to polarize Bem1 as well as Cdc42 at high temperature. Future work will be directed at understanding how GICs contribute to polarity establishment. Because many of the mechanisms and proteins involved in polarization are highly conserved, we anticipate our findings will help inform how this process regulated in higher eukaryotes.
Item Open Access A Systems-Level Analysis of an Epithelial to Mesenchymal Transition(2012) Saunders, Lindsay RoseEmbryonic development occurs with precisely timed morphogenetic cell movements directed by complex gene regulation. In this orchestrated series of events, some epithelial cells undergo extensive changes to become free moving mesenchymal cells. The transformation resulting in an epithelial cell becoming mesenchymal is called an epithelial to mesenchymal transition (EMT), a dramatic cell biological change that occurs throughout development, tissue repair, and disease. Extensive in vitro research has identified many EMT regulators. However, most in vitro studies often reduce the complicated phenotypic change to a binary choice between successful and failed EMT. Research utilizing models has generally been limited to a single aspect of EMT without considering the total transformation. Fully understanding EMT requires experiments that perturb the system via multiple channels and observe several individual components from the series of cellular changes, which together make a successful EMT.
In this study, we have taken a novel approach to understand how the sea urchin embryo coordinates an EMT. We use systems level methods to describe the dynamics of EMT by directly observing phenotypic changes created by shifting transcriptional network states over the course of primary mesenchyme cell (PMC) ingression, a classic example of developmental EMT. We systematically knocked down each transcription factor in the sea urchin's PMC gene regulatory network (GRN). In the first assay, one fluorescently labeled knockdown PMC precursor was transplanted onto an unperturbed host embryo and we observed the resulting phenotype in vivo from before ingression until two hours post ingression using time-lapse fluorescent microscopy. Movies were projected for computational analyses of several phenotypic changes relevant to EMT: apical constriction, apical basal polarity, motility, and de-adhesion.
A separate assay scored each transcription factor for its requirement in basement membrane invasion during EMT. Again, each transcription factor was knocked down one by one and embryos were immuno-stained for laminin, a major component of basement membrane, and scored on the presence or absence of a laminin hole at the presumptive entry site of ingression.
The measured results of both assays were subjected to rigorous unsupervised data analyses: principal component analysis, emergent self-organizing map data mining, and hierarchical clustering. This analytical approach objectively compared the various phenotypes that resulted from each knockdown. In most cases, perturbation of any one transcription factor resulted in a unique phenotype that shared characteristics with its upstream regulators and downstream targets. For example, Erg is a known regulator of both Hex and FoxN2/3 and all three shared a motility phenotype; additionally, Hex and Erg both regulated apical constriction but Hex additionally affected invasion and FoxN2/3 was the lone regulator of cell polarity. Measured phenotypic changes in conjunction with known GRN relationships were used to construct five unique subcircuits of the GRN that described how dynamic regulatory network states control five individual components of EMT: apical constriction, apical basal polarity, motility, de-adhesion, and invasion. The five subcircuits were built on top of the GRN and integrated existing fate specification control with the morphogenetic EMT control.
Early in the EMT study, we discovered one PMC gene, Erg, was alternatively spliced. We identified 22 splice variants of Erg that are expressed during ingression. Our Erg knockdown targeted the 5'UTR, present in all spliceoforms; therefore, the knockdown uniformly perturbed all native Erg transcripts (∑Erg). Specific function was demonstrated for the two most abundant spliceoforms, Erg-0 and Erg-4, by knockdown of ∑Erg and mRNA rescue with a single spliceoform; the mRNA expression constructs contained no 5'UTR and were not affected by the knockdown. Different molecular phenotypes were observed, and both spliceoforms targeted Tbr, Tel, and FoxO, only Erg-0 targeted FoxN2/3 and only Erg-4 targeted Hex. Neither targeted Tgif, which was regulated by ∑Erg knockdown sans rescue. Our results suggest the embryo employs a minimum of three unique roles in the GRN for alternative splicing of Erg.
Overall, these experiments increase the completeness and descriptive power of the GRN with two additional levels of complexity. We uncovered five sub-circuits of EMT control, which integrated into the GRN provide a novel view of how a complex morphogenetic movement is controlled by the embryo. We also described a new functional role for alternative splicing in the GRN where the transcriptional targets for two splice variants of Erg are unique subsets of the total set of ∑Erg targets.
Item Open Access A Three-Molecule Model of Structural Plasticity: the Role of the Rho family GTPases in Local Biochemical Computation in Dendrites(2015) Hedrick, Nathan GrayIt has long been appreciated that the process of learning might invoke a physical change in the brain, establishing a lasting trace of experience. Recent evidence has revealed that this change manifests, at least in part, by the formation of new connections between neurons, as well as the modification of preexisting ones. This so-called structural plasticity of neural circuits – their ability to physically change in response to experience – has remained fixed as a primary point of focus in the field of neuroscience.
A large portion of this effort has been directed towards the study of dendritic spines, small protrusions emanating from neuronal dendrites that constitute the majority of recipient sites of excitatory neuronal connections. The unique, mushroom-like morphology of these tiny structures has earned them considerable attention, with even the earliest observers suggesting that their unique shape affords important functional advantages that would not be possible if synapses were to directly contact dendrites. Importantly, dendritic spines can be formed, eliminated, or structurally modified in response to both neural activity as well as learning, suggesting that their organization reflects the experience of the neural network. As such, elucidating how these structures undergo such rearrangements is of critical importance to understanding both learning and memory.
As dendritic spines are principally composed of the cytoskeletal protein actin, their formation, elimination, and modification requires biochemical signaling networks that can remodel the actin cytoskeleton. As a result, significant effort has been placed into identifying and characterizing such signaling networks and how they are controlled during synaptic activity and learning. Such efforts have highlighted Rho family GTPases – binary signaling proteins central in controlling the dynamics of the actin cytoskeleton – as attractive targets for understanding how the structural modification of spines might be controlled by synaptic activity. While much has been revealed regarding the importance of the Rho GTPases for these processes, the specific spatial and temporal features of their signals that impart such structural changes remains unclear.
The central hypotheses of the following research dissertation are as follows: first, that synaptic activity rapidly initiates Rho GTPase signaling within single dendritic spines, serving as the core mechanism of dendritic spine structural plasticity. Next, that each of the Rho GTPases subsequently expresses a spatially distinct pattern of activation, with some signals remaining highly localized, and some becoming diffuse across a region of the nearby dendrite. The diffusive signals modify the plasticity induction threshold of nearby dendritic spines, and the spatially restricted signals serve to keep the expression of plasticity specific to those spines that receive synaptic input. This combination of differentially spatially regulated signals thus equips the neuronal dendrite with the ability to perform local biochemical computations, potentially establishing an organizational preference for the arrangement of dendritic spines along a dendrite. Finally, the consequences of the differential signal patterns also help to explain several seemingly disparate properties of one of the primary upstream activators of these proteins: brain-derived neurotrophic factor (BDNF).
The first section of this dissertation describes the characterization of the activity patterns of one of the Rho family GTPases, Rac1. Using a novel Förster Resonance Energy Transfer (FRET)- based biosensor in combination with two-photon fluorescence lifetime imaging (2pFLIM) and single-spine stimulation by two-photon glutamate uncaging, the activation profile and kinetics of Rac1 during synaptic stimulation were characterized. These experiments revealed that Rac1 conveys signals to both activated spines as well as nearby, unstimulated spines that are in close proximity to the target spine. Despite the diffusion of this structural signal, however, the structural modification associated with synaptic stimulation remained restricted to the stimulated spine. Thus, Rac1 activation is not sufficient to enlarge spines, but nonetheless likely confers some heretofore-unknown function to nearby synapses.
The next set of experiments set out to detail the upstream molecular mechanisms controlling Rac1 activation. First, it was found that Rac1 activation during sLTP depends on calcium through NMDA receptors and subsequent activation of CaMKII, suggesting that Rac1 activation in this context agrees with substantial evidence linking NMDAR-CaMKII signaling to LTP in the hippocampus. Next, in light of recent evidence linking structural plasticity to another potential upstream signaling complex, BDNF-TrkB, we explored the possibility that BDNF-TrkB signaling functioned in structural plasticity via Rac1 activation. To this end, we first explored the release kinetics of BDNF and the activation kinetics of TrkB using novel biosensors in conjunction with 2p glutamate uncaging. It was found that release of BDNF from single dendritic spines during sLTP induction activates TrkB on that same spine in an autocrine manner, and that this autocrine system was necessary for both sLTP and Rac1 activation. It was also found that BDNF-TrkB signaling controls the activity of another Rho GTPase, Cdc42, suggesting that this autocrine loop conveys both synapse-specific signals (through Cdc42) and heterosynaptic signals (through Rac1).
The next set of experiments detail one the potential consequences of heterosynaptic Rac1 signaling. The spread of Rac1 activity out of the stimulated spine was found to be necessary for lowering the plasticity threshold at nearby spines, a process known as synaptic crosstalk. This was also true for the Rho family GTPase, RhoA, which shows a similar diffusive activity pattern. Conversely, the activity of Cdc42, a Rho GTPase protein whose activity is highly restricted to stimulated spines, was required only for input-specific plasticity induction. Thus, the spreading of a subset of Rho GTPase signaling into nearby spines modifies the plasticity induction threshold of these spines, increasing the likelihood that synaptic activity at these sites will induce structural plasticity. Importantly, these data suggest that the autocrine BDNF-TrkB loop described above simultaneously exerts control over both homo- and heterosynaptic structural plasticity.
The final set of experiments reveals that the spreading of GTPase activity from stimulated spines helps to overcome the high activation thresholds of these proteins to facilitate nearby plasticity. Both Rac1 and RhoA, the activity of which spread into nearby spines, showed high activation thresholds, making weak stimuli incapable of activating them. Thus, signal spreading from a strongly stimulated spine can lower the plasticity threshold at nearby spines in part by supplementing the activation of high-threshold Rho GTPases at these sites. In contrast, the highly compartmentalized Rho GTPase Cdc42 showed a very low activation threshold, and thus did not require signal spreading to achieve high levels of activity to even a weak stimulus. As a result, synaptic crosstalk elicits cooperativity of nearby synaptic events by first priming a local region of the dendrite with several (but not all) of the factors required for structural plasticity, which then allows even weak inputs to achieve plasticity by means of localized Cdc42 activation.
Taken together, these data reveal a molecular pattern whereby BDNF-dependent structural plasticity can simultaneously maintain input-specificity while also relaying heterosynaptic signals along a local stretch of dendrite via coordination of differential spatial signaling profiles of the Rho GTPase proteins. The combination of this division of spatial signaling patterns and different activation thresholds reveals a unique heterosynaptic coincidence detection mechanism that allows for cooperative expression of structural plasticity when spines are close together, which in turn provides a putative mechanism for how neurons arrange structural modifications during learning.
Item Open Access Abl Family Kinases Regulate Endothelial Function(2013) Chislock, Elizabeth MarieThe vasculature has a crucial function in normal physiology, enabling the transport of oxygen and nutrients to cells throughout the body. In turn, endothelial cells, which form the inner-most lining of blood vessels, are key regulators of vascular function. In addition to forming a barrier which separates the circulation from underlying tissues, endothelial cells respond to diverse extracellular cues and produce a variety of biologically-active mediators in order to maintain vascular homeostasis. Disruption of normal vascular function is a prominent feature of a variety of pathological conditions. Thus, elucidating the signaling pathways regulating endothelial function is critical for understanding the role of endothelial cells in both normal physiology and pathology, as well as for potential development of therapeutic interventions.
In this dissertation, we use a combination of pharmacological inhibition and knockdown studies, along with generation of endothelial conditional knockout mice, to demonstrate an important role of the Abelson (Abl) family of non-receptor tyrosine kinases (Abl and Arg) in vascular function. Specifically, loss of endothelial expression of the Abl kinases leads to late-stage embryonic and perinatal lethality in conditional knockout mice, indicating a crucial requirement for Abl/Arg kinases in normal vascular development and function. Endothelial Abl/Arg-null embryos display focal regions of vascular loss and tissue damage, as well as increased endothelial cell apoptosis. An important pro-survival function for the Abl kinases is further supported by our finding that either microRNA-mediated Abl/Arg depletion or pharmacological inhibition of the Abl kinases increases endothelial cell susceptibility to stress-induced apoptosis in vitro. The Abl kinases are activated in response to treatment with the pro-angiogenic growth factors vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF). We show that both VEGF- and bFGF-mediated endothelial cell survival is impaired following Abl kinase inhibition.
These studies have uncovered a previously unappreciated role for the Abl kinases in the regulation of the angiopoietin/Tie2 signaling pathway, which functions to support endothelial cell survival and vascular stability. Loss of Abl/Arg expression leads to reduced mRNA and protein levels of the Tie2 receptor, resulting in impaired activation of intracellular signaling pathways by the Tie2 ligand angiopoietin-1 (Angpt1), as well as decreased Angpt1-mediated endothelial cell survival following serum-deprivation stress. Notably, we found that the Abl kinases are activated following Angpt1 stimulation, suggesting a unique dual role for Abl and Arg in Angpt/Tie2 signaling, potentially modulating Tie2 downstream signaling responses, as well as regulating Tie2 receptor expression.
Further, we show an important contribution of the Abl family kinases to the regulation of endothelial permeability responses both in vitro and in vivo. The Abl kinases are activated in response to a diverse group of permeability-inducing factors, including VEGF and the inflammatory mediators thrombin and histamine. We show that inhibition of Abl kinase activity, using either the ATP-competitive inhibitor imatinib or the allosteric inhibitor GNF-2, protects against disruption of endothelial barrier function by the permeability-inducing factors in vitro. VEGF-induced vascular permeability similarly is decreased in conditional knockout mice lacking endothelial Abl expression, as well as following treatment with Abl kinase inhibitors in vivo. Mechanistically, we show that loss of Abl kinase activity is accompanied by activation of the barrier-stabilizing GTPases (guanosine triphosphatases) Rac1 and Rap1, as well as inhibition of agonist-induced Ca2+ mobilization and generation of acto-myosin contractility.
Taken together, these results demonstrate involvement of the Abl family kinases in the regulation of endothelial cell responses to a broad range of pro-angiogenic and permeability-inducing factors, as well as a critical requirement for the endothelial Abl kinases in normal vascular development and function in vivo. These findings have implications for the clinical use of Abl kinase inhibitors.
Item Open Access Achieving Cell-Specific Delivery of Multiple Oligonucleotide Therapeutics with Aptamer Chimeras(2012) Kotula, Jonathan WCurrent standard cancer treatments such as chemotherapeutics, and radiation therapy are nearly as likely to kill the patient as cure the cancer. Therapies that have such a narrow window of efficacy are necessary for the treatment of aggressive diseases, but safer alternatives must be created. By discovering novel therapeutics that target specific disease processes within specific diseased cells, while leaving healthy cells unaltered, we can improve the lives of millions of cancer sufferers and their families. A therapeutic's window of efficacy can be measured by the therapeutic index. For many anti-cancer therapeutics, the therapeutic index is very small, the dose of treatment that kills cancer cells and shrinks tumors is nearly the dose that causes toxicity. In cancer patients, this toxicity causes many serious conditions such as gastrointestinal distress, organ damage, and death.
Recently, the model of cancer treatment has evolved from non-specific cytotoxic agents to more selective therapeutics that target cellular processes necessary for cancer cell survival. If a therapy can be targeted to selectively bind and internalize targeted cells, its toxicity would only impact the targeted cells and healthy cells in the immediate vicinity, which would greatly reduce the toxic effects on the rest of the body. Targeting cancer cells can be done through cancer biomarkers, which are cell surface proteins, expressed exclusively, or are much more abundant on the surface of cancer cells than on somatic cells.
Advances in antibody and aptamer technology have enabled researchers to design those molecules to bind specifically to cancer cells, and deliver drugs that alter specific cellular processes. An aptamer designed to bind PSMA, a prostate cancer biomarker, only bound to a specific subset of cancer cells, and delivered a therapeutic siRNA that prevented a specific survival process from occurring. While this technology is promising, it is currently limited to targeting small subsets of cancer types. To generate an aptamer therapeutic that would have greater utility and efficacy, I have examined the properties of a nucleolin aptamer-mediated delivery system that targets multiple types of cancer cells, and delivers various oligonucleotide therapeutics.
The nucleolin aptamer targeted cancer cells by binding to membrane–associated nucleolin. Nucleolin, a conserved protein found in all eukaryotes, shuttles from the nucleus, through the cytoplasm to the cell membrane. Cancer cells express a far greater amount of membrane–associated nucleolin than somatic cells, making nucleolin an ideal cancer biomarker. The shuttling, and oligonucleotide binding attributes of the protein enable it to deliver aptamer chimeras from the cell surface to the nucleus. Therefore the nucleolin aptamer has unique access to the nuclei of cancer cells, and can deliver therapeutic oligonucleotide cargoes through nucleolin binding.
The nucleolin aptamer delivered splice–switching oligonucleotides, a form of antisense technology, improving their efficacy, and potentially increasing their therapeutic viability. The ability to deliver antisense oligonucleotides to the nuclei of cancer cells has the potential for other therapeutic possibilities including the inhibition of transcription with antisense triplexes.
The nucleolin aptamer can also deliver therapeutic aptamers. The nucleolin aptamer–β–arrestin aptamer chimera prevented the stem cell renewal phenotype necessary for leukemia progression in human patient tissue samples. The ability to effectively deliver therapeutic aptamers may lead to clinical applications for many of the aptamers that have been selected against intracellular targets including transcriptional activators.
Oligonucleotide research continues to advance our understanding of potentially therapeutic oligonucleotides. Long non–coding RNAs for example, may impact epigenetics, and transcription. Additionally, locked nucleic acids have been developed to improve binding affinity, thus increasing the efficacy of antisense oligonucleotides. In order to bring these discoveries into the clinic, they must be safely and specifically delivered to their target cells.
This work demonstrated that the nucleolin aptamer could deliver oligonucleotide therapeutics to specific cancer cells. Nucleolin aptamer chimeras have the potential to develop into safe and effective cancer therapies, thus improving the treatment options for cancer sufferers.
Item Open Access Amino acid transporters regulate bone formation(2021) Shen, LeyaoBone development and homeostasis are governed by a number of developmental signals, transcription factors and cellular metabolism. This process is also dependent on the orchestration of multiple cell types including osteoblasts, chondrocytes, skeletal stem cells and osteoclasts. Osteoblasts are the principal bone forming cells responsible for producing and secreting the type I collagen rich extracellular bone matrix. Protein synthesis is an energetically and biosynthetically demanding process. This requires copious amounts of ATP and amino acids amongst other metabolites. However, the precise mechanisms and systems that osteoblasts utilize to meet these synthetic demands are poorly understood. Previous studies have shown amino acid consumption is increased in osteoblasts during differentiation. This process is regulated by transcription factors ATF4 and FOXO. Additionally, osteogenic signals like WNT and PTH can stimulate amino acid uptake. For example, WNT signaling can rapidly stimulate glutamine uptake and metabolism required for osteoblast differentiation. Unfortunately, transporters mediating glutamine uptake in osteoblasts are unknown. Moreover, the mechanism by which WNT stimulates increased glutamine consumption is also unknown. We identified two amino acid transporters, Slc7a7 and Slc1a5, as the primary glutamine transporters in response to WNT. Slc7a7 is responsible for the rapid WNT-induced glutamine uptake via the -catenin dependent pathway. Conversely, Slc1a5 sustains basal glutamine uptake, which is regulated by ATF4 downstream of the mTORC1 pathway. In summary, these data demonstrate the biphasic role of WNT signaling in regulating glutamine consumption, by two amino acid transporters Slc7a7 and Slc1a5, during osteoblast differentiation. While we have shown the importance of glutamine in bone cells, the role of other amino acids is not clear. Proline has long been considered as a critical amino acid due to its enrichment in collagens. Furthermore, PTH stimulates proline consumption in osteoblasts. The transport of proline is characterized by its dependency on sodium and sensitivity to MEAIB. However, the precise transport system responsible for proline import is not known. Here we identified the amino acid transporter Slc38a2, which encodes SNAT2, as the primary proline transporter in osteoblasts. Deletion of Slc38a2 results in defects in both intramembranous and endochondral ossifications. The phenotype is associated with defective osteoblast differentiation highlighted by reduction of proline enriched proteins (e.g. RUNX2, OSX and COL1A1). Slc38a2 provides proline to support osteoblast differentiation through two mechanisms. First, majority of proline is directly incorporated into proteins and does not contribute to amino acid biosynthesis. Second, proline oxidation regulates bioenergetics required for osteoblast differentiation. These findings highlight the multifaceted functions of proline, which is provided by Slc38a2, in osteoblast differentiation and bone formation. Collectively, my work demonstrates the critical role of amino acid transporters in osteoblast differentiation and provides novel insights in their potential applications in treatments of bone diseases like osteoporosis and bone fracture.
Item Open Access An Atat1/Mec-17-Myosin II axis controls ciliogenesis(2013) Rao, YanhuaPrimary cilia are evolutionarily conserved, acetylated microtubule-based organelles that transduce mechanical and chemical signals. Primary cilium assembly is tightly controlled and its deregulation causes a spectrum of human diseases. Formation of primary cilium is a collaborative effort of multiple cellular machineries, including microtubule, actin network and membrane trafficking. How cells coordinate these components to construct the primary cilia remains unclear. In this dissertation research, we utilized a combination of cell biology, biochemistry and light microscopy technologies to tackle the enigma of primary cilia formation, with particular focus on isoform-specific roles of non-muscle myosin II family members. We found that myosin IIB (Myh10) is required for cilium formation. In contrast, myosin IIA (Myh9) suppresses cilium formation. In Myh10 deficient cells, Myh9 inactivation significantly restores cilia formation. Myh10 antagonizes Myh9 and increases actin dynamics, permitting pericentrosomal preciliary complex formation required for cilium assembly. Importantly, Myh10 is upregulated upon serum starvation-induced ciliogenesis and this induction requires Atat1/Mec-17, the microtubule acetyltransferase. Our findings suggest that Atat1/Mec17-mediated microtubule acetylation is coupled to Myh10 induction, whose accumulation overcomes the Myh9-dependent actin cytoskeleton, thereby activating cilium formation. Thus, Atat1/Mec17 and myosin II coordinate microtubules and the actin cytoskeleton to control primary cilium biogenesis.
Item Open Access An Essential Role for Skeletal Muscle Progenitor Cells in Response to Ischemia in Vascular Disease(2020) Abbas, HasanPeripheral artery disease (PAD) is nearly as common as coronary artery disease, but few effective treatments exist, and it is associated with significant morbidity and mortality. Although PAD studies have focused on the vascular response to ischemia, studies from our lab indicate that skeletal muscle cells, particularly Pax7-expressing muscle progenitor cells (MPCs), also known as satellite cells, may play a critically important role in determining the phenotypic manifestation of PAD. Here, we demonstrate that genetic ablation of satellite cells in a murine model of PAD resulted in a complete absence of normal muscle regeneration following ischemic injury, despite a lack of morphological or physiological changes in resting muscle. Compared to ischemic muscle of control mice (Pax7WT), the ischemic limb of Pax7-deficient mice (Pax7∆) was unable to generate significant force 7- or 28-days after hind limb ischemia (HLI) in ex vivo force measurement studies. A dramatic increase in adipose infiltration was observed 28 days after HLI in Pax7∆ mice, which replaced functional muscle, a phenotype seen in PAD patients with severe disease. To investigate the mechanism of these adipogenic changes, we first investigated whether a pool of progenitor cells known as fibro-adipogenic progenitors (FAPs) was upregulated and demonstrated an increase in the expression of their canonical marker PDGFRα in Pax7∆ mice. Inhibition of FAPs using the drug batimastat resulted in a decrease in muscle adipose tissue and a corresponding increase in fibrosis. MPCs cultured from mouse muscle tissue failed to form myotubes in vitro following depletion of satellite cells in vivo, and they displayed an increased propensity to differentiate into fat in adipogenic medium. Importantly, this phenotype was recapitulated in patients with critical limb ischemia (CLI), the most severe form of PAD. Skeletal muscle samples from CLI patients demonstrated an increase in adipose deposition in more ischemic regions of muscle, which corresponded with a decrease in the number of satellite cells in those regions. Collectively, these data demonstrate that Pax7+ MPCs are required for normal muscle regeneration after ischemic injury, and they suggest that targeting muscle regeneration may be an important therapeutic approach to prevent muscle degeneration in PAD. Future studies will focus on the role of other supporting cells (such as pericytes) and the cross-talk between FAPs and satellite cells in ischemic muscle regeneration.
Item Open Access Analysis of crinkled Function in Drosophila melanogaster Hair and Bristle Morphogenesis(2012) Singh, VinayMutations in myosin VIIa (MyoVIIa), an unconventional myosin, have been shown to cause Usher Syndrome Type 1B in humans. Usher Syndrome Type 1B is characterized by congenital sensorineural deafness, vestibular dysfunction and pre-pubertal onset of retinitis pigmentosa. Mouse model studies show that sensorineural deafness and vestibular dysfunction in MyoVIIa mutants is caused by disruption in the structure of microvilli-like projections (stereocilia) of hair cells in the cochlea and vestibular organ. MyoVIIa has also been shown to affect adaptation of mechanoelectrical transduction channels in stereocilia.
In Drosophila melanogaster mutations in MyoVIIa encoded by crinkled (ck) cause defects in hair and bristle morphogenesis and deafness. Here we study the formation of bristles and hairs in Drosophila melanogaster to investigate the molecular basis of ck/MyoVIIa function and its regulation. We use live time-lapse confocal microscopy and genetic manipulations to investigate the requirement of ck/MyoVIIa function in various steps of morphogenesis of hairs and bristles. Here we show that null or near null mutations in ck/MyoVIIa lead to the formation of 8-10 short and thin hairs (split hairs) per epithelial cell that are likely the result of the failure of association of hair-actin bundles that in wild-type cells come together to form a single hair.
The myosin super family of motor proteins is divided into 17 classes by virtue of differences in the sequence of their motor domain, which presumably affect their physiological functions. In addition, substantial variety in the overall structure of their tail plays an important role in the differential regulation of myosin function. In this study we show that ck/MyoVIIa, that has two MyTH4 FERM domains in its tail separated by an SH3 domain, requires both MyTH4 FERM repeats for efficient association of hair-actin bundles to form hairs. We also show that the "multiple hair" phenotype of over-expression of ck/MyoVIIa requires both MyTH4 FERM domain function but not the tail-SH3 domain. We further demonstrate that the tail-SH3 domain of ck/MyoVIIa plays a role in keeping actin bundles, which run parallel to the length of the growing bristle, separate from each other. Our data also suggests that the tail-SH3 domain plays a role in the association of the actin filament bundles with the membrane and regulates F-actin levels in bristles.
We further demonstrate that over-expression of Quail (villin) can rescue the hair elongation defects seen in ck/MyoVIIa null or near null mutants but does not rescue the split hair defects. We show that over-expression of Alpha-actinin-GFP, another actin bundling protein, phenocopies the multiple hair phenotype of ck/MyoVIIa over-expression. Over-expression of Alpha-actinin-GFP in a ck/MyoVIIa null or near null background shows that Alpha-actinin-GFP cannot rescue the split or short hair phenotype of ck/MyoVIIa loss-of-function. However, cells over-expressing Alpha-actinin-GFP in a ck/MyoVIIa null or near null background have more than the normal 8-10 split hairs, suggesting that Alpha-actinin-GFP over-expression causes the formation of more than the normal complement of hair-actin bundles per cell, resulting in a multiple hair phenotype. We show that Twinfilin, an actin monomer sequestering protein implicated in negatively regulating F-actin bundle elongation in stereocilia in a MyoVIIa-dependent manner, is required for F-actin bundle stability.
In addition, we use yeast two-hybrid strategies to identify Slam as a protein that directly binds to ck/MyoVIIa. We show that Slam, a novel membrane-associated protein, likely functions to regulate ck/MyoVIIa function during hair and bristle morphogenesis. We show that over-expression of Slam and loss-of-function mutations in Slam phenocopy ck/MyoVIIa loss-of-function split and short hair phenotype. We also show that disruption of Slam and RhoGEF2 association causes split hair defects similar to ck/MyoVIIa loss-of-function phenotype suggesting that Slam probably regulates ck/MyoVIIa function via RhoGEF2.
Together our results show that ck/MyoVIIa plays an important role in regulating the actin cytoskeleton that underlies actin-based cellular protrusions like hairs and bristles.
Item Open Access Aneuploidy Tolerance in a Polyploid Organ(2016) Schoenfelder, Kevin PaulEndopolyploid cells (hereafter - polyploid cells), which contain whole genome duplications in an otherwise diploid organism, play vital roles in development and physiology of diverse organs such as our heart and liver. Polyploidy is also observed with high frequency in many tumors, and division of such cells frequently creates aneuploidy (chromosomal imbalances), a hallmark of cancer. Despite its frequent occurrence and association with aneuploidy, little is known about the specific role that polyploidy plays in diverse contexts. Using a new model tissue, the Drosophila rectal papilla, we sought to uncover connections between polyploidy and aneuploidy during organ development. Our lab previously discovered that the papillar cells of the Drosophila hindgut undergo developmentally programmed polyploid cell divisions, and that these polyploid cell divisions are highly error-prone. Time-lapse studies of polyploid mitosis revealed that the papillar cells undergo a high percentage of tripolar anaphase, which causes extreme aneuploidy. Despite this massive chromosome imbalance, we found the tripolar daughter cells are viable and support normal organ development and function, suggesting acquiring extra genome sets enables a cell to tolerate the genomic alterations incurred by aneuploidy. We further extended these findings by seeking mechanisms by which the papillar cells tolerated this resultant aneuploidy.
Item Open Access APOBEC Mutagenesis as a Driver of Tumor Evolution through Genetic Heterogeneity and Immunogenicity(2021) DiMarco, AshleyThe APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) family of cytidine deaminases is one of the most common endogenous sources of single base substitution mutations in human cancer. Accordingly, APOBEC enzymes represent a major source of intratumor genetic heterogeneity and have been associated with immunotherapy response in diverse cancer types. However, the consequences of APOBEC mutagenesis on tumor progression in vivo are not well understood. To address this, I developed several murine tumor models with inducible APOBEC3B expression and studied the contribution of APOBEC activity to tumor evolution and immunogenicity. First, I explored the effects of APOBEC activity on tumor relapse using a murine model of mammary tumor recurrence. APOBEC activity led to a significant acceleration in tumor recurrence following the strong selective pressure of oncogenic driver signaling loss. Recurrent APOBEC tumors had undifferentiated histological features and large, irregularly shaped nuclei containing defects like micronuclei, multinucleation, and chromatin bridges. I found that recurrent APOBEC tumors amplified the therapy resistance-associated oncogene, c-Met, on circular extrachromosomal DNA, likely driving the proliferation of the recurrent cancer cells. Second, because APOBEC mutational signatures are enriched in the majority of HER2-positive breast cancer patients, I used a syngeneic HER2-driven mammary tumor model to study the effects of APOBEC activity on the tumor immune microenvironment. I found that APOBEC activity induced an antitumor adaptive immune response and CD4+ T cell-mediated tumor growth inhibition. While polyclonal APOBEC tumors had a moderate growth defect, clonal APOBEC tumors were almost completely rejected by the immune system, suggesting that APOBEC-mediated genetic heterogeneity limits the antitumor adaptive immune response. In human breast cancers, the relationship between APOBEC mutagenesis and immunogenicity varied by breast cancer subtype and the frequency of subclonal mutations. Consistent with the observed immune infiltration in murine APOBEC tumors, APOBEC activity sensitized HER2-driven breast tumors to checkpoint inhibition. This work provides a mechanistic basis for the sensitivity of APOBEC tumors to checkpoint inhibitors and suggests a rationale for using APOBEC mutational signatures and clonality as biomarkers predicting immunotherapy response in HER2-positive breast cancers. In conclusion, I’ve identified a novel role for APOBEC activity in generating chromosomal instability, consisting of mitotic errors, oncogene amplification, and extrachromosomal DNA formation to promote tumor recurrence. Moreover, APOBEC activity also stimulated an antitumor adaptive immune response and sensitized tumors to immunotherapy.
Item Embargo Aptamers as Reversible Sorting Ligands in Dual FACS and MACS: Antisense and Nuclease-Mediated Approaches(2023) Requena, MartinFluorescence Activated Cell Sorting (FACS) and Magnetic Activated Cell Sorting (MACS) are two essential tools for cell separation in research and medicine. Antibodies, the gold standard in both of these methods, are effective ligands for cell-surface biomarkers, but their irreversible binding precludes a wide variety of downstream medical and experimental applications. Aptamers – nucleic acid ligands with a defined three-dimensional structure that enables them to bind a molecular target with a high degree of specificity – offer a viable alternative for this particular obstacle because their RNA- or DNA-based chemistry enables their removal from cellular targets. In these studies, we present examples of successful sorting of cells and removal of the targeting aptamers with MACS and FACS using both the previously-published antisense-based method of post-sorting aptamer removal and a more general approach using nuclease-based digestion of targeting aptamers on the cell surface after cell isolation. We believe this work can be used in a number of potential post-sorting applications where targeting ligands or attached magnetic or fluorescent moieties could interfere with experimental or clinical results.
Item Open Access Autophagy in Metabolism, Cell Death, and Leukemogenesis(2011) Altman, Brian JamesTissue homeostasis is controlled by the availability of growth factors, which sustain exogenous nutrient uptake and prevent apoptosis. Cancer cells, however, can express constitutively active oncogenic kinases such as BCR-Abl that promote these processes independent of extrinsic growth factors. When cells are deprived sufficient growth signals or when oncogenic kinases are inhibited, glucose metabolism decreases and cells activate the self-digestive process of autophagy, which clears damaged organelles and provides degradation products as an alternate fuel to support mitochondrial metabolism. Importantly, loss of growth signals can also lead to apoptosis mediated through Bcl-2 family proteins, and Bcl-2 has been reported to interfere with autophagy, potentially disrupting a key nutrient source just as glucose uptake becomes limiting. Since autophagy may support survival or lead to death depending on context, the role of this pathway in apoptosis-competent growth factor deprived cells remains unclear.
In this thesis, I examine the interactions of autophagy with Bcl-2 family proteins and apoptosis upon inhibition of growth signals in hematopoietic cells. In contrast to other studies, I found autophagy was rapidly induced in growth factor deprived cells regardless of Bcl-2 or Bcl-xL expression, and this led to increased production of fatty acids and amino acids for metabolism. While these data suggested autophagy may play a key role to support metabolism of growth factor deprived cells, provision of exogenous pyruvate or lipids as alternate fuel had little affect on cell survival. Instead, I found that autophagy modulated cell stress pathways and Bcl-2 family protein expression in a context specific fashion to impact cell fate.
My results show that autophagy's effect on cell survival is dependent on its level of induction within a cell. I observed that partial suppression of autophagy protects cells from stress and induction of pro-apoptotic Bcl-2 family expression, while complete inhibition of autophagy enhances stress and is pro-apoptotic. In experiments using shRNAi to partially suppress autophagy, I found increased survival upon growth factor deprivation in several different types of cells expressing anti-apoptotic Bcl-2 or Bcl-xL, indicating that autophagy promoted cell death in these instances. Cell death was not autophagic, but apoptotic, and relied on direct Chop-dependent transcriptional induction of the pro-apoptotic Bcl-2 family protein Bim. In contrast, complete acute disruption of autophagy through conditional Cre-mediated excision of the autophagy-essential gene Atg3 led to p53 phosphorylation, upregulation of p21 and the pro-apoptotic Bcl-2 family protein Puma, and rapid cell death of cells the presence or absence of growth factor. Importantly, transformed BCR-Abl-expressing cells had low basal levels of autophagy but were highly dependent on this process. Deletion of Atg3 or treatment with chemical autophagy inhibitors led to rapid apoptosis, and BCR-Abl expressing cells were unable to form leukemia in mice in without autophagy. Together, my data demonstrate a dual role for autophagy in cell survival or cell death and suggest that the level of autophagy in a cell is critical in determining its role in apoptosis and cell fate. Ultimately, these results may help to determine future approaches to modulate autophagy in cancer therapy.
Item Open Access B-cyclin/CDK Regulation of Mitotic Spindle Assembly through Phosphorylation of Kinesin-5 Motors in the Budding Yeast, Saccharomyces cerevisiae(2012) Chee, Mark Kuan LengAlthough it has been known for many years that B-cyclin/CDK complexes regulate the assembly of the mitotic spindle and entry into mitosis, the full complement of relevant CDK targets has not been identified. It has previously been shown in a variety of model systems that B-type cyclin/CDK complexes, kinesin-5 motors, and the SCFCdc4 ubiquitin ligase are required for the separation of spindle poles and assembly of a bipolar spindle. It has been suggested that in the budding yeast, Saccharomyces cerevisiae, B-type cyclin/CDK (Clb/Cdc28) complexes promote spindle pole separation by inhibiting the degradation of the kinesins-5 Kip1 and Cin8 by the anaphase-promoting complex (APCCdh1). I have determined, however, that the Kip1 and Cin8 proteins are actually present at wild-type levels in yeast in the absence of Clb/Cdc28 kinase activity. Here, I show that Kip1 and Cin8 are in vitro targets of Clb2/Cdc28, and that the mutation of conserved CDK phosphorylation sites on Kip1 inhibits spindle pole separation without affecting the protein's in vivo localization or abundance. Mass spectrometry analysis confirms that two CDK sites in the tail domain of Kip1 are phosphorylated in vivo. In addition, I have determined that Sic1, a Clb/Cdc28-specific inhibitor, is the SCFCdc4 target that inhibits spindle pole separation in cells lacking functional Cdc4. Based on these findings, I propose that Clb/Cdc28 drives spindle pole separation by direct phosphorylation of kinesin-5 motors.
In addition to the positive regulation of kinesin-5 function in spindle assembly, I have also found evidence that suggests CDK phosphorylation of kinesin-5 motors at different sites negatively regulates kinesin-5 activity to prevent premature spindle pole separation. I have also begun to characterize a novel putative role for the kinesins-5 in mitochondrial genome inheritance in S. cerevisiae that may also be regulated by CDK phosphorylation.
In the course of my dissertation research, I encountered problems with several established molecular biology tools used by yeast researchers that I have tried to address. I have constructed a set of 42 plasmid shuttle vectors based on the widely used pRS series for use in S. cerevisiae that can be propagated in the bacterium Escherichia coli. This set of pRSII plasmids includes new shuttle vectors that can be used with histidine and adenine auxotrophic laboratory yeast strains carrying mutations in the genes HIS2 and ADE1, respectively. My new pRSII plasmids also include updated versions of commonly used pRS plasmids from which common restriction sites that occur within their yeast-selectable biosynthetic marker genes have been removed in order to increase the availability of unique restriction sites within their polylinker regions. Hence, my pRSII plasmids are a complete set of integrating, centromere and 2 episomal plasmids with the biosynthetic marker genes ADE2, HIS3, TRP1, LEU2, URA3, HIS2 and ADE1 and a standardized selection of at least 16 unique restriction sites in their polylinkers. Additionally, I have expanded the range of drug selection options that can be used for PCR-mediated homologous replacement using pRS plasmid templates by replacing the G418-resistance kanMX4 cassette of pRS400 with MX4 cassettes encoding resistance to phleomycin, hygromycin B, nourseothricin and bialaphos. Finally, in the process of generating the new plasmids, I have determined several errors in existing publicly available sequences for several commonly used yeast plasmids. Using updated plasmid sequences, I constructed pRS plasmid backbones with a unique restriction site for inserting new markers in order to facilitate future expansion of the pRS/pRSII series.
Item Open Access Basement Membranes Link Together and Stretch to Withstand Mechanical Forces(2022) Gianakas, ClaireBasement membranes (BMs) are thin, dense sheets of extracellular matrix that surround most animal tissues and provide structural support. While the role of BMs in the structural support of tissues is well established, how these matrices can structurally support tissues while accommodating dynamic tissue function is not well understood. Using C. elegans, a powerful model organism that allows for live imaging, genetic analysis, and rapid screening, I was able to utilize endogenous knock-in fluorescent proteins, conditional RNAi, optogenetics, and quantitative live imaging to investigate how BM components contribute to the BM’s ability to withstand mechanical load in various circumstances. In Chapter 1, I discuss the known roles of BM, introduce BM proteins of interest, explore gaps in our understanding of BM’s function in withstanding mechanical force, and expand upon the utility of C. elegans as a model system to investigate these questions. In Chapter 2, I show that BM-to-BM linkages can function to resist the mechanical forces involved in egg-laying. In Chapter 3, I explore how BM stretches to accommodate dynamic tissue movement. In Chapter 4, I discuss future directions and the implications of these findings and in Chapter 5 I summarize my conclusions.