Biomarkers.

Hypertension is a major risk factor for the pathogenesis of vascular dementia and Alzheimer's disease. Chronic activation of the renin-angiotensin system (RAS) contributes substantially to neuroinflammation. We propose that neuroinflammation arising from chronic RAS activation can initiate and potentiate the onset of hypertension and related dementia. Neuroinflammation induced by chronic activation of the RAS plays a key role in the pathogenesis of dementia. Increased levels of pro-inflammatory cytokines tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and transforming growth factor (TGF)-β have been reported in brain tissue of vascular dementia patients and animal models of vascular dementia induced by either angiotensin II infusion or transverse aortic coarctation. It is proposed that neuronal cell death and synaptic dysfunction induced by neuroinflammation lead to cognitive impairment in dementia. The neuroprotective RAS pathway, regulated by angiotensin-converting enzyme 2 (ACE2) which converts angiotensin II into angiotensin-(1-7), can attenuate hypertension and dementia. Furthermore, the use of anti-hypertensive medications in preventing dementia or cognitive decline in hypertensive patients and animal models of dementia have mostly been beneficial. Current evidence suggests a strong link between RAS induced neuroinflammation and the onset of hypertension and dementia, which warrants further investigation. Strategies to counteract an overactive RAS and enhance the neuroprotective arm of the RAS may help prevent or improve cognitive impairment associated with hypertension.

IntroductionGraves' disease (GD), a common autoimmune thyroid disorder, is typified by hyperthyroidism and pervasive metabolic perturbations. Metabolomics, a burgeoning field instrumental in biomarker identification and elucidating systemic biological mechanisms, has recently shed light on the intricate pathophysiology of GD. The present study endeavors to delineate the metabolic aberrations in untreated GD patients from Shenzhen, China, leveraging LC-MS-based serum metabolomics.MethodsA cohort comprising 30 newly diagnosed, untreated GD patients and 32 healthy controls was assembled. Serum metabolite profiling was conducted via LC-MS, with subsequent identification and quantification of metabolites. Multivariate statistical analyses, encompassing principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA), were employed to discern significant metabolic discrepancies. Pathway enrichment analysis and receiver operating characteristic (ROC) curve analysis were utilized to assess the diagnostic efficacy of the identified metabolites.ResultsA total of 334 significantly dysregulated metabolites were uncovered, with a pronounced involvement of lipid and organic acid metabolic pathways. Notably, N-phenethylacetamide (AUC = 0.94), diaminopimelic acid (AUC = 0.93), and the dipeptide Gly-Val (AUC = 0.91) exhibited substantial diagnostic potential. Pathway enrichment analysis unveiled significant alterations in linoleic acid, alpha-linolenic acid, and arachidonic acid metabolism, underscoring the pivotal role of inflammatory lipid pathways and amino acid metabolism in GD.DiscussionThis study offers a granular metabolic profile of untreated Graves' disease, unmasking profound dysregulation within lipid and organic acid metabolism. The identified metabolites, particularly N-phenethylacetamide, diaminopimelic acid, and Gly-Val, emerge as promising high-performance serum biomarkers for GD diagnosis. These findings not only augment our comprehension of the metabolic reprogramming inherent to GD but also proffer potential targets for subsequent therapeutic endeavors. Subsequent investigations are imperative to elucidate the mechanistic roles of these metabolites in GD pathogenesis and their viability as clinical biomarkers.

BackgroundCisplatin and carboplatin are the primary first-line therapies for the treatment of ovarian cancer. However, resistance to these platinum-based drugs occurs in the large majority of initially responsive tumors, resulting in fully chemoresistant, fatal disease. Although the precise mechanism(s) underlying the development of platinum resistance in late-stage ovarian cancer patients currently remains unknown, CpG-island (CGI) methylation, a phenomenon strongly associated with aberrant gene silencing and ovarian tumorigenesis, may contribute to this devastating condition.MethodsTo model the onset of drug resistance, and investigate DNA methylation and gene expression alterations associated with platinum resistance, we treated clonally derived, drug-sensitive A2780 epithelial ovarian cancer cells with increasing concentrations of cisplatin. After several cycles of drug selection, the isogenic drug-sensitive and -resistant pairs were subjected to global CGI methylation and mRNA expression microarray analyses. To identify chemoresistance-associated, biological pathways likely impacted by DNA methylation, promoter CGI methylation and mRNA expression profiles were integrated and subjected to pathway enrichment analysis.ResultsPromoter CGI methylation revealed a positive association (Spearman correlation of 0.99) between the total number of hypermethylated CGIs and GI50 values (i.e., increased drug resistance) following successive cisplatin treatment cycles. In accord with that result, chemoresistance was reversible by DNA methylation inhibitors. Pathway enrichment analysis revealed hypermethylation-mediated repression of cell adhesion and tight junction pathways and hypomethylation-mediated activation of the cell growth-promoting pathways PI3K/Akt, TGF-beta, and cell cycle progression, which may contribute to the onset of chemoresistance in ovarian cancer cells.ConclusionSelective epigenetic disruption of distinct biological pathways was observed during development of platinum resistance in ovarian cancer. Integrated analysis of DNA methylation and gene expression may allow for the identification of new therapeutic targets and/or biomarkers prognostic of disease response. Finally, our results suggest that epigenetic therapies may facilitate the prevention or reversal of transcriptional repression responsible for chemoresistance and the restoration of sensitivity to platinum-based chemotherapeutics.

Single-cell chromatin accessibility sequencing (scCAS) technologies have enabled characterizing the epigenomic heterogeneity of individual cells. However, the identification of features of scCAS data that are relevant to underlying biological processes remains a significant gap. Here, we introduce a novel method Cofea, to fill this gap. Through comprehensive experiments on 5 simulated and 54 real datasets, Cofea demonstrates its superiority in capturing cellular heterogeneity and facilitating downstream analysis. Applying this method to identification of cell type-specific peaks and candidate enhancers, as well as pathway enrichment analysis and partitioned heritability analysis, we illustrate the potential of Cofea to uncover functional biological process.

Metabolic characteristics related to the hazardous effects of environmental arsenic on humans: A metabolomic review

This study aimed to identify potential biomarkers in high-risk human papillomavirus (HR-HPV) infections and related cervical lesions through the analysis of vaginal metabolic profiles. Forty cervicovaginal secretion samples were collected from healthy individuals, HR-HPV-positive individuals, low-grade squamous intraepithelial lesion patients, high-grade squamous intraepithelial lesion patients, and cervical cancer (CC) patients. All samples were analyzed using liquid chromatography-mass spectrometry (LC-MS). Metabolites with significant differences were identified using the variable importance in projection (VIP > 1) derived from the orthogonal least partial squares discriminant analysis (OPLS-DA) model and the p-value (p < 0.05) of the Student's t test. Utilizing hierarchical cluster analysis and receiver operating characteristic curve analysis, the optimal biomarkers were identified, and the diagnostic potential of these biomarkers was evaluated. Significantly enriched pathways of the differential metabolites were explored using metabolic pathway analysis. LC-MS analysis of the vaginal metabolomic profiles revealed unique molecular characteristics of different states of HR-HPV infection. Based on persistent HR-HPV infection, 3-Isochromanone increased, and DG(2:0/5-iso PGF2VI/0:0) and (4R,5S,7R,11x)-11,12-Dihydroxy-1(10)-spirovetiven-2-one 12-glucoside decreased (p < 0.05) with the aggravation of cervical lesions, suggesting their potential as biomarkers to predict various stages of cervical lesions. Additionally, analysis of metabolic pathway enrichment for differential metabolites identified the phenylalanine, tyrosine, and tryptophan biosynthesis pathways as the key metabolic pathways in the progression of cervical lesions. By measuring the metabolome of vaginal secretions, specific metabolites can effectively distinguish persistent HR-HPV infections and different grades of cervical lesions, which may become an important means for the early screening and diagnosis of CC.

The Intestinal Metabolome: An Intersection Between Microbiota and Host

Selenium (Se) is an essential trace element used for biosynthesis of selenoproteins and is acquired either through diet or cellular recycling mechanisms. Selenocysteine lyase (Scly) is the enzyme that supplies Se for selenoprotein biosynthesis via decomposition of the amino acid selenocysteine (Sec). Knockout (KO) of Scly in a mouse affected hepatic glucose and lipid homeostasis. Mice lacking Scly and raised on an Se-adequate diet exhibit hyperinsulinemia, hyperleptinemia, glucose intolerance, and hepatic steatosis, with increased hepatic oxidative stress, but maintain selenoprotein levels and circulating Se status. Insulin challenge of Scly KO mice results in attenuated Akt phosphorylation but does not decrease phosphorylation levels of AMP kinase alpha (AMPKα). Upon dietary Se restriction, Scly KO animals develop several characteristics of metabolic syndrome, such as obesity, fatty liver, and hypercholesterolemia, with aggravated hyperleptinemia, hyperinsulinemia, and glucose intolerance. Hepatic glutathione peroxidase 1 (GPx1) and selenoprotein S (SelS) production and circulating selenoprotein P (Sepp1) levels are significantly diminished. Scly disruption increases the levels of insulin-signaling inhibitor PTP1B. Our results suggest a dependence of glucose and lipid homeostasis on Scly activity. These findings connect Se and energy metabolism and demonstrate for the first time a unique physiological role of Scly in an animal model.

Trochlear dysplasia (TD) is a skeletal deformity that causes abnormal morphology of the trochlear groove, leading to patellar instability and related joint issues. Despite its clinical importance, the molecular mechanisms behind TD are not well understood. This study aims to explore these mechanisms using an integrated proteomic and metabolomic approach in a rat model of TD. A rat model was developed by inducing a flat trochlear groove and increasing the sulcus angle. Validation was performed using gross morphology and micro-CT. Subchondral bone loss was evaluated through micro-CT. Non-targeted metabolomics was applied to identify differential metabolites, and proteomics was conducted to identify altered proteins. Pathway enrichment and interaction analyses were used to interpret the data. The TD rat model exhibited significant morphological and bone density changes, including notable subchondral bone loss. Metabolomic analysis identified 52 differentially expressed metabolites, with creatine and L-malic acid prominently altered. Proteomic analysis revealed 204 differentially expressed proteins. KEGG analysis highlighted critical pathways such as glycine, serine, and threonine metabolism and the PI3K-Akt signaling pathway. Integrative analysis showed correlations between key metabolites and proteins, providing deeper insights into TD-related molecular changes. This study integrates proteomic and metabolomic analyses to uncover molecular alterations in a rat model of TD. Significant findings include upregulation of Col3a1 and altered metabolites such as creatine and L-malic acid. These results highlight the role of metabolic disturbances such as glycine, serine, and threonine metabolism and the PI3K-Akt signaling pathway in TD pathology. The study provides valuable biomarkers and insights into the mechanisms of TD, offering potential targets for future therapeutic and diagnostic strategies.

Pedunculate oak (Quercus robur L.) is an economically important forest-forming species in Poland that produces seeds that are sensitive to desiccation; therefore, short-lived seeds are classified as recalcitrant. Such seeds display active metabolism throughout storage. Acorns stored under controlled conditions (moisture content of 40%, temperature −3 °C) maintain viability for up to 1.5–2 years. Meanwhile, oaks only produce large numbers of seeds every few years during so-called mast years. This results in a scarcity of good-quality seeds for continuous nursery production and restoration. The recalcitrant storage behavior and the requirements of foresters make it necessary to develop a new protocol for longer acorn storage at lower temperatures. Two storage temperatures were tested: −3 °C (currently used in forest practice) and −7 °C. Our results showed that acorns stored for six months exhibited deterioration and reduced germination capacity, as well as reduced seedling performance, particularly when acorns were stored at −7 °C. To elucidate the decrease in quality during storage, an untargeted metabolomics study was performed for the first time and supported with the analysis of carbohydrates and percentages of carbon (C) and nitrogen (N). Embryonic axes were characterized by a lower C:N ratio and higher hydration. A total of 1985 metabolites were detected, and 303 were successfully identified and quantified, revealing 44 known metabolites that displayed significantly up- or downregulated abundance. We demonstrated for the first time that the significant deterioration of seed germination potential, particularly in seeds stored at −7 °C, was accompanied by an increased abundance of phenolic compounds and carbohydrates but also amino acids and phosphorylated monosaccharides, particularly in the embryonic axes. The increased abundance of defense-related metabolites (1,2,4-Benzenetriol; BTO), products of ascorbic acid degradation (threonic and isothreonic acid), as well as antifreezing compounds (sugar alcohols, predominantly threitol), was reported in seed stored at −7 °C. We hypothesize that seed deterioration was caused by freezing stress experienced during six months of storage at −7 °C, a decline in antioxidative potential and the unsuccessful rerouting of the energy-production pathways. Additionally, our data are a good example of the application of high-throughput metabolomic tools in forest management.

IntroductionObesity is an increasingly serious global health concern and is closely associated with gut dysbiosis and metabolic imbalance. Despite the considerable research conducted on the gut microbiota and metabolism over recent years, studies focusing on their correlation with obesity remain limited. In this study, we sought to characterize the gut microbiota and serum metabolic profiles of patients with obesity, aiming to identify potential biomarkers and therapeutic targets for this condition, and explore possible links between altered amino acid levels and gut microbial composition in its pathophysiology. The findings may offer novel insights into obesity prevention and treatment through microbiota modulation or amino acid regulation.MethodsForty adult volunteers with obesity (BMI = 30.9 ± 2.9 kg/m2) who met the diagnostic criteria were enrolled in this study. Pregnant or lactating women and individuals with severe comorbidities were excluded. The control group comprised 20 subjects with normal weight (BMI = 21.9 ± 1.7 kg/m2) and without metabolic disorders, recruited from among outpatients during the same period and matched for age and sex. Fecal microbiota profiling was performed using 16S rRNA sequencing. DNA was extracted from stool samples, and the V3–V4 region was amplified and sequenced on the Illumina platform. After rigorous quality control (QC) and chimera removal, effective tags were clustered into Operational Taxonomic Units (OTUs) based on sequence similarity. Alpha and beta diversity and intergroup differential abundance were assessed, with statistical significance determined by Welch's t-test. Serum metabolomic analysis was performed using standardized sample preparation and QC procedures, followed by LC–MS/MS-based targeted and untargeted metabolomics. Calibration curves with R2 > 0.99 were established, and relative metabolite concentrations were calculated from peak areas. In total, 28 amino acid metabolites were quantified and used for subsequent statistical analysis.ResultsSignificant differences in microbial composition were observed across multiple taxonomic levels between the controls and patients with obesity. At the phylum level, Proteobacteria was enriched in the obesity group (AUC = 0.709, 95% CI: 0.569–0.848; p = 0.006). At the class level, Gammaproteobacteria (AUC = 0.712, 95% CI: 0.573–0.852; p = 0.009) and Erysipelotrichia (AUC = 0.614, 95% CI: 0.471–0.757; p = 0.02) were found to be enriched in obesity. At the order level, enrichment was observed for Enterobacteriales (AUC = 0.734, 95% CI: 0.597–0.871; p = 0.008) and Erysipelotrichia (AUC = 0.614, 95% CI: 0.471–0.757; p = 0.029). At the family level, Enterobacteriaceae (AUC = 0.614, 95% CI: 0.471–0.757; p = 0.003) showed enrichment in obesity. Finally, at the genus level, Escherichia-Shigella (AUC = 0.71, 95% CI: 0.565–0.855; p = 0.028) was enriched in obesity, while at the species level, Bacteroides fragilis (AUC = 0.733, 95% CI: 0.593–0.873; p = 0.016) and Parabacteroides distasonis (AUC = 0.61, 95% CI: 0.466–0.754; p = 0.033) were noted to be enriched. Metabolomic analysis revealed that in patients with obesity, the abundance of carnosine (log2FC = 1.16, FDR = 0.0016, VIP = 0.707), creatinine (log2FC = 0.21, FDR = 0.0009, VIP = 2.02), and cystine (log2FC = 0.55, FDR = 0.009, VIP = 1.47) was significantly increased compared with that in the controls; in contrast, that of ornithine (log2FC = −0.59, FDR = 0.0009, VIP = 1.19), citrulline (log2FC = −0.59, FDR = 0.0003, VIP = 0.707), glycine (log2FC = −0.54, FDR = 0.0003, VIP = 1.41), and serine (log2FC = −0.38, FDR = 0.0019, VIP = 1.62) was significantly decreased. This suggested that these metabolites may have potential as early diagnostic biomarkers for obesity.ConclusionsObesity is associated with coordinated shifts in specific gut taxa and serum metabolites, with measurable effect sizes and strong discriminatory performance. Modulating amino acid levels or gut microbiota composition may represent a promising strategy for obesity prevention and treatment.

Metabolomics plays an important role in phytochemical genomics and crop breeding; however, metabolite annotation is a significant bottleneck in metabolomic studies. In particular, in liquid chromatography–mass spectrometry (MS)-based metabolomics, which has become a routine technology for the profiling of plant-specialized metabolites, a substantial number of metabolites detected as MS peaks are still not assigned properly to a single metabolite. Oryza sativa (rice) is one of the most important staple crops in the world. In the present study, we isolated and elucidated the structures of specialized metabolites from rice by using MS/MS and NMR. Thirty-six compounds, including five new flavonoids and eight rare flavonolignan isomers, were isolated from the rice leaves. The MS/MS spectral data of the isolated compounds, with a detailed interpretation of MS fragmentation data, will facilitate metabolite annotation of the related phytochemicals by enriching the public mass spectral data depositories, including the plant-specific MS/MS-based database, ReSpect.Electronic supplementary materialThe online version of this article (doi:10.1007/s11306-013-0619-5) contains supplementary material, which is available to authorized users.

Inhibition of metabolic disorders in vivo and in vitro by main constituent of Coreopsis tinctoria

Fructose-induced prediabetes causes persistent DNA methylation changes in white adipose tissue despite metabolic normalization.

Ultra-high-performance liquid chromatography-Q exactive orbitrap tandem mass spectrometry(UHPLC-QEOrbitrap-MS/MS) was used to explore the inhibitory effect and mechanism of ginkgo flavone aglycone(GA) combined with doxorubicin(DOX) on H22 cells. The effects of different concentrations of GA and DOX on the viability of H22 cells were investigated, and combination index(CI) was used to evaluate the effects. In the experiments, control(CON) group, DOX group, GA group, and combined GA and DOX(GDOX) group were constructed. Then the metabolomics strategy was employed to explore the metabolic markers that were significantly changed after combination therapy on the basis of single medication treatment, and by analyzing their biological significance, the effect and mechanism of the anti-tumor effect of GA combined with DOX were explained. The results revealed that when 30 μg·mL~(-1) GA and 0.5 μmol·L~(-1) DOX was determined as the co-administration concentration, the CI value was 0.808, indicating that the combination of GA and DOX had a synergistic anti-tumor effect. Metabolomics analysis identified 23 metabolic markers, including L-arginine, L-tyrosine and L-valine, mostly amino acids. Compared with the CON group, 22 and 17 metabolic markers were significantly down-regulated after DOX treatment and GA treatment, respectively. Compared with the DOX and GA groups, the treatment of GA combined with DOX further down-regulated the levels of these metabolic markers in liver cancer, which might contribute to the synergistic effect of the two. Five key metabolic pathways were found in pathway enrichment analysis, including glutathione metabolism, phenylalanine metabolism, arginine and proline metabolism, β-alanine metabolism, and valine, leucine and isoleucine degradation. These findings demonstrated that the combination of GA and DOX remarkably inhibited the viability of H22 cells and exerted a synergistic anti-tumor effect. The mechanism might be related to the influence of the energy supply of tumor cells by interfering with the metabolism of various amino acids.