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Investigation of the phosphatidylinositol 3-kinase pathway in B cellsMa, Kewei 05 1900 (has links)
There is hardly a cellular process that is not regulated in some way by phosphoinositides, which makes biochemical and physiological studies of these lipids extremely important. PI 3-kinases are key regulators of phosphoinositide metabolism and have been shown to affect a large variety of cellular responses. The key products of PI 3-kinases that have functional activity in higher eukaryotic cells are PI(3,4,5)P₃ and PI(3,4)P₂. PI(3,4,5)P₃ is universally accepted as one of the most important second messengers in signal transduction. However, our knowledge of the functions of PI(3,4)P₂ as a lipid second messenger is much less precise. In this dissertation, work was undertaken to elucidate the regulation of PI(3,4,5)P₃ and PI(3,4)P₂ production and downstream signaling in B cells. Cells with membrane targeted exogenous SHIP were utilized to manipulate phosphoinositide levels. The relationship of PI(3,4,5)P₃ and PI(3,4)P₂ levels to downstream PKB phosphorylation and activation was studied. PI(3,4,5)P₃ and PI(3,4)P₂ levels were found to closely correlate with PKB phosphorylation levels at Thr308 and Ser473, respectively. In addition, PI(3,4)P₂ levels determine the PKB activity in the cytosol; while PI(3,4,5)P₃ levels determine PKB activity at the plasma membrane. Different doses and different forms of B cell receptor (BCR) agonists were used for stimulation. PI 3-kinase activation was studied carefully following stimulation with low doses of anti-BCR antibody and F(ab')₂ fragments. Low concentrations of F(ab')₂ fragments produced higher levels of PI(3,4,5)P₃ than did a high concentration of F(ab')₂ fragments. Downstream PKB signaling was studied in these models. Similar conclusions were drawn from both SHIP over-expressing BJAB cells and dose-dependent BCR stimulations. We speculated that phosphoinositides’ regulation of the kinetics of PKB phosphorylation at Ser473 and Thr308 might be mediated by additional proteins. Investigation of plasma membrane-associated PKB showed that it formed a protein complex of around 400KD, which we attempted to characterize further with respect to PKB phosphorylation and association with lipids. In conclusion, phosphoinositide production is intricately regulated in vivo to control downstream signaling. The levels of PI(3,4)P₂ and PI(3,4,5)P₃ have precise and profound effects on PKB and other molecules such as TAPP and Bam32. This study has contributed new insight into the PI 3-kinase signaling pathway from the aspect of phosphoinositide lipid function.
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Investigation of the phosphatidylinositol 3-kinase pathway in B cellsMa, Kewei 05 1900 (has links)
There is hardly a cellular process that is not regulated in some way by phosphoinositides, which makes biochemical and physiological studies of these lipids extremely important. PI 3-kinases are key regulators of phosphoinositide metabolism and have been shown to affect a large variety of cellular responses. The key products of PI 3-kinases that have functional activity in higher eukaryotic cells are PI(3,4,5)P₃ and PI(3,4)P₂. PI(3,4,5)P₃ is universally accepted as one of the most important second messengers in signal transduction. However, our knowledge of the functions of PI(3,4)P₂ as a lipid second messenger is much less precise. In this dissertation, work was undertaken to elucidate the regulation of PI(3,4,5)P₃ and PI(3,4)P₂ production and downstream signaling in B cells. Cells with membrane targeted exogenous SHIP were utilized to manipulate phosphoinositide levels. The relationship of PI(3,4,5)P₃ and PI(3,4)P₂ levels to downstream PKB phosphorylation and activation was studied. PI(3,4,5)P₃ and PI(3,4)P₂ levels were found to closely correlate with PKB phosphorylation levels at Thr308 and Ser473, respectively. In addition, PI(3,4)P₂ levels determine the PKB activity in the cytosol; while PI(3,4,5)P₃ levels determine PKB activity at the plasma membrane. Different doses and different forms of B cell receptor (BCR) agonists were used for stimulation. PI 3-kinase activation was studied carefully following stimulation with low doses of anti-BCR antibody and F(ab')₂ fragments. Low concentrations of F(ab')₂ fragments produced higher levels of PI(3,4,5)P₃ than did a high concentration of F(ab')₂ fragments. Downstream PKB signaling was studied in these models. Similar conclusions were drawn from both SHIP over-expressing BJAB cells and dose-dependent BCR stimulations. We speculated that phosphoinositides’ regulation of the kinetics of PKB phosphorylation at Ser473 and Thr308 might be mediated by additional proteins. Investigation of plasma membrane-associated PKB showed that it formed a protein complex of around 400KD, which we attempted to characterize further with respect to PKB phosphorylation and association with lipids. In conclusion, phosphoinositide production is intricately regulated in vivo to control downstream signaling. The levels of PI(3,4)P₂ and PI(3,4,5)P₃ have precise and profound effects on PKB and other molecules such as TAPP and Bam32. This study has contributed new insight into the PI 3-kinase signaling pathway from the aspect of phosphoinositide lipid function.
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Investigation of the phosphatidylinositol 3-kinase pathway in B cellsMa, Kewei 05 1900 (has links)
There is hardly a cellular process that is not regulated in some way by phosphoinositides, which makes biochemical and physiological studies of these lipids extremely important. PI 3-kinases are key regulators of phosphoinositide metabolism and have been shown to affect a large variety of cellular responses. The key products of PI 3-kinases that have functional activity in higher eukaryotic cells are PI(3,4,5)P₃ and PI(3,4)P₂. PI(3,4,5)P₃ is universally accepted as one of the most important second messengers in signal transduction. However, our knowledge of the functions of PI(3,4)P₂ as a lipid second messenger is much less precise. In this dissertation, work was undertaken to elucidate the regulation of PI(3,4,5)P₃ and PI(3,4)P₂ production and downstream signaling in B cells. Cells with membrane targeted exogenous SHIP were utilized to manipulate phosphoinositide levels. The relationship of PI(3,4,5)P₃ and PI(3,4)P₂ levels to downstream PKB phosphorylation and activation was studied. PI(3,4,5)P₃ and PI(3,4)P₂ levels were found to closely correlate with PKB phosphorylation levels at Thr308 and Ser473, respectively. In addition, PI(3,4)P₂ levels determine the PKB activity in the cytosol; while PI(3,4,5)P₃ levels determine PKB activity at the plasma membrane. Different doses and different forms of B cell receptor (BCR) agonists were used for stimulation. PI 3-kinase activation was studied carefully following stimulation with low doses of anti-BCR antibody and F(ab')₂ fragments. Low concentrations of F(ab')₂ fragments produced higher levels of PI(3,4,5)P₃ than did a high concentration of F(ab')₂ fragments. Downstream PKB signaling was studied in these models. Similar conclusions were drawn from both SHIP over-expressing BJAB cells and dose-dependent BCR stimulations. We speculated that phosphoinositides’ regulation of the kinetics of PKB phosphorylation at Ser473 and Thr308 might be mediated by additional proteins. Investigation of plasma membrane-associated PKB showed that it formed a protein complex of around 400KD, which we attempted to characterize further with respect to PKB phosphorylation and association with lipids. In conclusion, phosphoinositide production is intricately regulated in vivo to control downstream signaling. The levels of PI(3,4)P₂ and PI(3,4,5)P₃ have precise and profound effects on PKB and other molecules such as TAPP and Bam32. This study has contributed new insight into the PI 3-kinase signaling pathway from the aspect of phosphoinositide lipid function. / Medicine, Faculty of / Medicine, Department of / Experimental Medicine, Division of / Graduate
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The role of LECT2 in liver carcinogenesisWu, Ping-Hsuan 24 August 2011 (has links)
Leukocyte cell-derived chemotaxin 2 (LECT2) is first isolated as a 16-kDa secreted protein from cultured fluid of phytohemagglutinin-activated human T-cell leukemia SKW-3 cells. Recently LECT2 has shown to be synthesized by human hepatocytes and stimulates the growth of chondrocytes. LECT2 is involved in chemotactic factor to neutrophils and may be associated with rheumatoid arthritis. Besides, LECT2 is evolutionarily conserved and acts as a repressor in the Wnt/£]-catenin signaling pathway. Wnt/£]-catenin signaling is implicated in liver carcinogenesis. However, the exact roles of LECT2 in liver carcinogenesis are not yet well characterized. This study is to investigate the extra roles of LECT2 in Wnt signaling. Our results showed that adenoviral administration of LECT2 over-expression suppress oncogenic processes such as migration, invasion, proliferation and colony formation, as well as alteration in cell cycle distributions. In animal model significantly suppress liver malignancies in orthotopic Novikoff hepatoma. In conclusion, we show that ad-LECT2 gene delivery attenuated cell carcinogenesis process via downregulated Wnt/£]-catenin signaling in vitro and suppressed tumor growth in vivo. Besides LECT2 over-expression represents a novel therapeutically factor for hepatocelluar carcinoma.
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Phosphorylated Motif Recognition and Mechanisms of Cell Signaling in Actin-cytoskeletal RegulationBlasutig, Ivan M. 20 January 2009 (has links)
The actin cytoskeleton is critical to the proper function of cells and its misregulation can lead to human disease states. As a consequence, actin dynamics is tightly controlled. To gain further insight into the mechanisms controlling actin dynamics, my studies have focused on two families of proteins implicated in actin regulation.
The Nck proteins act as molecular adaptors in signal propagation by linking upstream mediators, which they recognize through the Nck SH2 domain, to downstream effectors, which bind the Nck SH3 domains. I have found that Nck is required in podocyte cells for proper foot process formation, a process involving actin cytoskeletal reorganization, and therefore for proper kidney function. Furthermore, I show that Nck links the podocyte adhesion protein nephrin to actin polymerization. In cell-based assays, nephrin-induced actin polymerization is dependent on an interaction with functional Nck, which occurs through binding of three phosphorylated tyrosine sites within the cytoplasmic tail of nephrin to the Nck SH2 domain. Finally, I demonstrate that the enteropathogenic E.coli protein Tir reorganizes the cytoskeleton by molecular-mimicry of nephrin-like signaling.
The srGAP proteins are GTPase activating proteins that attenuate the activity Rho GTPases, proteins directly involved in actin cytoskeletal control. The regulatory mechanisms that control srGAP activity are unclear. I have found that the srGAP family members srGAP1, srGAP2, and srGAP3 interact, through their carboxy-terminal region with 14-3-3 proteins, and that this interaction is dependent on protein kinase C-induced phosphorylation of srGAP. 14-3-3 binding does not affect the activity of srGAP2, as determined using cell-based GAP assays. Further studies are required to clarify the biological significance of this interaction to srGAP regulation.
The data presented in this thesis furthers our understanding of signaling networks that control the actin cytoskeleton, and brings us closer to the goal of fully understanding actin dynamics and cellular signaling.
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Phosphorylated Motif Recognition and Mechanisms of Cell Signaling in Actin-cytoskeletal RegulationBlasutig, Ivan M. 20 January 2009 (has links)
The actin cytoskeleton is critical to the proper function of cells and its misregulation can lead to human disease states. As a consequence, actin dynamics is tightly controlled. To gain further insight into the mechanisms controlling actin dynamics, my studies have focused on two families of proteins implicated in actin regulation.
The Nck proteins act as molecular adaptors in signal propagation by linking upstream mediators, which they recognize through the Nck SH2 domain, to downstream effectors, which bind the Nck SH3 domains. I have found that Nck is required in podocyte cells for proper foot process formation, a process involving actin cytoskeletal reorganization, and therefore for proper kidney function. Furthermore, I show that Nck links the podocyte adhesion protein nephrin to actin polymerization. In cell-based assays, nephrin-induced actin polymerization is dependent on an interaction with functional Nck, which occurs through binding of three phosphorylated tyrosine sites within the cytoplasmic tail of nephrin to the Nck SH2 domain. Finally, I demonstrate that the enteropathogenic E.coli protein Tir reorganizes the cytoskeleton by molecular-mimicry of nephrin-like signaling.
The srGAP proteins are GTPase activating proteins that attenuate the activity Rho GTPases, proteins directly involved in actin cytoskeletal control. The regulatory mechanisms that control srGAP activity are unclear. I have found that the srGAP family members srGAP1, srGAP2, and srGAP3 interact, through their carboxy-terminal region with 14-3-3 proteins, and that this interaction is dependent on protein kinase C-induced phosphorylation of srGAP. 14-3-3 binding does not affect the activity of srGAP2, as determined using cell-based GAP assays. Further studies are required to clarify the biological significance of this interaction to srGAP regulation.
The data presented in this thesis furthers our understanding of signaling networks that control the actin cytoskeleton, and brings us closer to the goal of fully understanding actin dynamics and cellular signaling.
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Mapping the cellular mechanisms regulating atrial natriuretic peptide secretionTaskinen, P. (Panu) 01 June 1999 (has links)
Abstract
Atrial natriuretic peptide (ANP) and B-type natriuretic peptide (BNP) are cardiac hormones, which are involved in the regulation of blood pressure and fluid homeostasis. The major determinant for ANP and BNP release are atrial and ventricular wall stretch, but also some vasoactive factors such as endothelin-1 (ET-1) can enhance cardiac hormone secretion. The mechanical stretch rapidly activates multiple signal transduction pathways in cardiac cells, but the cellular mechanisms mediating stretch-induced ANP secretion are still unknown. The aim of the present study was to examine the cellular mechanisms of autocrine/paracrine factors and stretch-induced ANP secretion.
Genistein, a potent protein tyrosine kinase (PTK) inhibitor, rapidly increased cardiac contractile force and ANP secretion in perfused rat heart. This effect of genistein may be unrelated to the inhibition of PTKs since this stimulation was blocked by a L-type calcium channel antagonist and Ca2+/calmodulin-dependent protein kinase II inhibitor. Pregnancy hormone relaxin increased heart rate and ANP secretion in perfused spontaneously beating heart, suggesting that relaxin may have a role in modulating cardiac function. Cellular mechanisms of atrial wall stretch-induced ANP secretion were also studied. This enhanced secretion was blocked by sarcoplasmic reticulum Ca2+-ATPase inhibitor thapsigargin and PTK inhibitor lavendustin A, indicating that thapsigargin sensitive Ca2+ pools and activation of PTK orPTK cascade have an important role in the regulation of stretch-secretion coupling. In addition, protein phosphatase inhibitor okadaic acid accelerated stretch-induced ANP secretion, suggesting that precise balance of protein kinase and phosphatase activity plays a role in mechanical stretch-induced ANP secretion. Finally interactions of endothelial factors regulating ANP exocytosis were studied. The potent nitric oxide synthase inhibitor L-NAME increased basal and atrial wall stretch-induced ANP secretion in the presence of ET-1, suggesting that nitric oxide may tonically inhibit ANP secretion.
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Mechanisms Governing the Tumor Suppressive Functions of the A-alpha Subunit of Protein Phosphatase 2AO'Connor, Caitlin M. 28 August 2019 (has links)
No description available.
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Development and Application of Network Algorithms for Prediction of Gene Function and Response to Viral Infection and ChemicalsLaw, Jeffrey Norman 09 December 2020 (has links)
The complex molecular machinery of the cell controls its response to various signals and environmental conditions. A natural approach to study these molecular mechanisms and cellular processes is with protein interaction networks. Due to the complexity of these networks,
sophisticated computational techniques are required to extract biological insights from them.
In this thesis, I develop and apply network-based algorithms for three different challenges.
1. I develop a novel, highly-scalable algorithm for network-based label prediction methods
that enables the integration of functional annotations and interaction networks across
many species in order to predict the functions of genes in newly-sequenced bacteria.
2. To overcome the limitations of experimental approaches to find human proteins and
processes that are hijacked by SARS-CoV-2, I adapt network propagation approaches
for predicting human interactors of the virus.
3. Large-scale experimental techniques to screen chemicals for toxicity have tested their
effects on many individual proteins. I integrate human protein-protein interactions with
this data to gain insights into the molecular networks those chemicals affect.
For each of these research problems, I perform comprehensive evaluations and downstream
analyses to demonstrate both the accuracy of our approaches and their utility in obtaining a
broader understanding of the molecular systems in question. / Doctor of Philosophy / The functions of all living cells are governed by complex networks of molecular interactions.
A major goal of systems biology is to understand the components of this machinery and
how they regulate each other to control the cell's response to various conditions and signals.
Advances in experimental techniques to understand these systems over the past couple
of decades have led to an explosion of data that probe various aspects of a cell such as
genome sequencing, which reads the DNA blueprint, gene expression, which measures the
amount of each gene's products in the cell, and the interactions between those products
(i.e., proteins). To extract biological insights from these datasets, increasingly sophisticated
computational methods are required. A powerful approach is to model the datasets as networks where the individual molecules are the nodes and the interactions between them are
the edges. In this thesis, I develop and apply network-based algorithms to utilize molecular
systems data for three related problems: (i) predicting the functions of genes in bacterial
species, (ii) predicting human proteins and processes that are hijacked by the SARS-CoV-2
virus, and (iii) suggesting cellular signaling pathways affected by exposure to a chemical.
Developments such as those presented in these three projects are critical to obtaining a
broader understanding of the functions of genes in the cell. Therefore, I make the methods
and results for each project easily accessible to aid other researchers in their efforts.
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Utilizing Systems Level Approaches to Identify Key Mechanisms of Drug Resistance in BRAF Mutated MelanomaParaiso, Kim H.T. 18 February 2015 (has links)
In the last four years, seven new drugs have been FDA approved for the treatment of late stage melanoma, for the field of melanoma, this marks an incredibly exciting. Three of these new therapies, vemurafenib, dabrafenib and trametinib are small molecule kinase inhibitors that target the MAPK pathway and as such have been approved for the treatment of BRAFV600 mutant melanomas. Yet despite recent advances, mechanisms of intrinsic and acquired BRAF inhibitor resistance continue to undermine uniform and long-lasting therapeutic responses. Several studies have shown that the reactivation of MAPK signaling is a critical event leading to BRAF inhibitor resistance. These studies lead to the evaluation and subsequent FDA approval of frontline BRAF (dabrafenib) plus MEK (trametinib) inhibitors to delay drug resistance.
Though this approach has meaningful clinical benefit, there are still a number of patients who do not respond to therapy or who, through unknown mechanisms, succumb to refractory disease. In an effort to identify drivers of MAPK inhibitor resistance, several studies have relied on traditional genomics methods. While gene-based approaches have guided precision medicine, they do not address the dynamics of the global signaling changes that occur following acquired resistance.
The dissertation herein will describe our efforts to fill these gaps of knowledge and will expand upon the evolution and development of our understanding of intrinsic and acquired MAPK pathway inhibitor resistance. This work will elaborate on our early understanding of single agent BRAF inhibitor resistance, the use of genomic and proteomic approaches to further elucidate these mechanisms, and evidence based approaches to delay and overcome single agent BRAF inhibitor resistance. This work will describe global phosphoproteomic and bioinformatics methodologies to elucidate the underlying processes of both single (BRAF) and dual agent (BRAF plus MEK) inhibitor resistance as well as strategies to constrain dual agent BRAF plus MEK inhibitor resistance.
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