Browsing by Subject "UPR"

Now showing 1 - 4 of 4

Open Access
Lipotoxic endoplasmic reticulum stress-associated inflammation : molecular mechanisms and modification by a bioactive lipokine
(2012) Demirsoy, Şeyma
Physiologic or pathologic processes that disturb protein folding in the endoplasmic reticulum (ER) activate a signaling pathway named the unfolded protein response (UPR). UPR promotes cell survival by reducing misfolded protein levels. The three proximal stress sensors of the UPR are known as PKR-resemble like ER kinase (PERK), inositol-requiring enzyme-1 (IRE1) and activating transcription factor 6 (ATF6), which monitor the quality of protein folding in the ER membrane and relay that information to the rest of the cell. If ER homeostasis can not be restored, prolonged UPR signaling can lead to cell death. Recent studies have shown metabolic overload, particularly high levels of fatty acids and cholesterol can induce ER stress and activate UPR signaling. These studies also demonstrated ER stress is a central mechanism that underlies the pathogenesis of metabolic diseases including obesity, type 2 diabetes, insulin resistance, atherosclerosis and hepatosteatosis. Understanding how nutrient excess activates the UPR and its novel molecular mechanisms of operation during metabolic stress could facilitate the development of novel and effective future therapeutics aiming to restore ER homeostasis. The molecular mechanisms of lipid induced activation of UPR and how the three proximal UPR stress sensors are linked to lipid metabolism and inflammation is not well understood. One of the UPR stress sensors, PERK, is a trans-membrane serine/threonine kinase with only two known downstream substrates, the eukaryotic translation initiation factor (eIF2) that controls translation initiation, and an antioxidant transcription factor, Nuclear factor eryhthroid-2-related factor-2 (Nrf2), that keeps redox homeostasis. One of the existing road blocks in studying PERK signaling has been the lack of molecular or chemical tools to regulate its activity. For my thesis studies, I developed a chemical-genetic approach to specifically modify PERK’s kinase activity. In this approach, the ATP binding pocket of a particular kinase is altered via site-directed mutagenesis in order to accommodate a bulky ATP analog that is not an effective substrate for the wild type kinase. Thus, only the mutated kinase can be targeted by the activatory or inhibitory bulky ATP analogs and this form of the kinase is referred to as ATP analog sensitive kinase (ASKA). Furthermore, I identified specific siRNA sequences that can be efficiently delivered to mouse macrophages and significantly reduce PERK expression. Both of these methods can be applied to study the direct impact of PERK activity on lipotoxic ER stress- associated inflammation. The results of the siRNA mediated PERK expression silencing experiments showed that PERK has a direct contribution to lipid-induced pro-inflammatory response in macrophages. Finally, I examined whether palmitoleate, a bioactive monounsaturated fatty acid previously shown to reduce lipid-induced ER stress and death, could also modify lipotoxic ER stress-associated inflammation. Based on the results from my experiments, palmitoleate is highly effective in preventing lipid induce inflammation. Unexpectedly, I also observed that palmitoleate could significantly block LPS-induced inflammation, too. In summary, during my thesis study I generated several useful tools including siRNA mediated knock-down of PERK and a novel chemical-genetic tool to directly and specifically modify PERK kinase activity. The findings from my studies demonstrate that PERK plays a significant role in lipid-induced inflammation, suggesting modification of PERK activity or its direct pro-inflammatory substrates could become desirable approaches to inhibit obesity-induced inflammation that contributes to the pathogenesis of diabetes and atherosclerosis. The outcome of my studies also showed that palmitoleate can significantly reduce lipotoxic-ER stress associated inflammation, which may explain its beneficial impact on both insulin resistance and atherosclerosis. Furthermore, the ATP-analog sensitive PERK mutant developed in my thesis can be coupled with proteomics to identify the full repertoire of PERK substrates during metabolic stress. In conclusion, the findings and tools developed in my thesis studies can form the basis of future studies to identify the molecular details of PERK’s involvement in lipid induced inflammation, the identification of novel PERK substrates during metabolic stress and the development of new therapeutic strategies against metabolically induced inflammation in obesity, diabetes and atherosclerosis.
Open Access
Prevention of fatty acid-induced inflammasome activation by a bioactive lipokine
(2014-08) Koyuncu, Seda
Exposure to excess lipids such as fatty acids and cholesterol leads to cellular stress, release of reactive oxygen species (ROS), inflammation dysfunction and death. These responses have important role in the pathogenesis of chronic metabolic and inflammatory diseases such asobesity, diabetes and atherosclerosis. Recent studies show that fatty acids also cause the formation of inflammatoryprotein complexes that are called inflammasome. Inflammasome promotesthe activation of caspase-1 protein and cleavage of inactive interleukin-1 beta(IL-1β) and interleukin-18 (IL-18) into their active, secreted forms.Two signals are required for the activation of inflammasome. The first signal (also known as priming step) is needed for the inducing the expression ofthe proinflammatory factors pro-IL-1β and pro-IL-18 andthe nucleotide-binding oligomerization domain receptor (NOD-like receptor) family, pyrin domain containing-3 (NLRP3) proteins through the activation of nuclear factor kappa beta (NF-κB),a transcription factor. The second signal is needed for the activation of caspase-1 and formation of the inflammasome complex. Saturated free fatty acids such as palmitate are known to cause the activation of inflammasome through generation of mitochondrial ROS as a second signal for inflammasome complex formation. In this study, I investigated the effect of palmitoleate, a bioactive monounsaturated fatty acidpreviously shown to counteract lipid-induced ER stress and enhance insulin sensitivity, on palmitate-induced activation of inflammasome complex. I observed that palmitoleate lead to a significant reduction in palmitate-stimulatedIL-1β transcription. Moreover, it reduced the expression of palmitate-stimulated secondary proinflammatory factors such as tumor necrosis factor alpha(TNF-a).Palmitoleate also diminished the palmitate induced activation of caspase-1, maturation and secretion of IL-1β in macrophages. To further understand the mechanism of the protective role of palmitoleate on palmitate induced inflammasome activation,I analyzed the effect of palmitoleate on palmitate-induced mtROS in macrophages cells were analyzed. These studies showed palmitoleate decreased palmitate induced mitochondrial oxygen species in macrophages. Moreover, I investigated the effect of palmitoleate on palmitate-induced inactivation of 5' AMP-activated protein kinase (AMPK)controls autopaghy and clearance of dysfunctional mitochondria, thereby reducing mtROS formation. Palmitoleate blocked the suppression of AMPK phosphorylation that was suppressed by palmitate, suggesting PAO's impact on mtROS secretion and inflammasome activation occurs by this upstream mechanism. Saturated fatty acids like palmitate are also known to cause endoplasmic reticulum (ER) stress, whichbe counteracted by palmitolate treatment. When ER stress happens, cells try to solve stress by activating the unfolded protein response (UPR). There are three arms of the UPR are Protein Kinase R-resemble like protein kinase (PERK), inositol-requiring enzyme-1 (IRE1) and activating factor 6 (ATF6). In this thesis, contribution of PERK and IRE1 on palmitate-induced activation of inflammasome was investigated. First, the relation between PERK and IRE1 with palmitate-stimulated mtROS was analyzedusing PERK- and IRE1- deficient mouse embryonic fibroblast cells (MEFs).The results of this study show PERK leads to a marked reduction in the formation of mtROS while IRE1 enhanced palmitate induced mtROS.Furthermore, palmitoleate suppressed palmitate-induced autophosphorylation of IRE1 while there was no effect of palmitoleate on palmitate-induced phosphorylation of PERK. In summary, palmitate-induced inflammasome activation can be inhibited by palmitoleate in boththe priming step and the second step.Palmitoleate blocks palmitate-induced suppression of phosphorylation of AMPK, leading to its reactivation and subsequent reduction in mtROS formation. Palmitate is a well-known inducer of ER stress, which can be counteracted by palmitoleic acid. Moreover, the IRE1 branch of the UPR has been shown to control inflammasome activationby regulating of mtROS production under lipotoxicity. The outcome of my studies show that the UPR branches initiated by PERK and IRE1 regulate mtROS production and therefore, palmitoleate may also block inflammasome activation induced by palmitate through this alternative mechanism.These findings imply that palmitoleate may have therapeutic applications inthe management of diseases where inflammasome activation has been shown to play a causal role such as obesity, diabetes and atherosclerosis.
Open Access
The role of Protein Kinase R in lipotoxicity
(2013) Yağabasan, Büşra
Endoplasmic reticulum (ER) is a central organelle for cellular homeostasis through its myriad of functions including protein and lipid biosynthesis, protein folding and secretion and calcium homeostasis. When protein folding or secretion is disrupted, ER elicits a unique signaling response initiated at its membranes called the unfolded protein response (UPR). UPR attempts to restore cellular homeostasis and survival via reducing unfolded protein levels, however, if this cannot be achieved or the stress is prolonged the UPR could lead to apoptosis. Three specific ER membrane proteins, inositol-requiring enzyme-1 (IRE1), Protein Kinase R-resemble like ER kinase (PERK) and activating transcription factor 6 (ATF6), act as ER stress sensors and initiate distinct but interlaced signaling pathways to restore ER homeostasis. Recently, studies demonstrated that over nutrition, especially high amount of saturated fatty acids or cholesterol in the circulation, leads to the induction of ER stress in metabolic tissues, resulting in the activation of UPR signaling pathways. Furthermore, ER stress was shown to play a causal role in the pathogenesis of metabolic diseases such as obesity, insulin resistance, type 2 diabetes and atherosclerosis. Interferon inducible double strand RNA activated protein kinase R (PKR) is also known to be activated during ER stress. Recent studies showed it can be activated by lipids during ER stress in cells and in metabolic tissues of obese mice. Genetic ablation or inhbition of PKR enhances systemic glucose homeostasis and insulin sensitivity in obesity in rodent models. However, it is not known how PKR becomes activated by overnutrition or by ER stress. In fact, many of the specific cellular components and molecular mechanisms in lipid induced cellular stress or death, namely lipotoxicity, is not completely understood. PKR is one of the serine/threonine kinase that is known to be activated during lipid induced ER stress, but only a few specific downstream substrates are known and these fall short of explaining PKR’s role in lipotoxicity in chronic metabolic disease pathogenesis. PKR also plays a crucial role in activation of inflammasomes through interacting with the inflammasome components. There is a gap in our knowledge regarding PKR’s specific molecular actions in nutrient-induced inflammation and metabolism in chronic metabolic diseases. In this thesis study, my major goal was to develop specific tools to modulate PKR’s activity and search for its specific substrates in lipotoxicity and its role in mediating lipid-induced ER stress response. For this purpose, I developed a novel chemical-genetic approach to specifically modify PKR’s kinase activity during ER stress. In this approach, the bulky sidechain of a gatekeeper amino acid (such as methionine) in the ATP binding cavity of PKR has been altered to a smaller side-chain amino acid (such as glycine) in order to slightly enlarge the cavity to accommodate bulky ATP analogs (activating or inhibiting). This mutant of the PKR has been named the analog sensitive kinase allele (ASKA) of PKR and was shown to utilize normal ATP as well as the bulky ATP analogs in kinase reactions. Furthermore, I demonstrated the specific inhibition of PKR kinase with the inhibitory, bulky ATP analogs such as4-Amino-1-tert-butyl-3-(1’-naphthyl)pyrazolo[3,4-d]pyrimidine (NAPP1) or 4-Amino- 1-tert-butyl-3-(1’-naphthylmethyl)pyrazolo[3,4-d]pyrimidine (1-NMPP1). In order to move one step closer to identification of potential PKR substrates, I also optimized kinase reactions for immunoprecipitated PKR ASKA mutant and visualized several potential downstream substrates in my initial experiments Finally, I studied a unique relationship between two ER stress related kinases IRE1 and PKR in lipid induced ER stress conditions. I observed specific inhibition of IRE1’s endoribonuclease activity with an inhibitor, but not its kinase activity, completely blocks PKR activation by lipids. These findings strongly support hat IRE1’s RNAse activity is necessary for PKR kinase activation by lipids. This function of IRE1 RNAse domain is novel and unsuspected. The future goals of this research should be directed to discovering the RNA mediators of IRE1-PKR coupling and understanding their role in mediating the inflammatory and metabolic pathologies associated with chronic metabolic diseases. In conclusion, in my thesis study, I developed novel chemical-genetic approach to specifically modify PKR kinase activity that could be useful in discovering novel PKR substrates. Based on the preliminary findings in this thesis, PKR appears to have many unidentified substrates regulated during lipid induced ER stress. Furthermore, using the chemical-genetic PKR as a tool as well as several other approaches I demonstrated the existence of a unique, functional relationship between IRE1 and PKR in lipotoxicity. In addition, the results in my thesis shows that IRE1’s endoribonuclease activity is required and sufficient for PKR kinase activation by lipids. These findings and tools developed during my studies can be further utilized for analyzing the specific role of PKR in lipotoxicity, which is important for the health consequences of metabolic diseases.
Open Access
Unfolded protein response regulated mirnas in lipotoxic endoplasmic reticulum stress in macrophages
(2014-07) Terzi, Erdem Murat
The proper functioning and the development of the cell is essential to the fitness of the multicellular organisms - any significant disturbances in cellular mechanisms can lead to a multitude of diseases or death. Among these conditions, the global rise in metabolic diseases like obesity, diabetes and atherosclerosis draw significant research interest focus. Since the prevalence of metabolic disorders in the developed and underdeveloped world is expected to increase further in next decade; understanding the contributing cellular mechanisms is vital for the development of new and effective diagnostic and therapeutic tools against this devastating disease cluster. Among the homeostatic cellular pathways important for health the Unfolded Protein Response (UPR) is highly conserved from yeast to mammals. Aside from most conserved UPR branch Inositol-requiring protein 1(IRE1), the mammalian UPR is composed of three different pathways regulated by IRE1, eukaryotic translation initiation factor 2-alpha kinase 3 (PERK), and activating transcription factor 6 (ATF6). The UPR signaling is activated in response to the accumulation of unfolded or misfolded proteins in ER that leads to endoplasmic reticulum (ER) stress. The goal of the UPR is to re-establish ER homeostasis via inhibition of further protein translation and promoting protein folding. In the case of severe or unresolved ER stress, UPR instead triggers a programmed cell death. Recent studies indicate that noncoding regulatory RNAs such as microRNAs (miRNAs) play important role in both upstream and downstream of the UPR. In this thesis, the regulation of miRNA expression by the different UPR arms are examined in macrophages under lipidinduced or lipotoxic ER stress conditions. The results of PCR array studies of RNA obtained from mouse macrophages stressed with a saturated fatty acid, palmitate (PA) , revealed multiple differentially regulated miRNAs. Among these miRNAs, significantly regulated ones were further examined for their regulation by the different arms of the UPR. Towards this end several complementary approaches were taken: First, significantly regulated microRNAs from microRNA PCR array results were analyzed. Next, macrophages were treated with palmitate after transfection with IRE1 and PERK silencer RNA (siRNA) to assess the role of UPR arms in lipid regulated miRNA regulation and the expression of relevant miRNAs was examined in treated macrophages. As an alternative method, macrophages were treated simultaneously with palmitate and specific inhibitors for IRE1’s endoribonuclease or PERK’s kinase activity. Then miRNA expressions were further examined in IRE1 knock-out mouse embryonic fibroblast (MEF) cell lines transfected with the wild type (WT) IRE or the endoribonuclease domain inactive (RD) mutant of IRE1 to verify the specific regulation of the miRNA by the IRE1’s endoribonuclease activity. As a result, upregulation of miR-2137 expression by palmitate was determined as IRE1-endoribonuclease dependent. Next, potential target mRNAs were examined by the overexpression or knock-down of miR-2137 in macrophages. One possible target mRNA was found to be inositol polyphosphate phosphatase-like 1 (Innpl1) . Aside from miR-2137, miR-33 also showed significant alteration upon PA treatment in macrophages. Since the role of miR-33 in atherosclerosis, obesity and insulin resistance is well established, its expression was studied further in RAW 264.7 macrophage cell line and bone marrow-derived primary macrophages after IRE1 and PERK knock-down with siRNA. ATP-binding cassette, sub-family A (ABC1), member 1 (ABCA1), a known target of miR-33, was investigated as down-stream target of miR-33 in PA treated macrophages, in an IRE1 dependent manner. The results of this study uncovered new UPR regulated miRNAs under lipid stress in macrophages. Excess lipid is one of the prominent causes in metabolic diseases – obesity, atherosclerosis, insulin resistance – and these UPR regulated miRNAs may explain the underlying mechanism behind this set of diseases. Furthermore, the possible gene targets for these miRNAs could be responsible for progression of such conditions. Further studies are needed to reveal the exact mechanisms that can lead to the development of novel therapeutic approaches.