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Project description:Whether and how the reactive oxygen species generated by hepatic stellate cells (HSCs) promote immune evasion of hepatocellular carcinoma (HCC) remains mysteriouss. Therefore, investigating the function of superoxide anion, the firstly generated reactive oxygen species, during the immune evasion become necessary. In this work, we establish a novel in situ imaging method for visualization of superoxide anion changes in HSCs based on a new two-photon fluorescence probe TPH. TPH comprises recognition group for superoxide anion and HSCs targeting peptides. We observe that superoxide anion in HSCs gradually rose, impairing the infiltration of CD8+ T cells in HCC mice. Further studies reveal that the cyclin-dependent kinase 4 is deactivated by superoxide anion, and then cause the up-regulation of PD-L1. Our work provides molecular insights into HSC-mediated immune evasion of HCC, which may represent potential targets for HCC immunotherapy.
2024-04-08 | PXD051328 |
Project description:Superoxide radical anion and other Reactive Oxygen Species are constantly produced during respiration. In mitochondria, the dismutation of the superoxide radical anion is accelerated by the mitochondrial superoxide dismutase 2 (SOD2), an enzyme that has been traditionally associated with antioxidant protection. However, increases in SOD2 expression promote oxidative stress, indicating that there may be a prooxidant role for SOD2. We show that SOD2, which normally binds manganese, can incorporate iron and generate an alternative isoform with peroxidase activity. The switch from manganese to iron allows FeSOD2 to utilize H2O2 to promote oxidative stress. We found that FeSOD2 is formed in cultured cells. FeSOD2 causes mitochondrial dysfunction and higher levels of oxidative stress in cultured cells. We show that formation of FeSOD2 converts an antioxidant defense into a prooxidant peroxidase that leads to cellular changes seen in multiple human diseases.
2017-12-05 | GSE106206 | GEO
Project description:Global Gene Expression Analysis Reveals Differences in Cellular Responses to Hydroxyl- and Superoxide Anion Radical-...
| PRJNA115869 | ENA
Project description:Investigation of whole genome gene expression level changes in Arabidopsis roots by the effect of light. Plant growth is sustained by a continuous cell division in meristems followed by cell differentiation and elongation. We have found that in Arabidopsis thaliana roots, flavonols play a key role in regulating the transition from cell division to differentiation. Using an engineered device to grow roots in darkness, but shoot in light cycle, coupled with transcriptomic and metabolomics analysis, we deciphered that flavonols accumulation regulates proliferation-promoting levels of auxin-PLETHORA and superoxide anion (O2-). High flavonols levels restrict auxin transport and the PLETHORA gradient but also superoxide radical content, promoting an accelerated cell differentiation. Furthermore, cytokinin-SHY2 and H2O2-UPB1 pathways, which promote differentiation and, respectively, antagonize auxin and O2- activity, increase flavonols biosynthesis establishing mutual interactions among these pathways. Flavonols function as positional signals integrating hormonal and ROS pathways to determine final organ growth. This work analyze the effect of root illumination in gene transcription. Details of how plants and roots are grown are described in Silva et al. (submitted) A six chip study using total RNA extracted from three independent experiments of Arabidopsis roots growing in presence of light and three independent experiments of Arabidopsis roots growing without light.
2016-04-01 | E-GEOD-68093 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in Arabidopsis roots by the effect of light. Plant growth is sustained by a continuous cell division in meristems followed by cell differentiation and elongation. We have found that in Arabidopsis thaliana roots, flavonols play a key role in regulating the transition from cell division to differentiation. Using an engineered device to grow roots in darkness, but shoot in light cycle, coupled with transcriptomic and metabolomics analysis, we deciphered that flavonols accumulation regulates proliferation-promoting levels of auxin-PLETHORA and superoxide anion (O2-). High flavonols levels restrict auxin transport and the PLETHORA gradient but also superoxide radical content, promoting an accelerated cell differentiation. Furthermore, cytokinin-SHY2 and H2O2-UPB1 pathways, which promote differentiation and, respectively, antagonize auxin and O2- activity, increase flavonols biosynthesis establishing mutual interactions among these pathways. Flavonols function as positional signals integrating hormonal and ROS pathways to determine final organ growth. This work analyze the effect of root illumination in gene transcription. Details of how plants and roots are grown are described in Silva et al. (submitted)
2016-04-01 | GSE68093 | GEO
Project description:The development of whole-genome bisulfite sequencing (WGBS) has led to a number of exciting discoveries about how genomes utilize DNA methylation and has led to a plethora of novel testable hypotheses. Methods for constructing sodium bisulfite-converted and amplified libraries have recently excelled to the point that the bottleneck for experiments that use WGBS has shifted to data analysis and interpretation. Here we present empirical evidence for an over-representation of methylated DNA from WGBS. This enrichment for methylated DNA is exacerbated by higher cycles of PCR and is influenced by the type of uracil-insensitive DNA polymerase used for amplifying the sequencing library. Future efforts to computationally correct for this enrichment bias will be essential to increasing the accuracy of determining methylation levels for individual cytosines. MethylC-Seq of Arabidopsis thaliana
2014-09-11 | E-GEOD-58217 | biostudies-arrayexpress
Project description:We used unbiased whole genome bisulfite sequencing (WGBS) to identify DNA methylation changes in the intestinal stem cells (ISCs) or their progeny during the suckling period of mouse colon development. Lgr5-EGFP mice were used to identify ISC populations in the colons. WGBS were performed using EGFP labeled Lgr5+ ISCs and epithelial cell adhesion molecule (EpCAM) labeled epithelial cells isolated at the beginning and end of the suckling period (postnatal day 0-P0 and P21).
2015-08-25 | E-GEOD-58532 | biostudies-arrayexpress
Project description:Purpose: Lactococcus lactis is the primary constituent of many industrial starter cultures used in food fermentations. However, this bacterium is exposed to several stressful conditions during the industrial process. L. lactis TOMSC161 has been shown to resist better to freeze-drying and storage when cells are harvested at the late stationary compared to the early stationary phase. Methods: In this work, the physiological changes that occur during growth (early and late stationary phases) were studied using transcriptomic, proteomic and cytometric approaches in order to elucidate the cell mechanisms involved in the stress tolerance of L. lactis TOMSC161 to freeze-drying and storage processes. Results: The majority of altered abundances for genes determined by transcriptomic analysis indicated a slowdown at the late stationary phase in general metabolism and in the incomplete reduction of O2 leading to reactive oxygen species (ROS), in comparison to the early stationary phase. Furthermore, the expression of genes involved in general and oxidative stress responses was over-expressed at the late stationary phase when compared to the early stationary phase, thus explaining the better resistance to freeze-drying and the storage of cells harvested after six hours of stationary phase. Superoxide anion detection was performed by flow cytometry and related to the ROS production of starters. Superoxide anion concentration was lower for cells harvested at the late stationary phase when compared to cells harvested at the early stationary phase. Conclusions: L. lactis TOMSC161 was thus able to develop an oxidative stress “pre-adaptation” during the stationary phase making it possible to better resist freeze-drying and storage stresses and especially oxidative stress.
2018-10-30 | GSE74554 | GEO
Project description:Whole genome bisulfite sequencing (WGBS) of the NA18507 (Yoruba) lymphoblastoid cell line high resolution methylome of one cell type
2016-02-25 | E-GEOD-66285 | biostudies-arrayexpress
Project description:Although the accumulation of neutrophils in the lungs and airways is common to many inflammatory lung diseases, including acute lung injury, the alterations that neutrophils undergo as they leave the peripheral circulation and migrate into the lungs have not been well characterized. Human volunteers were exposed to endotoxin by bronchoscopic instillation. The resulting air space neutrophil accumulation and peripheral blood neutrophils were isolated 16 h later, compared with circulating neutrophils isolated before or after to the pulmonary endotoxin exposure, and compared with circulating neutrophils exposed to endotoxin in vitro. Microarray analysis was performed on air space, circulatory, and in vitro endotoxin-stimulated neutrophils. Functional analysis included the determination of neutrophil apoptosis, chemotaxis, release of cytokines and growth factors, and superoxide anion release. Dramatic gene expression differences were apparent between air space and circulating neutrophils: approximately 15% of expressed genes have altered expression levels, including broad increases in inflammatory- and chemotaxis-related genes, as well as antiapoptotic and IKK-activating pathways. Functional analysis of air space compared with circulating neutrophils showed increased superoxide release, diminished apoptosis, decreased IL-8-induced chemotaxis, and a pattern of IL-8, macrophage inflammatory protein-1beta, monocyte chemoattractant protein-1, and tumor necrosis factor-alpha release different from either unstimulated or LPS-stimulated circulating neutrophils. Many of these changes are not elicited by in vitro treatment with endotoxin. Limited differences were detected between circulating neutrophils isolated before and 16 h after pulmonary endotoxin instillation. These results suggest that neutrophils sequestered in the lung become fundamentally different from those resident in the circulation, and this difference is distinct from in vitro activation with endotoxin.
2007-10-02 | E-GEOD-2322 | biostudies-arrayexpress