cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1603014.v2
title: Soluble mediators

description: Measurement of cytokines (IL-10, IL-12 p70, IFN-gamma, TGF-beta), soluble CD83 and Prostaglandin E2 (PGE2)
DOI: 10.6084/m9.figshare.1602765.v1
title: The Tm7sf2 Gene Deficiency Protects Mice against Endotoxin-Induced Acute Kidney Injury

description: INTRODUCTION: <em>Tm7sf2</em> gene codifies for 3β-hydroxysterol Δ14-reductase, an endoplasmic reticulum resident protein involved in cholesterol biosynthesis (1, 2). Cholesterol is an essential component of plasma membranes, and it can also contribute to multiple cellular functions or to injury response. Connection between cholesterol metabolism and inflammation is exemplified by <em>Tm7sf2</em>-KO mice, that under stress conditions show an inflammatory phenotype (NF-kB activation and TNFα upregulation) (3). In mouse skin, the loss of <em>Tm7sf2</em> gene reduces cholesterol/cholesterol sulfate levels following inflammatory insults, and increases susceptibility to skin papillomas formation (4). AIM OF THE STUDY: Investigation of the role of <em>Tm7sf2</em> gene in renal cholesterol/lipid metabolism and inflammatory response, in an in vivo model of acute kidney injury induced by the administration of lipopolysaccharide (LPS). MATERIALS AND METHODS: Male C57BL/6, <em>Tm7sf2+/+</em>, and<em> Tm7sf2-/-</em> mice were intraperitoneally injected with a single dose of LPS (5mg/Kg) or vehicle (0.9% saline) and sacrificed at selected time points. - Blood urea nitrogen (BUN) and serum creatinine assessment - Hematoxylin/eosin (HE), Oil Red O (ORO) stain, and immunohistochemistry on kidney sections - Renal cortex lipid content (TLC); mRNA and protein analysis by qPCR or Western blotting, respectively RESULTS: <em>Tm7sf2</em>-null mice are protected against LPS-induced acute kidney injury without affecting kidney cholesterol levels. <em>Tm7sf2</em> insufficiency reduces renal LPS-triggered NF-κB activation and iNOS expression <em>Tm7sf2</em> deficiency reduces neutral lipids accumulation in kidney The lack of <em>Tm7sf2</em> gene leads to FXR activation CONCLUSIONS: - The lack of <em>Tm7sf2</em> gene results in kidney endotoxin tolerance state contributing to dampen the inflammatory response generated by LPS exposure, i.e. NF-kB activation/iNOS expression - Lower ectopic accumulation of triglycerides (TG) in KO kidney could reduce the lipotoxicity due to secondary metabolites generation - We hypotesize that increased FXR activation in Tm7sf2-/- kidney antagonizes NF-kB/iNOS proinflammatory pathway and TG biogenesis process
DOI: 10.6084/m9.figshare.1603017.v3
title: The polyunsaturated fatty acids arachidonic acid and docosahexaenoic acid induce mouse dendritic cells maturation but reduce T-cell responses in vitro

description: The polyunsaturated fatty acids arachidonic acid and docosahexaenoic acid induce mouse dendritic cells maturation but reduce T-cell responses in vitro
DOI: 10.6084/m9.figshare.1602762
title: Gaussian Job Archive for C18H30Br8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1603014.v1
title: Soluble mediators

description: Measurement of cytokines (IL-10, IL-12 p70, IFN-gamma, TGF-beta), soluble CD83 and Prostaglandin E2 (PGE2)
DOI: 10.6084/m9.figshare.1602762.v1
title: Gaussian Job Archive for C18H30Br8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1602010
title: The histone demethylase KDM5A is a key factor for the resistance to temozolomide in glioblastoma

description: Notwithstanding current multimodal treatment, including surgery, radiotherapy and chemotherapy with temozolomide (TMZ), median survival of glioblastoma (GBM) patients is about 14 months, due to the rapid emergence of cell clones resistant to treatment. Therefore, understanding the mechanisms underlying chemoresistance is mandatory to improve treatments' outcome. We generated TMZ resistant cells (TMZ-R) from a GBM cell line and from cancer stem cell-enriched cultures isolated from human GBMs. We demonstrated that TMZ resistance is partially reverted by “drug wash-out” suggesting the contribution of epigenetic mechanisms in drug resistance and supporting the possibility of TMZ rechallenge in GBM patients after prior drug exposure. The expression of histone lysine demethylase genes (<i>KDMs</i>) was increased in TMZ-R cells compared to parental cells, and TMZ resistance or restored sensitivity was mimicked by over-expressing or inactivating <i>KDM5A</i>. Methylation and expression of O6-methylguanine-DNA methyltransferase (MGMT) and drug efflux mechanisms were not altered in TMZ-R cells compared to parental TMZ sensitive cells. TMZ-R cells transiently acquired morphologic and molecular characteristics of differentiated tumor cells, features that were lost after drug wash-out. In conclusion, we demonstrated that treatment-induced TMZ resistance in GBM involves epigenetic mechanisms in a subset of slow-cycling and transiently partially differentiated cells that escape drug cytotoxicity, overcome G2 checkpoint and sustain clonal growth. We found that TMZ-R cells are sensitive to histone deacethylase inhibitors (HDACi) that synergize with TMZ. This strong synergism could be exploited to develop novel combined adjuvant therapies for this rapidly progressing and invariably lethal cancer.
DOI: 10.6084/m9.figshare.1603017.v4
title: The polyunsaturated fatty acids arachidonic acid and docosahexaenoic acid induce mouse dendritic cells maturation but reduce T-cell responses in vitro

description: The polyunsaturated fatty acids arachidonic acid and docosahexaenoic acid induce mouse dendritic cells maturation but reduce T-cell responses in vitro
DOI: 10.6084/m9.figshare.1602009
title: Longevity of U cells of differentiated yeast colonies grown on respiratory medium depends on active glycolysis

description: Colonies of <i>Saccharomyces cerevisiae</i> laboratory strains pass through specific developmental phases when growing on solid respiratory medium. During entry into the so-called alkali phase, in which ammonia signaling is initiated, 2 prominent cell types are formed within the colonies: U cells in upper colony regions, which have a longevity phenotype and activate the expression of a large number of metabolic genes, and L cells in lower regions, which die more quickly and exhibit a starvation phenotype. Here, we performed a detailed analysis of the activities of enzymes of central carbon metabolism in lysates of both cell types and determined several fermentation end products, showing that previously reported expression differences are reflected in the different enzymatic capabilities of each cell type. Hence, U cells, despite being grown on respiratory medium, behave as fermenting cells, whereas L cells rely on respiratory metabolism and possess active gluconeogenesis. Using a spectrum of different inhibitors, we showed that glycolysis is essential for the formation, and particularly, the survival of U cells. We also showed that β-1,3-glucans that are released from the cell walls of L cells are the most likely source of carbohydrates for U cells.
DOI: 10.6084/m9.figshare.1603017.v6
title: The polyunsaturated fatty acids arachidonic acid and docosahexaenoic acid induce mouse dendritic cells maturation but reduce T-cell responses in vitro

description: The polyunsaturated fatty acids arachidonic acid and docosahexaenoic acid induce mouse dendritic cells maturation but reduce T-cell responses in vitro
DOI: 10.6084/m9.figshare.1602008
title: Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis

description: The nucleolus is considered to be a stress sensor and rDNA-based regulation of cellular senescence and longevity has been proposed. However, the role of rDNA in the maintenance of genome integrity has not been investigated in detail. Using genomically diverse industrial yeasts as a model and array-based comparative genomic hybridization (aCGH), we show that chromosome level may be balanced during passages and as a response to alcohol stress that may be associated with changes in rDNA pools. Generation- and ethanol-mediated changes in genes responsible for protein and DNA/RNA metabolism were revealed using next-generation sequencing. Links between redox homeostasis, DNA stability, and telomere and nucleolus states were also established. These results suggest that yeast genome is dynamic and chromosome homeostasis may be controlled by rDNA.
DOI: 10.6084/m9.figshare.1603017.v5
title: The polyunsaturated fatty acids arachidonic acid and docosahexaenoic acid induce mouse dendritic cells maturation but reduce T-cell responses in vitro

description: The polyunsaturated fatty acids arachidonic acid and docosahexaenoic acid induce mouse dendritic cells maturation but reduce T-cell responses in vitro
DOI: 10.6084/m9.figshare.1602010.v2
title: The histone demethylase KDM5A is a key factor for the resistance to temozolomide in glioblastoma

description: Notwithstanding current multimodal treatment, including surgery, radiotherapy and chemotherapy with temozolomide (TMZ), median survival of glioblastoma (GBM) patients is about 14 months, due to the rapid emergence of cell clones resistant to treatment. Therefore, understanding the mechanisms underlying chemoresistance is mandatory to improve treatments' outcome. We generated TMZ resistant cells (TMZ-R) from a GBM cell line and from cancer stem cell-enriched cultures isolated from human GBMs. We demonstrated that TMZ resistance is partially reverted by “drug wash-out” suggesting the contribution of epigenetic mechanisms in drug resistance and supporting the possibility of TMZ rechallenge in GBM patients after prior drug exposure. The expression of histone lysine demethylase genes (<i>KDMs</i>) was increased in TMZ-R cells compared to parental cells, and TMZ resistance or restored sensitivity was mimicked by over-expressing or inactivating <i>KDM5A</i>. Methylation and expression of O6-methylguanine-DNA methyltransferase (MGMT) and drug efflux mechanisms were not altered in TMZ-R cells compared to parental TMZ sensitive cells. TMZ-R cells transiently acquired morphologic and molecular characteristics of differentiated tumor cells, features that were lost after drug wash-out. In conclusion, we demonstrated that treatment-induced TMZ resistance in GBM involves epigenetic mechanisms in a subset of slow-cycling and transiently partially differentiated cells that escape drug cytotoxicity, overcome G2 checkpoint and sustain clonal growth. We found that TMZ-R cells are sensitive to histone deacethylase inhibitors (HDACi) that synergize with TMZ. This strong synergism could be exploited to develop novel combined adjuvant therapies for this rapidly progressing and invariably lethal cancer.
DOI: 10.6084/m9.figshare.1602009.v2
title: Longevity of U cells of differentiated yeast colonies grown on respiratory medium depends on active glycolysis

description: Colonies of <i>Saccharomyces cerevisiae</i> laboratory strains pass through specific developmental phases when growing on solid respiratory medium. During entry into the so-called alkali phase, in which ammonia signaling is initiated, 2 prominent cell types are formed within the colonies: U cells in upper colony regions, which have a longevity phenotype and activate the expression of a large number of metabolic genes, and L cells in lower regions, which die more quickly and exhibit a starvation phenotype. Here, we performed a detailed analysis of the activities of enzymes of central carbon metabolism in lysates of both cell types and determined several fermentation end products, showing that previously reported expression differences are reflected in the different enzymatic capabilities of each cell type. Hence, U cells, despite being grown on respiratory medium, behave as fermenting cells, whereas L cells rely on respiratory metabolism and possess active gluconeogenesis. Using a spectrum of different inhibitors, we showed that glycolysis is essential for the formation, and particularly, the survival of U cells. We also showed that β-1,3-glucans that are released from the cell walls of L cells are the most likely source of carbohydrates for U cells.
DOI: 10.6084/m9.figshare.1602008.v2
title: Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis

description: The nucleolus is considered to be a stress sensor and rDNA-based regulation of cellular senescence and longevity has been proposed. However, the role of rDNA in the maintenance of genome integrity has not been investigated in detail. Using genomically diverse industrial yeasts as a model and array-based comparative genomic hybridization (aCGH), we show that chromosome level may be balanced during passages and as a response to alcohol stress that may be associated with changes in rDNA pools. Generation- and ethanol-mediated changes in genes responsible for protein and DNA/RNA metabolism were revealed using next-generation sequencing. Links between redox homeostasis, DNA stability, and telomere and nucleolus states were also established. These results suggest that yeast genome is dynamic and chromosome homeostasis may be controlled by rDNA.
DOI: 10.6084/m9.figshare.1602010.v1
title: The histone demethylase KDM5A is a key factor for the resistance to temozolomide in glioblastoma

description: Notwithstanding current multimodal treatment, including surgery, radiotherapy and chemotherapy with temozolomide (TMZ), median survival of glioblastoma (GBM) patients is about 14 months, due to the rapid emergence of cell clones resistant to treatment. Therefore, understanding the mechanisms underlying chemoresistance is mandatory to improve treatments' outcome. We generated TMZ resistant cells (TMZ-R) from a GBM cell line and from cancer stem cell-enriched cultures isolated from human GBMs. We demonstrated that TMZ resistance is partially reverted by “drug wash-out” suggesting the contribution of epigenetic mechanisms in drug resistance and supporting the possibility of TMZ rechallenge in GBM patients after prior drug exposure. The expression of histone lysine demethylase genes (<i>KDMs</i>) was increased in TMZ-R cells compared to parental cells, and TMZ resistance or restored sensitivity was mimicked by over-expressing or inactivating <i>KDM5A</i>. Methylation and expression of O6-methylguanine-DNA methyltransferase (MGMT) and drug efflux mechanisms were not altered in TMZ-R cells compared to parental TMZ sensitive cells. TMZ-R cells transiently acquired morphologic and molecular characteristics of differentiated tumor cells, features that were lost after drug wash-out. In conclusion, we demonstrated that treatment-induced TMZ resistance in GBM involves epigenetic mechanisms in a subset of slow-cycling and transiently partially differentiated cells that escape drug cytotoxicity, overcome G2 checkpoint and sustain clonal growth. We found that TMZ-R cells are sensitive to histone deacethylase inhibitors (HDACi) that synergize with TMZ. This strong synergism could be exploited to develop novel combined adjuvant therapies for this rapidly progressing and invariably lethal cancer.
DOI: 10.6084/m9.figshare.1602008.v1
title: Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis

description: The nucleolus is considered to be a stress sensor and rDNA-based regulation of cellular senescence and longevity has been proposed. However, the role of rDNA in the maintenance of genome integrity has not been investigated in detail. Using genomically diverse industrial yeasts as a model and array-based comparative genomic hybridization (aCGH), we show that chromosome level may be balanced during passages and as a response to alcohol stress that may be associated with changes in rDNA pools. Generation- and ethanol-mediated changes in genes responsible for protein and DNA/RNA metabolism were revealed using next-generation sequencing. Links between redox homeostasis, DNA stability, and telomere and nucleolus states were also established. These results suggest that yeast genome is dynamic and chromosome homeostasis may be controlled by rDNA.
DOI: 10.6084/m9.figshare.1602009.v1
title: Longevity of U cells of differentiated yeast colonies grown on respiratory medium depends on active glycolysis

description: Colonies of <i>Saccharomyces cerevisiae</i> laboratory strains pass through specific developmental phases when growing on solid respiratory medium. During entry into the so-called alkali phase, in which ammonia signaling is initiated, 2 prominent cell types are formed within the colonies: U cells in upper colony regions, which have a longevity phenotype and activate the expression of a large number of metabolic genes, and L cells in lower regions, which die more quickly and exhibit a starvation phenotype. Here, we performed a detailed analysis of the activities of enzymes of central carbon metabolism in lysates of both cell types and determined several fermentation end products, showing that previously reported expression differences are reflected in the different enzymatic capabilities of each cell type. Hence, U cells, despite being grown on respiratory medium, behave as fermenting cells, whereas L cells rely on respiratory metabolism and possess active gluconeogenesis. Using a spectrum of different inhibitors, we showed that glycolysis is essential for the formation, and particularly, the survival of U cells. We also showed that β-1,3-glucans that are released from the cell walls of L cells are the most likely source of carbohydrates for U cells.
DOI: 10.6084/m9.figshare.1602000
title: Mitophagy is required for mitochondrial biogenesis and myogenic differentiation of C2C12 myoblasts

description: Myogenesis is a crucial process governing skeletal muscle development and homeostasis. Differentiation of primitive myoblasts into mature myotubes requires a metabolic switch to support the increased energetic demand of contractile muscle. Skeletal myoblasts specifically shift from a highly glycolytic state to relying predominantly on oxidative phosphorylation (OXPHOS) upon differentiation. We have found that this phenomenon requires dramatic remodeling of the mitochondrial network involving both mitochondrial clearance and biogenesis. During early myogenic differentiation, autophagy is robustly upregulated and this coincides with DNM1L/DRP1 (dynamin 1-like)-mediated fragmentation and subsequent removal of mitochondria via SQSTM1 (sequestosome 1)-mediated mitophagy. Mitochondria are then repopulated via PPARGC1A/PGC-1α (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha)-mediated biogenesis. Mitochondrial fusion protein OPA1 (optic atrophy 1 [autosomal dominant]) is then briskly upregulated, resulting in the reformation of mitochondrial networks. The final product is a myotube replete with new mitochondria. Respirometry reveals that the constituents of these newly established mitochondrial networks are better primed for OXPHOS and are more tightly coupled than those in myoblasts. Additionally, we have found that suppressing autophagy with various inhibitors during differentiation interferes with myogenic differentiation. Together these data highlight the integral role of autophagy and mitophagy in myogenic differentiation.
DOI: 10.6084/m9.figshare.1602000.v1
title: Mitophagy is required for mitochondrial biogenesis and myogenic differentiation of C2C12 myoblasts

description: Myogenesis is a crucial process governing skeletal muscle development and homeostasis. Differentiation of primitive myoblasts into mature myotubes requires a metabolic switch to support the increased energetic demand of contractile muscle. Skeletal myoblasts specifically shift from a highly glycolytic state to relying predominantly on oxidative phosphorylation (OXPHOS) upon differentiation. We have found that this phenomenon requires dramatic remodeling of the mitochondrial network involving both mitochondrial clearance and biogenesis. During early myogenic differentiation, autophagy is robustly upregulated and this coincides with DNM1L/DRP1 (dynamin 1-like)-mediated fragmentation and subsequent removal of mitochondria via SQSTM1 (sequestosome 1)-mediated mitophagy. Mitochondria are then repopulated via PPARGC1A/PGC-1α (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha)-mediated biogenesis. Mitochondrial fusion protein OPA1 (optic atrophy 1 [autosomal dominant]) is then briskly upregulated, resulting in the reformation of mitochondrial networks. The final product is a myotube replete with new mitochondria. Respirometry reveals that the constituents of these newly established mitochondrial networks are better primed for OXPHOS and are more tightly coupled than those in myoblasts. Additionally, we have found that suppressing autophagy with various inhibitors during differentiation interferes with myogenic differentiation. Together these data highlight the integral role of autophagy and mitophagy in myogenic differentiation.
DOI: 10.6084/m9.figshare.1602002.v2
title: Disruption of microtubules in plants suppresses macroautophagy and triggers starch excess-associated chloroplast autophagy

description: Microtubules, the major components of cytoskeleton, are involved in various fundamental biological processes in plants. Recent studies in mammalian cells have revealed the importance of microtubule cytoskeleton in autophagy. However, little is known about the roles of microtubules in plant autophagy. Here, we found that ATG6 interacts with TUB8/β-tubulin 8 and colocalizes with microtubules in <i>Nicotiana benthamiana</i>. Disruption of microtubules by either silencing of tubulin genes or treatment with microtubule-depolymerizing agents in <i>N. benthamiana</i> reduces autophagosome formation during upregulation of nocturnal or oxidation-induced macroautophagy. Furthermore, a blockage of leaf starch degradation occurred in microtubule-disrupted cells and triggered a distinct ATG6-, ATG5- and ATG7-independent autophagic pathway termed starch excess-associated chloroplast autophagy (SEX chlorophagy) for clearance of dysfunctional chloroplasts. Our findings reveal that an intact microtubule network is important for efficient macroautophagy and leaf starch degradation.
DOI: 10.6084/m9.figshare.1602002.v1
title: Disruption of Microtubules in Plants Suppresses Macroautophagy and Triggers Starch Excess-Associated Chloroplast Autophagy

description: Microtubules, the major components of cytoskeleton, are involved in various fundamental biological processes in plants. Recent studies in mammalian cells have revealed the importance of microtubule cytoskeleton in autophagy. However, little is known about the roles of microtubules in plant autophagy. Here, we found that ATG6 (AUTOPHAGY 6) interacts with TUB8/β-tubulin 8 (TUBULIN BETA 8) and colocalizes with microtubules in <i>Nicotiana benthamiana</i>. Disruption of microtubules by either silencing of tubulin genes or treatment with microtubule-depolymerizing agents in <i>N. benthamiana</i> reduces autophagosome formation during upregulation of nocturnal or oxidation-induced macroautophagy. Furthermore, a blockage of leaf starch degradation occurred in microtubule-disrupted cells and triggered a distinct ATG6-, ATG5- and ATG7-independent autophagic pathway termed starch excess-associated chloroplast autophagy (SEX chlorophagy) for clearance of dysfunctional chloroplasts. Our findings reveal that an intact microtubule network is important for efficient macroautophagy and leaf starch degradation.