Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrated metabolomics and transcriptomics reveal the anti-aging effect of melanin from Sepiella maindroni ink (MSMI) on D-galactose-induced aging mice.

ABSTRACT: Sepiella maindroni ink, a flavoring and coloring agent in food, has attracted considerable attention due to its various pharmacological activities. Our previous study showed that the melanin of Sepiella maindroni ink (MSMI) can alleviate oxidative damage and delay aging in D-galactose(D-gal)-induced aging mice. This study aimed to reveal the possible mechanisms of the anti-aging effect of MSMI. In this article, a comprehensive analysis of gas chromatography-mass spectrometry (GC-MS)-based metabolomics and microarray-based transcriptomics revealed that 221 mRNAs were differentially expressed and 46 metabolites were significantly changed in the anti-aging progress of MSMI. Integrated analysis of transcript and metabolic profiles indicated that MSMI mainly altered carbohydrate metabolism, lipid metabolism, and insulin signaling pathway. MSMI achieved anti-aging effects not only by reducing oxidative damage and sorbitol toxicity but also by regulating lipid metabolism, improving insulin sensitivity, and reducing the formation of advanced glycation end products (AGEs). Moreover, our findings firstly demonstrated that MSMI could increase the expression of interferon-induced proteins and might be a potential antiviral compound.

SUBMITTER: Zhou Y

PROVIDER: S-EPMC8109126 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Integrated Transcriptomics and Metabolomics Analysis Reveal Key Metabolism Pathways Contributing to Cold Tolerance in Peanut.

Project description:Low temperature (non-freezing) is one of the major limiting factors in peanut (Arachis hypogaea L.) growth, yield, and geographic distribution. Due to the complexity of cold-resistance trait in peanut, the molecular mechanism of cold tolerance and related gene networks were largely unknown. In this study, metabolomic analysis of two peanut cultivars subjected to chilling stress obtained a set of cold-responsive metabolites, including several carbohydrates and polyamines. These substances showed a higher accumulation pattern in cold-tolerant variety SLH than cold-susceptible variety ZH12 under cold stress, indicating their importance in protecting peanut from chilling injuries. In addition, 3,620 cold tolerance genes (CTGs) were identified by transcriptome sequencing, and the CTGs were most significantly enriched in the "phenylpropanoid biosynthesis" pathway. Two vital modules and several novel hub genes were obtained by weighted gene co-expression network analysis (WGCNA). Several key genes involved in soluble sugar, polyamine, and G-lignin biosynthetic pathways were substantially higher and/or responded more quickly in SLH (cold tolerant) than ZH12 (cold susceptible) under low temperature, suggesting they might be crucial contributors during the adaptation of peanut to low temperature. These findings will not only provide valuable resources for study of cold resistance in peanut but also lay a foundation for genetic modification of cold regulators to enhance stress tolerance in crops.

| S-EPMC8652294 | biostudies-literature

Transcriptomics Integrated With Metabolomics Reveal the Effects of Ultraviolet-B Radiation on Flavonoid Biosynthesis in Antarctic Moss.

Project description:Bryophytes are the dominant vegetation in the Antarctic continent. They have suffered more unpleasant ultraviolet radiation due to the Antarctic ozone layer destruction. However, it remains unclear about the molecular mechanism of Antarctic moss acclimation to UV-B light. Here, the transcriptomics and metabolomics approaches were conducted to uncover transcriptional and metabolic profiling of the Antarctic moss Leptobryum pyriforme under UV-B radiation. Totally, 67,290 unigenes with N50 length of 2,055 bp were assembled. Of them, 1,594 unigenes were significantly up-regulated and 3353 unigenes were markedly down-regulated under UV-B radiation. These differentially expressed genes (DEGs) involved in UV-B signaling, flavonoid biosynthesis, ROS scavenging, and DNA repair. In addition, a total of 531 metabolites were detected, while flavonoids and anthocyanins accounted for 10.36% of the total compounds. There were 49 upregulated metabolites and 41 downregulated metabolites under UV-B radiation. Flavonoids were the most significantly changed metabolites. qPCR analysis showed that UVR8-COP1-HY5 signaling pathway genes and photolyase genes (i.e., LpUVR3, LpPHR1, and LpDPL) were significantly up-regulated under UV-B light. In addition, the expression levels of JA signaling pathway-related genes (i.e., OPR and JAZ) and flavonoid biosynthesis-related genes were also significantly increased under UV-B radiation. The integrative data analysis showed that UVR8-mediated signaling, jasmonate signaling, flavonoid biosynthesis pathway and DNA repair system might contribute to L. pyriforme acclimating to UV-B radiation. Therefore, these findings present a novel knowledge for understanding the adaption of Antarctic moss to polar environments and provide a foundation for assessing the impact of global climate change on Antarctic land plants.

| S-EPMC8692278 | biostudies-literature

Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126.

Project description:Chemical pollutant exposure is a risk factor contributing to the growing epidemic of non-alcoholic fatty liver disease (NAFLD) affecting human populations that consume a western diet. Although it is recognized that intoxication by chemical pollutants can lead to NAFLD, there is limited information available regarding the mechanism by which typical environmental levels of exposure can contribute to the onset of this disease. Here, we describe the alterations in gene expression profiles and metabolite levels in the human HepaRG liver cell line, a validated model for cellular steatosis, exposed to the polychlorinated biphenyl (PCB) 126, one of the most potent chemical pollutants that can induce NAFLD. Sparse partial least squares classification of the molecular profiles revealed that exposure to PCB 126 provoked a decrease in polyunsaturated fatty acids as well as an increase in sphingolipid levels, concomitant with a decrease in the activity of genes involved in lipid metabolism. This was associated with an increased oxidative stress reflected by marked disturbances in taurine metabolism. A gene ontology analysis showed hallmarks of an activation of the AhR receptor by dioxin-like compounds. These changes in metabolome and transcriptome profiles were observed even at the lowest concentration (100 pM) of PCB 126 tested. A decrease in docosatrienoate levels was the most sensitive biomarker. Overall, our integrated multi-omics analysis provides mechanistic insight into how this class of chemical pollutant can cause NAFLD. Our study lays the foundation for the development of molecular signatures of toxic effects of chemicals causing fatty liver diseases to move away from a chemical risk assessment based on in vivo animal experiments.

| S-EPMC6063328 | biostudies-literature

Integrated transcriptomics and metabolomics reveal tolerance mechanisms to hypoxia stress in Yesso scallop, Mizuhopecten yessoensis

Project description:Global warming and human activities have led to an increased frequency of hypoxia in coastal regions. Hypoxia not only affects the growth and development of scallops but can also cause death, posing a significant challenge to the health and sustainability of aquaculture. Its effects on scallop growth and immune system have been widely reported, but studies on the effects of hypoxic stress on the metabolism of Yesso scallop Mizuhopecten yessoensis are not fully understood. Additionally, the molecular mechanisms of hypoxic stress on damage to the Yesso scallop are still limited. In this study, we deploy high-throughput RNA sequencing (RNA-Seq) and non-targeted liquid chromatography-mass spectrometry (LC-MS) based metabolomics analysis to investigate the alterations in key genes and metabolites in scallops after 24 hours of hypoxia stress (DO: 1 ± 0.1 mg/L). A total of 704 differentially expressed genes (DEGs) and 302 differentially expressed metabolites (DEMs) were identified in the gill tissues of Yesso scallops under hypoxic conditions, respectively. DEGs and DEMs were involved in energy metabolism, antioxidant responses, immune responses, and inflammatory responses, as well as processes of cell apoptosis and cell proliferation. KEGG enrichment analysis shows that the mTOR signaling pathway is a significantly enriched pathway shared by DEGs and DEMs. These findings suggest that Yesso scallops cope with acute hypoxic stress by changing energy metabolism, inhibiting cell apoptosis and proliferation, and increasing immune defense strategies. Overall, the results of this study provide a new understanding of how Yesso scallops respond to hypoxia and provide target genes for the selection and breeding of low-oxygen-tolerant scallops.

2024-09-01 | GSE252091 | GEO

Anti-Aging Effect of Chitosan Oligosaccharide on d-Galactose-Induced Subacute Aging in Mice.

Project description:Chitosan oligosaccharide (COS), a natural polysaccharide with good antioxidant and anti-inflammatory properties, is the depolymerized product of chitosan possessing various biological activities. The present study was designed to investigate the possible anti-aging effect of COS on the aging model mouse induced by d-galactose (d-gal) and explore the underlying mechanism. In the experiment, 48 male Kunming mice (KM mice) were randomly divided into the normal group, model group, positive group, and low-medium-high dose polysaccharide groups (300, 600, 1200 mg/kg/day). The results showed that COS, by intragastric gavage after subcutaneous injection of d-gal (250 mg/kg/day) into the neck of mice consecutively for eight weeks, gradually recovered the body weight, the activity of daily living, and organ indices of mice, as well as effectively ameliorated the histological deterioration of the liver and kidney in mice triggered by d-gal. To be specific, COS obviously improved the activities of antioxidant enzymes in liver and kidney of KM mice, including catalase (CAT), glutathione peroxidase (GSH-Px), and superoxide dismutase (SOD), as well as decreased malondialdehyde (MDA) levels when compared with those in model group mice. Furthermore, COS not only elevated the diminished levels of serum immunoglobulin G (IgG) and IgM induced by d-gal, but also significantly inhibited the d-gal-caused upregulation of serum alanine aminotransferase (ALT), aspartate transaminase (AST), alkaline phosphatase (ALP), uric acid (UA) and creatinine (CREA) levels as compared with those of mice in the model group. These results demonstrate that COS has an obvious anti-aging activity in d-gal-induced subacute aging mice, the mechanism of which, to some extent, is associated with enhancing the antioxidant defenses, reducing oxidative stress, and improving the immune function of aging model mice.

| S-EPMC6025514 | biostudies-literature

Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum.

Project description:CB-1 and K326 are closely related tobacco cultivars; however, their cold tolerance capacities are different. K326 is much more cold tolerant than CB-1.We studied the transcriptomes and metabolomes of CB-1 and K326 leaf samples treated with cold stress. Totally, we have identified 14,590 differentially expressed genes (DEGs) in CB-1 and 14,605 DEGs in K326; there was also 200 differentially expressed metabolites in CB-1 and 194 in K326. Moreover, there were many overlapping genes (around 50%) that were cold-responsive in both plant cultivars, although there were also many differences in the cold responsive genes between the two cultivars. Importantly, for most of the overlapping cold responsive genes, the extent of the changes in expression were typically much more pronounced in K326 than in CB-1, which may help explain the superior cold tolerance of K326. Similar results were found in the metabolome analysis, particularly with the analysis of primary metabolites, including amino acids, organic acids, and sugars. The large number of specific responsive genes and metabolites highlight the complex regulatory mechanisms associated with cold stress in tobacco. In addition, our work implies that the energy metabolism and hormones may function distinctly between CB-1 and K326.Differences in gene expression and metabolite levels following cold stress treatment seem likely to have contributed to the observed difference in the cold tolerance phenotype of these two tobacco cultivars.

| S-EPMC5492280 | biostudies-literature

Integrated Transcriptomics and Metabolomics Analyses of Stress-Induced Murine Hair Follicle Growth Inhibition.

Project description:Psychological stress plays an important role in hair loss, but the underlying mechanisms are not well-understood, and the effective therapies available to regrow hair are rare. In this study, we established a chronic restraint stress (CRS)-induced hair growth inhibition mouse model and performed a comprehensive analysis of metabolomics and transcriptomics. Metabolomics data analysis showed that the primary and secondary metabolic pathways, such as carbohydrate metabolism, amino acid metabolism, and lipid metabolism were significantly altered in skin tissue of CRS group. Transcriptomics analysis also showed significant changes of genes expression profiles involved in regulation of metabolic processes including arachidonic acid metabolism, glutathione metabolism, glycolysis gluconeogenesis, nicotinate and nicotinamide metabolism, purine metabolism, retinol metabolism and cholesterol metabolism. Furthermore, RNA-Seq analyses also found that numerous genes associated with metabolism were significantly changed, such as Hk-1, in CRS-induced hair growth inhibition. Overall, our study supplied new insights into the hair growth inhibition induced by CRS from the perspective of integrated metabolomics and transcriptomics analyses.

| S-EPMC8859263 | biostudies-literature

Sulfated polysaccharide of Sepiella maindroni ink targets Akt and overcomes resistance to the FGFR inhibitor AZD4547 in bladder cancer.

Project description:Rapid appearance of resistance to fibroblast growth factor receptor (FGFR) inhibitors hampers targeted regimens in bladder cancer. In the present study, we evaluated whether SIP-SII, a sulphated derivative of the polysaccharide in Sepiella maindroni (spineless cuttlefish) ink used in traditional Chinese medicine, could attenuate resistance to FGFR inhibition in bladder cancer cells. In vitro assays indicated that SIP-SII reduced cell viability and migration, restricted cell cycle progression, and increased apoptosis in parallel with decreased AKT phosphorylation and downregulation of CDK4, MMP2, and Bcl-2 in RT112 and JMSU1 cells. Synergistic effects on cell viability were observed when SIP-SII was combined with the small-molecule FGFR inhibitor AZD4547. Specific Akt targeting by SIP-SII was suggested by the fact that neither Akt knockdown nor the selective PI3K inhibitor BKM120 enhanced the inhibitory effects of SIP-II, while expression of a constitutively active Akt mutant rescued SIP-SII effects. Furthermore, subcutaneous transplantation of RT112 xenografts confirmed the superiority and tolerability of combined SIP-SII and AZD4547 administration over monotherapy regimens. The present study thus provides pre-clinical evidence of the ability of SIP-SII to improve FGFR-targeted therapies for bladder cancer by inhibiting Akt.

| S-EPMC6782013 | biostudies-literature

Integrated Metabolomics and Transcriptomics Unravel the Metabolic Pathway Variations for Different Sized Beech Mushrooms.

Project description:Beech mushrooms (Hypsizygus marmoreus) are largely relished for their characteristic earthy flavor, chewy-texture, and gustatory and nutritional properties in East Asian societies. Intriguingly, the aforementioned properties of beech mushroom can be subsumed under its elusive metabolome and subtle transcriptome regulating its various stages of growth and development. Herein, we carried out an integrated metabolomic and transcriptomic profiling for different sized beech mushrooms across spatial components (cap and stipe) to delineate their signature pathways. We observed that metabolite profiles and differentially expressed gene (DEGs) displayed marked synergy for specific signature pathways according to mushroom sizes. Notably, the amino acid, nucleotide, and terpenoid metabolism-related metabolites and genes were more abundant in small-sized mushrooms. On the other hand, the relative levels of carbohydrates and TCA intermediate metabolites as well as corresponding genes were linearly increased with mushroom size. However, the composition of flavor-related metabolites was varying in different sized beech mushrooms. Our study explores the signature pathways associated with growth, development, nutritional, functional and organoleptic properties of different sized beech mushrooms.

| S-EPMC6928633 | biostudies-literature

Integrated Metabolomics and Transcriptomics Analysis of Monolayer and Neurospheres from Established Glioblastoma Cell Lines.

Project description:Altered metabolic processes contribute to carcinogenesis by modulating proliferation, survival and differentiation. Tumours are composed of different cell populations, with cancer stem-like cells being one of the most prominent examples. This specific pool of cells is thought to be responsible for cancer growth and recurrence and plays a particularly relevant role in glioblastoma (GBM), the most lethal form of primary brain tumours. Here, we have analysed the transcriptome and metabolome of an established GBM cell line (U87) and a patient-derived GBM stem-like cell line (NCH644) exposed to neurosphere or monolayer culture conditions. By integrating transcriptome and metabolome data, we identified key metabolic pathways and gene signatures that are associated with stem-like and differentiated states in GBM cells, and demonstrated that neurospheres and monolayer cells differ substantially in their metabolism and gene regulation. Furthermore, arginine biosynthesis was identified as the most significantly regulated pathway in neurospheres, although individual nodes of this pathway were distinctly regulated in the two cellular systems. Neurosphere conditions, as opposed to monolayer conditions, cause a transcriptomic and metabolic rewiring that may be crucial for the regulation of stem-like features, where arginine biosynthesis may be a key metabolic pathway. Additionally, TCGA data from GBM patients showed significant regulation of specific components of the arginine biosynthesis pathway, providing further evidence for the importance of this metabolic pathway in GBM.

| S-EPMC8001840 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data