Ontology highlight
ABSTRACT:
PROVIDER: PRJNA872936 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21203690_1.fastq.gz | Fastqsanger.gz |
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Project description:HDXMS data on isocitrate dehydrogenase (IDH1) and variants of the enzyme bound to cofactors and substrates.
2024-02-24 | MSV000094158 | MassIVE
Project description:Nowadays, the common octopus (Octopus vulgaris) culture is hampered by massive mortalities occurring during early life-cycle stages (paralarvae). Despite the causes of the high paralarvae mortality are not yet well defined and understood, the nutritional stress caused by inadequate diets is pointed out as one of the main factors. In this study the effects of diet on paralarvae is analyzed through a proteomic approach, to search for novel biomarkers of nutritional stress. A total of 43 proteins showing differential expression in the different conditions studied have been identified. The analysis highlights proteins related with the carbohydrate metabolism: glyceraldehyde-3-phosphate-dedydrogenase (GAPDH), triosephosphate isomerase; other ways of energetic metabolism: NADP+-specific isocitrate dehydrogenase, arginine kinase; detoxification: glutathione-S-transferase (GST); stress: heat shock proteins (HSP70); structural constituent of eye lens: S-crystallin 3; and cytoskeleton: actin, actin-beta/gamma1, beta actin. These results allow defining characteristic proteomes of paralarvae depending on the diet; as well as the use of several of these proteins as novel biomarkers to evaluate their welfare linked to nutritional stress. Notably, the changes of proteins like S-crystallin 3, arginine kinase and NAD+ specific isocitrate dehydrogenase, may be related to fed versus starving paralarvae, particularly in the first 4 days of development.
2019-11-25 | PXD006241 | Pride
Project description:Nowadays, the common octopus (Octopus vulgaris) culture is hampered by massive mortalities occurring during early life-cycle stages (paralarvae). Despite the causes of the high paralarvae mortality are not yet well defined and understood, the nutritional stress caused by inadequate diets is pointed out as one of the main factors. In this study the effects of diet on paralarvae is analyzed through a proteomic approach, to search for novel biomarkers of nutritional stress. A total of 43 proteins showing differential expression in the different conditions studied have been identified. The analysis highlights proteins related with the carbohydrate metabolism: glyceraldehyde-3-phosphate-dedydrogenase (GAPDH), triosephosphate isomerase; other ways of energetic metabolism: NADP+-specific isocitrate dehydrogenase, arginine kinase; detoxification: glutathione-S-transferase (GST); stress: heat shock proteins (HSP70); structural constituent of eye lens: S-crystallin 3; and cytoskeleton: actin, actin-beta/gamma1, beta actin. These results allow defining characteristic proteomes of paralarvae depending on the diet; as well as the use of several of these proteins as novel biomarkers to evaluate their welfare linked to nutritional stress. Notably, the changes of proteins like S-crystallin 3, arginine kinase and NAD+ specific isocitrate dehydrogenase, may be related to fed versus starving paralarvae, particularly in the first 4 days of development.
2022-03-01 | PXD006242 | Pride
Project description:Immune landscape of Isocitrate Dehydrogenase (IDH) stratified human gliomas
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Project description:Pancreatic cancer cells alter their metabolism to survive cancer-associated stress. For example, cancer cells must adapt to steep nutrient gradients that characterize the natural tumor microenvironment. In the absence of adaptive strategies, harsh metabolic conditions promote free radicals and impair energy production in tumor cells. Towards this end, wild-type isocitrate dehydrogenase 1 (IDH1) activity is a metabolic requirement for cancer cells living in a harsh metabolic milieu. The cytosolic enzyme interconverts isocitrate and α-ketoglutarate (αKG) and uses NADP(H) as a cofactor. We show that under low nutrient conditions, the enzymatic reaction favors oxidative decarboxylation to yield NADPH and αKG. Metabolic studies showed that the IDH1 products directly support an antioxidant defense and mitochondrial function in stressed cancer cells. Genetic IDH1 suppression reduced pancreatic cancer cells' growth in vitro under low nutrient conditions and in mouse models of pancreatic cancer. Thus, intrinsic tumor microenvironment conditions sensitized wild-type IDH1 to FDA-approved AG-120 (ivosidenib) and revealed the drug to be a potent single-agent therapeutic in cell culture and diverse in vivo cancer models. This work identified a potentially new repertoire of safe cancer therapies, including a clinically available compound, to treat multiple wild-type IDH1 cancers, including pancreatic cancer.
2021-11-01 | GSE161073 | GEO
Project description:Reactive oxygen species (ROS) production is a conserved immune response, primarily mediated in Arabidopsis by the respiratory burst oxidase homolog D (RBOHD), a nicotinamide adenine dinucleotide phosphate (NADPH) oxidase associated with the plasma membrane. A rapid increase in NADPH is necessary to fuel RBOHD proteins and hence maintain ROS production. However, the molecular mechanism underlying the NADPH generation for fueling RBOHD remains unclear. In this study, we isolated a new mutant allele of flagellin-insensitive 4 (FIN4), encoding the first enzyme in de novo NAD biosynthesis. fin4 mutants show reduced NADPH levels and impaired ROS production. However, FIN4 and other genes involved in the NAD- and NADPH-generating pathways are not highly upregulated upon elicitor treatment. Therefore, we hypothesized that a cytosolic NADP-linked dehydrogenase might be post-transcriptionally activated to keep the NADPH supply close to RBOHD. RPM1-INDUCED PROTEIN KINASE (RIPK), a receptor-like cytoplasmic kinase, regulates broad-spectrum ROS signaling in plant immunity. We then isolated the proteins associated with RIPK and identified NADP-malic enzyme 2 (NADP-ME2), an NADPH-generating enzyme. Compared with wild-type plants, nadp-me2 mutants display decreased NADP-ME activity, lower NADPH levels, as well as reduced ROS production in response to immune elicitors. Furthermore, we found that RIPK can directly phosphorylate NADP-ME2 and enhance its activity in vitro. The phosphorylation of NADP-ME2 S371 residue contributes to ROS production upon immune elicitor treatment and the susceptibility to the necrotrophic bacterium, Pectobacterium carotovorum. Overall, our study suggests that RIPK activates NADP-ME2 to rapidly increase cytosolic NADPH, hence fueling RBOHD to sustain ROS production in plant immunity.
2022-03-10 | GSE198017 | GEO
Project description:2-hydroxyglutarate (2-HG) is an oncometabolite accumulating in certain cancers and some neurometabolic diseases. In cancers 2-HG accumulation is induced by a gain-of-function mutation in isocitrate dehydrogenase (IDH) genes, leading to conversion of alpha-ketoglutarate (a-KG) into 2-HG
2023-04-15 | E-MTAB-11328 | biostudies-arrayexpress
Project description:Immune landscape of Isocitrate Dehydrogenase (IDH) stratified human gliomas [RNA-Seq]
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Project description:Immune landscape of Isocitrate Dehydrogenase (IDH) stratified human gliomas [scRNA-seq]
| PRJNA922463 | ENA
Project description:The purpose of this study was to characterize the molecular phenotype and function of tumor-infiltrating myeloid cells isolated from genetically engineered glioma mouse model expressing wild-type IDH1 or mutated IDH1 (isocitrate dehydrogenase).
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