Browsing by Subject "Inflammation"
Now showing 1 - 9 of 9
Results Per Page
Sort Options
Item Open Access Angiogenic peptide nanofibers improve wound healing in STZ-induced diabetic rats(American Chemical Society, 2016-06) Senturk, B.; Mercan, S.; Delibasi, T.; Güler, Mustafa O.; Tekinay, A. B.Low expressions of angiogenic growth factors delay the healing of diabetic wounds by interfering with the process of blood vessel formation. Heparin mimetic peptide nanofibers can bind to and enhance production and activity of major angiogenic growth factors, including VEGF. In this study, we showed that heparin mimetic peptide nanofibers can serve as angiogenic scaffolds that allow slow release of growth factors and protect them from degradation, providing a new therapeutic way to accelerate healing of diabetic wounds. We treated wounds in STZ-induced diabetic rats with heparin mimetic peptide nanofibers and studied repair of full-thickness diabetic skin wounds. Wound recovery was quantified by analyses of re-epithelialization, granulation tissue formation and blood vessel density, as well as VEGF and inflammatory response measurements. Wound closure and granulation tissue formation were found to be significantly accelerated in heparin mimetic gel treated groups. In addition, blood vessel counts and the expressions of alpha smooth muscle actin and VEGF were significantly higher in bioactive gel treated animals. These results strongly suggest that angiogenic heparin mimetic nanofiber therapy can be used to support the impaired healing process in diabetic wounds.Item Open Access Identification of RNA-based biomarkers associated with manic episodes and lithium response in bipolar disorder(Bilkent University, 2022-12) Niaz, NoorBipolar disorder (BD) is one of the major mood disorders. A person afflicted with this neuropsychiatric disease undergoes episodes of depression and mania. BD ranks as the highest amongst all the mood disorders for having the most negative affect on a person's life. It is a lifelong illness, which requires constant monitoring and medication. From psychotic behaviours to suicide ideation, this disease is a burden on the afflicted and their families. Although, BD has been shown to have a high heritability factor, none of the studies done so far have been able to identify any biomarkers that could be causative for this disease. It is due to the fact that this disease is multifactorial, in which environment is a major contributing factor. Therefore, we believe that a more 'pattern-seeking' approach would lead to novel findings. We performed gene-set enrichment analysis (GSEA) with BD datasets that consisted of 3 different biological phenotypes; euthymic BD, manic BD and lithium treated BD samples. Since a long time, lithium has been used as 'the leading' drug to treat BD because it functions as a mood stabilizer. Therefore, we also included BD cohorts that had undergone lithium treatment in our analysis. As a result of GSEA, we were able to discover 2 novel patterns. In pattern 1, specific genes were found to up-regulated in euthymic BD and lithium treated cohorts, while the same genes were down-regulated in manic BD cohorts. In pattern 2, the opposite trend was observed, that is; another list of specific genes was down-regulated in euthymic BD and lithium treated cohorts, while they were found to be up-regulated in manic BD. The novelty of utilizing GSEA in our analysis was in the fact that we created our own custom gene-sets. The gene-sets were formed after performing differential gene expression (DEG) analysis on all the 3 types of BD datasets. The advantage of using custom gene-sets was that these were genes representing differential expression in different BD phenotypes, therefore, they were biologically relevant to BD. In the publically available curation of gene-sets on various databases, very few gene-sets represent BD. Hence, the custom gene-sets are more relevant and specific to the disease. Then we proceeded to extract core-enriched genes and performed further analysis, such as, plotting fold-change graphs and performing non-parametric tests. In light of these results, we propose putative biomarkers associated with manic episodes and lithium response in bipolar disorder. We put forth the hypothesis that these patterns can diagnose BD accurately, indicate if a patient is responding to lithium or not, and predict an oncoming manic episode. Therefore, we propose the genes adhering to the discovery patterns as putative biomarkers. Simultaneously, we performed biological analyses and literature review with the list of putative biomarkers. We found out inflammation as a potential underlying cause of pathogenicity in BD. We hypothesize that the process of inflammation is disrupted in BD patients, especially between the different mood states and that in order to treat this disease, inflammation as a pathway should also be targeted. We highlight TNFa as one of the main cytokines that 3 of our biomarkers; ADAMTS9, IL-1 B and STCJ are associated through various pathways, and this disruption of the inflammatory pathway may occur due to alteration in TNFa and biomarkers' levels. We hope that after further, subsequent research, the inclusion of our biomarkers in the clinics will help with the issue of BD misdiagnosis, help save precious treatment time, help with the choice of medication, and help indicate a patient's mood state. Overall, it will help the clinicians to tailor the treatment to every patient's specific profile, making the it easier to design a more personalized treatment strategy.Item Open Access IKKs and tumor cell plasticity(Wiley-Blackwell Publishing Ltd., 2018) Göktuna, Serkan İsmail; Diamanti, M. A.; Chau, T. L.Nuclear factor κB (NF-κB) transcription factors are the central hubs of signaling pathways connecting proinflammatory signals to cell survival, proliferation and cytokine production. In cancers, NF-κB signaling influences many aspects of tumor development, from initiation to metastasis. These functions are mediated by tumor-induced plasticity that allows tumor cells to adapt and survive in changing conditions within the tumor microenvironment. Tumor cell plasticity is shaped by the inflammatory microenvironment in tumors. This review focuses on inhibitor of NF-κB kinases, the direct upstream elements of NF-κB regulation, specifically on their conventional and non-conventional functions in animal models of tumorigenesis from the recent literature.Item Open Access Immunomodulatory potential of human umbilical cord tissue-derived mesenchymal stromal cell (UCX®) exosomes in combination with immunosuppressive “A151” oligodeoxynucleotide(Bilkent University, 2019-07) Bulut, ÖzlemMesenchymal stromal or stem cells (MSCs) modulate immune responses apart from their regenerative capacities. Accumulating evidence suggests that MSCs exert their paracrine effects through extracellular vesicles known as exosomes. In this study, we utilized a particular human umbilical cord tissue-derived MSC type termed as UCX®. UCX® is superior to the gold-standard bone marrow-derived MSCs in terms of immunosuppressive properties. We aimed to characterize and employ UCX® exosomes as cell-free immunosuppressive therapeutic agents. Another aim was to compare the functionalities of exosomes either isolated from 2-dimensional (2D) cultures or isolated from 3-dimensional (3D) spheroid cultures. 3D culture provides better cell-to-cell and cell-to-matrix interactions thereby mimics the in vivo environment better. A synthetic oligodeoxynucleotide called A151 ODN, which consists of 4 repeats of the mammalian telomeric TTAGGG motif, has broad immunosuppressive effects. Delivery of A151 ODN within liposomes or exosomes protects it from degradation by nucleases and improve the desired outcome. We also aimed to combine the immunomodulatory potentials of UCX® exosomes and A151 ODN through direct loading of A151 ODN into exosomes with ~95% efficiency via a dehydration-rehydration-based lyophilization method. First, we determined the binding and internalization kinetics of exosomes with different immune cells. 3D-exosomes interacted with the target cells much faster and more efficiently. Next, we investigated how UCX® exosomes influence Toll-like receptor (TLR) signaling in mouse splenocytes and bone marrow-derived macrophages (BMDMs). 3D-exosomes compared to 2D-exosomes were more potent to suppress IFNγ, IL6, IL12, and to a lesser extent TNFα production mediated by TLR1/2, TLR4, TLR7/8 and TLR9 but not by TLR3 triggering. A151 ODN-loading to either 2D- or 3D-exosomes improved the inhibition of all the above mentioned pro-inflammatory cytokines. Especially 3D-exosomes downregulated co-stimulatory molecules CD80 and CD86 along with MHC-II on BMDMs following TLR stimulation. Macrophage polarization experiments revealed that UCX® exosomes reprogram BMDMs to produce high amounts of nitric oxide and arginase-1 which are the key immunomodulatory factors induced by myeloid-derived suppressor cells (MDSCs) to inhibit T- and NK-cell activity. Besides shifting macrophages to an MDSC-like suppressive phenotype, exosomes also supported expansion of MDSC populations in vivo upon intraperitoneal injection. Next, we tested the therapeutic efficiency of UCX® exosomes with or without A151 ODN in zymosan-induced peritonitis and dextran sodium sulfate (DSS)-induced colitis models in mice. Exosomes could not alleviate zymosan-induced peritonitis which is an acute and severe inflammation. However, 3D-exosomes and A151 ODN-loaded versions of both 2D- and 3D-exosomes remarkably prevented DSS-induced colitis progression. A151 ODN itself was also therapeutic, albeit to a lesser degree. Standalone 3D-exosomes and A151 ODN-loaded exosomes prevented weight loss and colon shortening. All treatments except for 2D-exosomes could restore DSS-induced loss of T-cell numbers and cytokine-producing capacities in mesenteric lymph nodes and spleen. All treatments except for A151 ODN prevented DSS-induced macrophage accumulation in the lymph nodes. 3D-exosomes and A151 ODN-loaded versions of both exosomes normalized serum IL6 levels while only A151 ODN-loaded 3D-exosomes could impact the cytokine production capacities of macrophages. Finally, we tested the effects of UCX® exosomes with or without A151 ODN on wound healing. In vitro, 2D- and 3D-exosomes differentially upregulated the productions of wound healing-related cytokines and growth factors such as IL1α, TGFβ and VEGFα from fibroblast and keratinocyte cell lines. In vivo, in an excisional wound healing model, free or A151 ODN-loaded exosomes did not accelerate wound closure. However, they caused systemic immunosuppression at the late stages of wound healing. Systemic outcomes include reduced inflammatory capacity of macrophages and higher granulocytic MDSC numbers in spleen. A151 ODN-loaded 3D-exosomes also reduced T-cell numbers in spleen and pro-inflammatory cytokine levels in circulation. Taken together, this study revealed that 2D- but more importantly 3D-culturing of umbilical cord MSCs result in functionally different exosomes, 3D culture-derived exosomes display higher immunosuppressive potential, A151 ODN-loading into these exosomes improves immunosuppressive capacity and A151 ODN-loaded UCX® exosomes could be a valuable therapeutic agent for inflammatory and autoimmune disorders.Item Open Access Mesenchymal stem cell derived extracellular vesicles: promising immunomodulators against autoimmune, autoinflammatory disorders and SARS-CoV-2 infection(Scientific and Technical Research Council of Turkey, 2020) Bulut, Özlem; Gürsel, İhsanDiscovery of novel and broad-acting immunomodulators is of critical importance for the prevention and treatment of disorders occurring due to overexuberant immune responseincluding SARS-CoV-2 triggered cytokine storm leading to lung pathology and mortality during the ongoing viral pandemic. Mesenchymal stem/stromal cells (MSCs), highly regarded for their regenerative capacities, also possessesremarkable immunoregulatory functions affecting all types of innate and adaptive immune cells. Owing to that, MSCs have been heavily investigated in clinic for the treatment of autoimmune and inflammatory diseases along with transplant rejection. Extensive research in the last decaderevealed that MSCs carry out most of their functions through paracrine factors which are soluble mediators and extracellular vesicles (EVs). EVs, including exosomes and microvesicles, are an efficient way of intercellular communication due to their unique ability to carry biological messages such as transcription factors, growth factors, cytokines, mRNAs and miRNAs over long distances. EVs originate through direct budding of the cell membrane or the endosomal secretion pathway and they consist of the cytosolic and membrane components of their parent cell. Therefore, they are able to mimic the characteristics of the parent cell, affecting the target cells upon binding or internalization. EVs secreted by MSCs are emerging as a cell-free alternative to MSC-based therapies. MSC EVs are being tested in preclinical and clinical settings where they exhibit exceptional immunosuppressivecapacity. They regulate the migration, proliferation, activation and polarization of various immune cells, promoting a tolerogenic immune response while inhibiting inflammatory response. Being as effective immunomodulators as their parent cells, MSC EVs are also preferable over MSC-based therapies due to their lower risk of immunogenicity, tumorigenicity and overall superior safety. In this review, we present the outcomes of preclinical and clinical studies utilizing MSC EVs as therapeutic agents for the treatment of a wide variety of immunological disorders.Item Open Access Metabolomics approaches in experimental allergic encephalomyelitis(Elsevier, 2018) Battini, B.; Bund, C.; Moussallieh, F. M.; Çiçek, A. Ercüment; De Sèze, J.; Namer, I. J.A myelin basic protein (MBP)-induced experimental allergic encephalomyelitis (EAE) involves paraplegia due to a reversible thoracolumbar spinal cord impairment. The aims of this study were thus to find significant metabolic biomarkers of inflammation and identify the site of inflammation in the central nervous system (CNS) during the acute signs in of the disease using metabolomics. All the EAE samples were associated with higher levels of lactate, ascorbate, glucose and amino acids, and decreased level of N-acetyl-aspartate (NAA) compared to the control group. A decreased NAA level has been particularly shown in lumbar spinal cord in relationship with the clinical signs.Item Open Access Opposing roles of the aldo-keto reductases AKR1B1 and AKR1B10 in colorectal cancer(Springer Netherlands, 2017-09) Taskoparan, B.; Seza, E. G.; Demirkol, S.; Tuncer, S.; Stefek, M.; Gure, A. O.; Banerjee, S.Purpose: Aldo-keto reductases (including AKR1B1 and AKR1B10) constitute a family of oxidoreductases that have been implicated in the pathophysiology of diabetes and cancer, including colorectal cancer (CRC). Available data indicate that, despite their similarities in structure and enzymatic functions, their roles in CRC may be divergent. Here, we aimed to determine the expression and functional implications of AKR1B1 and AKR1B10 in CRC. Methods: AKR1B1 and AKR1B10 gene expression levels were analyzed using publicly available microarray data and ex vivo CRC-derived cDNA samples. Gene Set Enrichment Analysis (GSEA), The Cancer Genome Atlas (TCGA) RNA-seq data and The Cancer Proteome Atlas (TCPA) proteome data were analyzed to determine the effect of high and low AKR1B1 and AKR1B10 expression levels in CRC patients. Proliferation, cell cycle progression, cellular motility, adhesion and inflammation were determined in CRC-derived cell lines in which these genes were either exogenously overexpressed or silenced. Results: We found that the expression of AKR1B1 was unaltered, whereas that of AKR1B10 was decreased in primary CRCs. GSEA revealed that, while high AKR1B1 expression was associated with increased cell cycle progression, cellular motility and inflammation, high AKR1B10 expression was associated with a weak inflammatory phenotype. Functional studies carried out in CRC-derived cell lines confirmed these data. Microarray data analysis indicated that high expression levels of AKR1B1 and AKR1B10 were significantly associated with shorter and longer disease-free survival rates, respectively. A combined gene expression signature of AKR1B10 (low) and AKR1B1 (high) showed a better prognostic stratification of CRC patients independent of confounding factors. Conclusions: Despite their similarities, the expression levels and functions of AKR1B1 and AKR1B10 are highly divergent in CRC, and they may have prognostic implications.Item Open Access Therapeutic potential of an immunosuppressive oligodeoxynucleotide encapsulated within liposomes on bleomycin-induced mouse model of lung inflammation and fibrosis(Bilkent University, 2019-05) Kılıç, GizemSystemic sclerosis (SSc) is an autoimmune/autoinflammatory disease with unknown etiology. It is characterized by vascular dysfunction, inflammation and disseminated fibrosis of skin or internal organs. Although its prevalence is low, development of fibrosis on internal organs and lack of a curative treatment result in high morbidity. Current therapies targeting specific symptoms such as interstitial lung disease, Raynaud’s phenomenon and pulmonary arterial hypertension are inefficient, and at best, temporarily relieves the symptoms throughout the course of the treatment. Herein, we investigated the therapeutic potential of an immunosuppressive oligodeoxynucleotide expressing TTAGGG telomeric repeats which is known as the “A151 ODN” on bleomycin-induced mouse model of systemic sclerosis. A151 ODN is the single stranded synthetic form of the telomeric repeat sequence expressed on mammalian chromosome, and it contains four repeats of “TTAGGG” motif. In order to enhance the therapeutic effectivity while protecting its digestion from nuclease activity following administration, we encapsulated A151 ODN within anionic liposomes. Since pattern recognition receptors and their signaling pathways were demonstrated to initiate inflammation in SSc, we first explored the immunosuppressive capacity of A151 ODN by analyzing in vitro cytokine productions and surface marker expression levels. Similar with the previous findings, A151 ODN was highly potent to abolish cytokine production in response to TLR9 induction. Although A151 ODN by itself was not very effective to suppress cytokine secretion following TLR1/2 and TLR4 induction, encapsulation within anionic liposomes further improved the immunosuppressive potential in response to TLR engagement. Furthermore, flow cytometry analyses revealed that A151 ODN decreased antigen presentation capacity and activation of bone-marrow derived macrophages (BMDMs) in response to TLR stimulation which was demonstrated by the reduction in levels of surface MHCII and co-stimulatory molecules as well as proteins having role on macrophage adherence and migration. A151 ODN also inhibited transcription of two major genes known to play a critical role on the development of fibrosis, TGFβ and Col1a1, from fibroblasts. Following these promising results on A151 ODN’s immunosuppressive and anti-fibrotic potential, we tested its therapeutic role on bleomycin-induced lung inflammation and fibrosis on mice which reflects different phases of systemic sclerosis. First in vivo experiment that A151 ODN was used prior to bleomycin administration revealed that A151 ODN could prevent development of systemic sclerosis by reducing immune cell recruitment into alveolar space and suppressing the secretion of inflammatory cytokines. After that, we investigated if A151 ODN could abolish established lung inflammation triggered by bleomycin instillation. For that, we treated animals with an A151 ODN either in free form or encapsulated within anionic liposomes after lung inflammation was initiated following bleomycin instillation. Data indicated that A151 ODN reduced macrophage activation marker expressions, monocyte and neutrophil infiltration into alveolar space. Moreover, suppression on immune cells activation in bronchoalveolar lavage fluid (BALF) correlated with the inhibited cytokine production. As a result of reduced inflammation, pro-fibrotic gene expressions were less in A151 ODN-treated mice. Of note, liposomal encapsulation provided reduced gene expressions while failed to further enhance the immunosuppressive potential on surface marker expression or cytokine secretion of A151 ODN. Lastly, we tested whether treatment with liposome-encapsulated A151 ODN is still effective to regress fibrosis once it has been developed; therefore, we treated mice with single injection of liposomal A151 on different time points. Unfortunately, single instillation was insufficient to decrease fibrosis and macrophage activation as well as cytokine production. Taken together, our findings indicated that liposome-encapsulated A151 ODN is very potent to attenuate the lung inflammation whereas single injection was ineffective to regress established lung fibrosis.Item Open Access Vesicular HMGB1 release from neurons stressed with spreading depolarization enables confined inflammatory signaling to astrocytes(BioMed Central Ltd., 2023-12-11) Kaya, Z.; Belder, N.; Sever-Bahcekapili, M.; Donmez-Demir, B.; Erdener, Ş.; Bozbeyoğlu, Naz; Bagci, C.; Eren-Kocak, E.; Yemisci, M.; Karatas, H.; Erdemli, E.; Gürsel, İhsan; Dalkara, T.The role of high mobility group box 1 (HMGB1) in inflammation is well characterized in the immune system and in response to tissue injury. More recently, HMGB1 was also shown to initiate an “inflammatory signaling cascade” in the brain parenchyma after a mild and brief disturbance, such as cortical spreading depolarization (CSD), leading to headache. Despite substantial evidence implying a role for inflammatory signaling in prevalent neuropsychiatric disorders such as migraine and depression, how HMGB1 is released from healthy neurons and how inflammatory signaling is initiated in the absence of apparent cell injury are not well characterized. We triggered a single cortical spreading depolarization by optogenetic stimulation or pinprick in naïve Swiss albino or transgenic Thy1-ChR2-YFP and hGFAP-GFP adult mice. We evaluated HMGB1 release in brain tissue sections prepared from these mice by immunofluorescent labeling and immunoelectron microscopy. EzColocalization and Costes thresholding algorithms were used to assess the colocalization of small extracellular vesicles (sEVs) carrying HMGB1 with astrocyte or microglia processes. sEVs were also isolated from the brain after CSD, and neuron-derived sEVs were captured by CD171 (L1CAM). sEVs were characterized with flow cytometry, scanning electron microscopy, nanoparticle tracking analysis, and Western blotting. We found that HMGB1 is released mainly within sEVs from the soma of stressed neurons, which are taken up by surrounding astrocyte processes. This creates conditions for selective communication between neurons and astrocytes bypassing microglia, as evidenced by activation of the proinflammatory transcription factor NF-ĸB p65 in astrocytes but not in microglia. Transmission immunoelectron microscopy data illustrated that HMGB1 was incorporated into sEVs through endosomal mechanisms. In conclusion, proinflammatory mediators released within sEVs can induce cell-specific inflammatory signaling in the brain without activating transmembrane receptors on other cells and causing overt inflammation.