Expression Profiles Of Metabolism-related Genes Research Articles

Investigation of ENO2 as a promising novel marker for the progression of colorectal cancer with microsatellite instability-high

BackgroundMicrosatellite instability-high (MSI-H) has emerged as a significant biological characteristic of colorectal cancer (CRC). Studies reported that MSI-H CRC generally had a better prognosis than microsatellite stable (MSS)/microsatellite instability-low (MSI-L) CRC, but some MSI-H CRC patients exhibited distinctive molecular characteristics and experienced a less favorable prognosis. In this study, our objective was to explore the metabolic transcript-related subtypes of MSI-H CRC and identify a biomarker for predicting survival outcomes.MethodsSingle-cell RNA sequencing (scRNA-seq) data of MSI-H CRC patients were obtained from the Gene Expression Omnibus (GEO) database. By utilizing the copy number variation (CNV) score, a malignant cell subpopulation was identified at the single-cell level. The metabolic landscape of various cell types was examined using metabolic pathway gene sets. Subsequently, functional experiments were conducted to investigate the biological significance of the hub gene in MSI-H CRC. Finally, the predictive potential of the hub gene was assessed using a nomogram.ResultsThis study revealed a malignant tumor cell subpopulation from the single-cell RNA sequencing (scRNA-seq) data. MSI-H CRC was clustered into two subtypes based on the expression profiles of metabolism-related genes, and ENO2 was identified as a hub gene. Functional experiments with ENO2 knockdown and overexpression demonstrated its role in promoting CRC cell migration, invasion, glycolysis, and epithelial-mesenchymal transition (EMT) in vitro. High expression of ENO2 in MSI-H CRC patients was associated with worse clinical outcomes, including increased tumor invasion depth (p = 0.007) and greater likelihood of perineural invasion (p = 0.015). Furthermore, the nomogram and calibration curves based on ENO2 showed potential prognosis predictive performance.ConclusionOur findings suggest that ENO2 serves as a novel prognostic biomarker and is associated with the progression of MSI-H CRC.

Regulatory Role of Trehalose Metabolism in Cold Stress of Harmonia axyridis Laboratory and Overwinter Populations

Trehalose is a non-reducing disaccharide that plays a key role in the response to cold and other environmental stressors in insects. Harmonia axyridis (Pallas) is an important natural predator of insect pests and has become a cosmopolitan invasive species, causing negative ecological impacts worldwide. In this study, the relative survival ability, trehalose and glycogen contents, trehalose activity and trehalose metabolism-related gene-expression profiles over a cold storage period were compared in a natural overwintering population and an indoor laboratory (experimental) population. Yellow adults were dominant in the overwintering population. The survival rate of the overwintering population during the cold storage period was higher than that of the experimental population after the fifth day. The contents of trehalose and glycogen in the overwinter population were higher than those of the experimental population during cold storage. Trehalose and glycogen contents initially increased and then decreased in the overwinter population, but decreased consistently over the cold storage period in the experimental population. Nevertheless, trehalose levels were relatively higher during the cold storage period in the overwinter population, with higher expression of TPS and TRE and trehalase activity. More importantly, the experiment showed that yellow adults have a better ability to regulate trehalose metabolism under cold storage compared to black adults. A strong resilience against cold stress and long-term cold storage ability could contribute to a better understanding of the invasiveness of H. axyridris.

Construction of a prognostic signature in Ewing's sarcoma: Based on metabolism-related genes

ObjectiveBy combining the expression profiles of metabolism-related genes (MRGS) with clinical information, the expression quantities of MRGS and the influence on development and prognosis were systematically analyzed, so as to provide a theoretical basis for the clinical study on the prognosis of Ewing's sarcoma. MethodsMRGs expression profiles of 64 patients with Ewing's sarcoma were obtained from GEO dataset. Univariate Cox regression analysis was used to identify metabolization-related differentially expressed genes (DEGs) related with prognosis in Ewing's sarcoma patients. Then, multivariate Cox analysis was used to calculate novel prognostic markers based on metabolism-related DEGs. Besides, We validate the model using ICGC datasets. Finally, the new prognostic index was verified on the basis of the prognostic models. ResultsMultivariate Cox regression analysis identified 74 metabolization-related DEGs, 25 of which were associated with Ewing's sarcoma patients' overall survival. Subsequently, we used 25 DEGs to construct metabolism-related prognostic signature for patients with Ewing's sarcoma. Based on the 18 DEGs regression coefficient, we propose the formula of each patient's risk score, and then divided the patients into high-risk group and low-risk group. The results indicated that the survival rate and survival time were higher in the low-risk group and lower in the high-risk group. Multivariate Cox analysis showed that risk score index was an independent prognostic factor for Ewing's sarcoma. ConclusionThe experimental results suggest that the 18 metabolism-related DEGs marker may be effective in predicting the prognosis of Ewing's sarcoma to some extent, helping to individualize treatment of patients at different risks.

Identification of a Prognostic Index Based on a Metabolic-Genomic Landscape Analysis of Hepatocellular Carcinoma (HCC).

BackgroundMetabolic disorders have attracted increasing attention from scientists who conduct research on various tumours, especially hepatocellular carcinoma (HCC). The purpose of this study was to assess the prognostic significance of metabolism in HCC.MethodsThe expression profiles of metabolism-related genes (MRGs) of 349 surviving HCC patients were extracted from The Cancer Genome Atlas (TCGA) database. Subsequently, a series of biomedical computational algorithms were used to identify a seven-MRG signature as a prognostic model. GSEA indicated the function and pathway enrichment of these MRGs. Then, drug sensitivity analysis was used to identify the hub gene, which was tested using IHC staining.ResultsA total of 420 differential MRGs and 116 differentially expressed transcription factors (TFs) were identified in HCC patients based on data from the TCGA database. The GO and KEGG enrichment analyses indicated that metabolic disturbance might be involved in the development of HCC. LASSO regression analysis was used to construct a seven-MRG signature (DHDH, ENO1, G6PD, LPCAT1, PDE6D, PIGU and PPAT) that could predict the prognosis of HCC patients. GSEA revealed the functional and pathway enrichment of these seven MRGs. Then, drug sensitivity analysis indicated that G6PD might play a key role in the prognosis of HCC by promoting chemoresistance. Finally, we used IHC staining to demonstrate the relationship between G6PD expression levels and clinical parameters in HCC patients.ConclusionThe results of this study provide a potential method for predicting the prognosis of HCC patients and avenues for further studies of HCC metabolism. Moreover, the function of G6PD may play a key role in the development and progression of HCC.

Effects of Plant Sterols Intake on Systematic and Tissue Specific Lipid Metabolism in C57BL/6J Mice

Abstract Objectives To investigate the effects of plant sterols intake on systematic and tissue specific lipid metabolism in C57BL/6J mice. Methods Male C57BL/6J mice were randomly divided into control diet group (CS) and plant sterol group (PS, 2% plant sterols). After 28 weeks of continuous feeding, the serum of the mice were collected for biochemical and mass spectrometry tests. Serum levels of total cholesterol (TC), triglyceride (TG) and free sterols were determined. The livers and lungs were collected for free sterol quantification and RNA-seq analysis. Results Compared with the CS group, 2% plant sterols intake significantly reduced the levels of TC in the serum of mice (P < 0.05), with the TG level unchanged. The quantitative results of free sterols showed that the concentration of campesterol were increased, and the cholestanol levels were decreased significantly in the serum and liver of the PS group mice. The results of RNA-seq analysis were used to further evaluate its impact on the lipid metabolism related gene expression profile in the livers and lungs. The results showed that HMGCR, SQLE, HMGCS1, SREBF1, and other genes related to cholesterol synthesis in the PS group were significantly up-regulated in the liver, but not in the lung; Among the first 20 targeting pathways related to the action of plant sterols, the liver differentially expressed genes were enriched in lipid metabolism (steroid biosynthesis, terpenoid skeleton biosynthesis, peroxisome, bile acid secretion, PPAR, MAPK, fatty acid metabolism.), inflammation related (Cell adhesion molecules, leukocyte trans-endothelial migration) and amino acid metabolism (glutathione, valine, leucine and isoleucine metabolism). The differential genes in lung tissue are enriched in lipid metabolism (acetone metabolism, fatty acid metabolism, insulin resistance, terpenoid skeleton biosynthesis, iron death, PPAR), cell function (internal Swallowing, aging) and vascular smooth muscle contraction etc. Conclusions Differentially expressed gene networks reflect the multi-dimensional regulation of plant sterols on tissue specific lipid metabolism, which lays a good foundation for further revealing its mechanism. Funding Sources Yihaikerry Nutrition and Food Safety Foundation, Chinese Nutrition Society; Project of Technology Innovation and Application, Chongqing, China

Identification of a metabolism-related gene expression prognostic model in endometrial carcinoma patients

BackgroundMetabolic abnormalities have recently been widely studied in various cancer types. This study aims to explore the expression profiles of metabolism-related genes (MRGs) in endometrial cancer (EC).MethodsWe analyzed the expression of MRGs using The Cancer Genome Atlas (TCGA) data to screen differentially expressed MRGs (DE-MRGs) significantly correlated with EC patient prognosis. Functional pathway enrichment analysis of the DE-MRGs was performed. LASSO and Cox regression analyses were performed to select MRGs closely related to EC patient outcomes. A prognostic signature was developed, and the efficacy was validated in part of and the entire TCGA EC cohort. Moreover, we developed a comprehensive nomogram including the risk model and clinical features to predict EC patients’ survival probability.ResultsForty-seven DE-MRGs were significantly correlated with EC patient prognosis. Functional enrichment analysis showed that these MRGs were highly enriched in amino acid, glycolysis, and glycerophospholipid metabolism. Nine MRGs were found to be closely related to EC patient outcomes: CYP4F3, CEL, GPAT3, LYPLA2, HNMT, PHGDH, CKM, UCK2 and ACACB. Based on these nine DE-MRGs, we developed a prognostic signature, and its efficacy in part of and the entire TCGA EC cohort was validated. The nine-MRG signature was independent of other clinical features, and could effectively distinguish high- and low-risk EC patients and predict patient OS. The nomogram showed excellent consistency between the predictions and actual survival observations.ConclusionsThe MRG prognostic model and the comprehensive nomogram could guide precise outcome prediction and rational therapy selection in clinical practice.

Identification of an ATP metabolism-related signature associated with prognosis and immune microenvironment in gliomas.

As the core element of material and energy metabolism pathways, the biological functions and prognostic significance of ATP metabolism in diffuse gliomas have so far remained unclear. Based on comprehensive analysis of ATP metabolism‐related gene expression profiles, we constructed an ATP metabolism‐related risk signature to determine the role of ATP metabolism. We found that this ATP metabolism‐related gene expression profile could divide patients into 2 robust groups with distinct clinical characteristics and prognosis. Patients in the high‐risk group tended to be predicted as malignant entities, indicating that the activation of ATP metabolism may promote the malignant progress of diffuse gliomas. Cox regression and Kaplan‐Meier analyses suggested that this risk signature was an independent predictor for prognosis. Furthermore, we constructed an individualized prognosis prediction model through nomogram and time‐dependent receiver operating characteristic (ROC) curve analyses. Functional analysis suggested that, in addition to material and energy metabolism, ATP metabolism also played an essential role in the regulation of the tumor immune microenvironment. In brief, the ATP metabolism‐related signature was tightly associated with regulation of the tumor immune microenvironment and could serve as an independent prognostic biomarker in diffuse gliomas.

Establishment of the Prognostic Index Reflecting Tumor Immune Microenvironment of Lung Adenocarcinoma Based on Metabolism-Related Genes.

Background: The incidence of lung adenocarcinoma (LUAD) increased substantially in recent years. A systematic investigation of the metabolic genomics pattern is critical to improve the treatment and prognosis of LUAD. This study aimed to analyze the relationship between tumor microenvironment (TME) and metabolism-related genes of LUAD.Methods: The data was extracted from TCGA and GEO datasets. The metabolism-related gene expression profile and the corresponding clinical data of LUAD patients were then integrated. The survival-related genes were screened out using univariate COX regression and lasso regression analysis. The latent properties and molecular mechanisms of these LUAD-specific metabolism-related genes were investigated by computational biology.Results: A novel prognostic model was established based on 8 metabolism-related genes, including TYMS, ALDH2, PKM, GNPNAT1, LDHA, ENTPD2, NT5E, and MAOB. The immune infiltration of LUAD was also analyzed using CIBERSORT algorithms and TIMER database. In addition, the high- and low-risk groups exhibited distinct layout modes in the principal component analysis.Conclusions: In summary, our studies identified clinically significant metabolism-related genes, which were potential signature for LUAD diagnosis, monitoring, and prognosis.

P.718 Procognitive effect of a single dose of magnesium in novel object recognition test, in healthy and corticosterone treated rats

By combining the expression profiles of metabolism-related genes (MRGS) with clinical information, the expression quantities of MRGS and the influence on development and prognosis were systematically analyzed, so as to provide a theoretical basis for the clinical study on the prognosis of Ewing's sarcoma.MRGs expression profiles of 64 patients with Ewing's sarcoma were obtained from GEO dataset. Univariate Cox regression analysis was used to identify metabolization-related differentially expressed genes (DEGs) related with prognosis in Ewing's sarcoma patients. Then, multivariate Cox analysis was used to calculate novel prognostic markers based on metabolism-related DEGs. Besides, We validate the model using ICGC datasets. Finally, the new prognostic index was verified on the basis of the prognostic models.Multivariate Cox regression analysis identified 74 metabolization-related DEGs, 25 of which were associated with Ewing's sarcoma patients' overall survival. Subsequently, we used 25 DEGs to construct metabolism-related prognostic signature for patients with Ewing's sarcoma. Based on the 18 DEGs regression coefficient, we propose the formula of each patient's risk score, and then divided the patients into high-risk group and low-risk group. The results indicated that the survival rate and survival time were higher in the low-risk group and lower in the high-risk group. Multivariate Cox analysis showed that risk score index was an independent prognostic factor for Ewing's sarcoma.The experimental results suggest that the 18 metabolism-related DEGs marker may be effective in predicting the prognosis of Ewing's sarcoma to some extent, helping to individualize treatment of patients at different risks.

The copper-sensing transcription factor Mac1, the histone deacetylase Hst1, and nicotinic acid regulate de novo NAD+ biosynthesis in budding yeast

NADH (NAD+) is an essential metabolite involved in various cellular biochemical processes. The regulation of NAD+ metabolism is incompletely understood. Here, using budding yeast (Saccharomyces cerevisiae), we established an NAD+ intermediate-specific genetic system to identify factors that regulate the de novo branch of NAD+ biosynthesis. We found that a mutant strain (mac1Δ) lacking Mac1, a copper-sensing transcription factor that activates copper transport genes during copper deprivation, exhibits increases in quinolinic acid (QA) production and NAD+ levels. Similar phenotypes were also observed in the hst1Δ strain, deficient in the NAD+-dependent histone deacetylase Hst1, which inhibits de novo NAD+ synthesis by repressing BNA gene expression when NAD+ is abundant. Interestingly, the mac1Δ and hst1Δ mutants shared a similar NAD+ metabolism-related gene expression profile, and deleting either MAC1 or HST1 de-repressed the BNA genes. ChIP experiments with the BNA2 promoter indicated that Mac1 works with Hst1-containing repressor complexes to silence BNA expression. The connection of Mac1 and BNA expression suggested that copper stress affects de novo NAD+ synthesis, and we show that copper stress induces both BNA expression and QA production. Moreover, nicotinic acid inhibited de novo NAD+ synthesis through Hst1-mediated BNA repression, hindered the reuptake of extracellular QA, and thereby reduced de novo NAD+ synthesis. In summary, we have identified and characterized novel NAD+ homeostasis factors. These findings will expand our understanding of the molecular basis and regulation of NAD+ metabolism.

Hepatic PHD2/HIF-1α axis is involved in postexercise systemic energy homeostasis.

Exercise plays an important role in the prevention and treatment of chronic liver disease and associated metabolic disorders. A single bout of exercise induces tissue blood flow redistribution, which decreases splanchnic circulation and leads to physiologic hypoxia in the gastrointestinal system and liver. The transcription factor, hypoxia inducible factor-1α (HIF-1α), and its regulator, prolylhydroxylase 2 (PHD2), play pivotal roles in the response to oxygen flux by regulating downstream gene expression levels in the liver. We hypothesized that exercise increases the HIF-1α levels in the liver, and that the hepatic PHD2/HIF-1α axis is involved in postexercise restoration of systemic energy homeostasis. Through constant O2 consumption, CO2 production, food and water intake, and physical activity detection with metabolic chambers, we observed that one 30-min session of swimming exercise enhances systemic energy metabolism in mice. By using the noninvasive bioluminescence imaging ROSA26 oxygen-dependent domain Luc mouse model, we reveal that exercise increases in vivo HIFα levels in the liver. Intraperitoneal injections of the PHD inhibitor, dimethyloxalylglycine, mimicked exercise-induced HIFα increase, whereas the HIF-1α inhibitor, PX-478, blocked this effect. We next constructed liver-specific knockout (LKO) mouse models with albumin- Cre-mediated, hepatocyte-specific Hif1a and Phd2 deletion. Compared with their controls, Hif1a-LKO and Phd2-LKO mice exhibited distinct patterns of hepatic metabolism-related gene expression profiles. Moreover, Hif1a-LKO mice failed to restore systemic energy homeostasis after exercise. In conclusion, the current study demonstrates that a single bout of exercise disrupts systemic energy homeostasis, increasing the HIF-1α levels in the liver. These findings also provide evidence that the hepatic PHD2/HIF-1α axis is involved in postexercise systemic metabolic homeostasis.-Luo, B., Xiang, D., Wu, D., Liu, C., Fang, Y., Chen, P., Hu, Y.-P. Hepatic PHD2/HIF-1α axis is involved in postexercise systemic energy homeostasis.

Gene expression and plasma lipid content in relation to intramuscular fat in Chinese indigenous Wuhua chicken

SUMMARY The deposition pattern of intramuscular fat (IMF), inosine monophosphate (IMP), and fat metabolism related gene expression profiles were studied in Wuhua chickens. A total of 160 healthy birds (80 of each gender) was reared. Ten birds from each gender were randomly selected at 90, 120, 150, and 180 d of age for blood and tissue sample collection. There were no changes in male IMF content that ranged from 0.9 to 1.79 mg/g. In females, there were large differences in IMF content, which increased from 0.62 mg/g at 90 d to the highest level of 2.61 mg/g at 150 d (P = 0.015). No statistical changes were observed in IMP content in both males and females. In females, very low density lipoprotein (VLDL) exhibited an age dependent manner and reached the highest level of 64.93 mg/mL at 180 d, while the low density lipoprotein (LDL) reached the highest level at 120 d (1.35 nmol/L). Serum triglycerides (TG) increased to the highest level of 1.3 nmol/L at 180 d (P = 0.0003). In males, TG reached the highest level at 120 d (P = 0.035). The A-FABP mRNA expression was highest at 180 d of age in males (P = 0.017). The Apo-B and PPAR-γ genes expressed the highest levels around 150 d of age in female chickens. Higher plasma TG was associated with greater breast IMF in both males and females. The correlation coefficient between IMF and PPAR-γ expression was 0.875 (P = 0.065) in females. Plasma TG might be used as a potential index for breast IMF selection, and PPAR-γ might be used as a candidate gene for IMF selection in females.

Transcription Profiles Reveal Sugar and Hormone Signaling Pathways Mediating Flower Induction in Apple (Malus domestica Borkh.).

Flower induction in apple (Malus domestica Borkh.) is regulated by complex gene networks that involve multiple signal pathways to ensure flower bud formation in the next year, but the molecular determinants of apple flower induction are still unknown. In this research, transcriptomic profiles from differentiating buds allowed us to identify genes potentially involved in signaling pathways that mediate the regulatory mechanisms of flower induction. A hypothetical model for this regulatory mechanism was obtained by analysis of the available transcriptomic data, suggesting that sugar-, hormone- and flowering-related genes, as well as those involved in cell-cycle induction, participated in the apple flower induction process. Sugar levels and metabolism-related gene expression profiles revealed that sucrose is the initiation signal in flower induction. Complex hormone regulatory networks involved in cytokinin (CK), abscisic acid (ABA) and gibberellic acid pathways also induce apple flower formation. CK plays a key role in the regulation of cell formation and differentiation, and in affecting flowering-related gene expression levels during these processes. Meanwhile, ABA levels and ABA-related gene expression levels gradually increased, as did those of sugar metabolism-related genes, in developing buds, indicating that ABA signals regulate apple flower induction by participating in the sugar-mediated flowering pathway. Furthermore, changes in sugar and starch deposition levels in buds can be affected by ABA content and the expression of the genes involved in the ABA signaling pathway. Thus, multiple pathways, which are mainly mediated by crosstalk between sugar and hormone signals, regulate the molecular network involved in bud growth and flower induction in apple trees.

Microarray analysis of differentially expressed genes engaged in fruit development between table and wine grape.

Microarray analysis of genes can provide individual gene-expression profiles and new insights for elucidating biological mechanisms responsible for fruit development. To obtain an overall view on expression profiles of metabolism-related genes involved in fruit development of table and wine grapes, a microarray system comprising 15,403 ESTs was used to compare the expressed genes. The expression patterns from the microarray analysis were validated with quantitative real-time polymerase chain reaction analysis of 18 selected genes of interest. During the entire fruit development stage, 2,493 genes exhibited at least 2.0-fold differences in expression levels with 1,244 genes being up-regulated and 1,249 being down-regulated. Following gene ontology analysis, only 929 differentially expressed (including 403 up-regulated and 526 down-regulated) genes were annotated in table and wine grapes. These differentially expressed genes were found to be mainly involved in carbohydrate metabolism, biosynthesis of secondary metabolites as well as energy, lipid and amino acid metabolism via KEGG. Our results provide new insights into the molecular mechanisms and expression profiles of genes in the fruit development stage of table and wine grapes.

Possible involvement and the mechanisms of excess trans-fatty acid consumption in severe NAFLD in mice

Excessive trans-fatty acids (TFA) consumption has been thought to be a risk factor mainly for coronary artery diseases while less attention has been paid to liver disease. We aimed to clarify the impact of TFA-rich oil consumption on the hepatic pathophysiology compared to natural oil. Mice were fed either a low-fat (LF) or high-fat (HF) diet made of either natural oil as control (LF-C or HF-C) or partially hydrogenated oil, TFA-rich oil (LF-T or HF-T) for 24 weeks. We evaluated the liver and body weight, serological features, liver lipid content and composition, liver histology and hepatic lipid metabolism-related gene expression profile. In addition, primary cultures of mice Kupffer cells (KCs) were evaluated for cytokine secretion and phagocytotic ability after incubation in cis- or trans-fatty acid-containing medium. The HF-T-fed mice showed significant increases of the liver and body weights, plasma alanine-aminotransferase, free fatty acid and hepatic triglyceride content compared to the HF-C group, whereas the LF-T group did not differ from the LF-C group. HF-T-fed mice developed severe steatosis, along with increased lipogenic gene expression and hepatic TFA accumulation. KCs showed increased tumor necrosis factor secretion and attenuated phagocytotic ability in the TFA-containing medium compared to its cis-isomer. Excessive consumption of the TFA-rich oil up-regulated the lipogenic gene expression along with marked hepatic lipid accumulation. TFA might be pathogenic through causing severe steatosis and modulating the function of KCs. The quantity and composition of dietary lipids could be responsible for the pathogenesis of non-alcoholic steatohepatitis.