Metabolomics-driven identification of perturbations in amino acid and sphingolipid metabolism as therapeutic targets in a rat model of anorexia nervosa disease using chemometric analysis and a multivariate analysis platform

Metabolomics for Clinical Biomarker Discovery and Therapeutic Target Identification

As links between genotype and phenotype, small-molecule metabolites are attractive biomarkers for disease diagnosis, prognosis, classification, drug screening and treatment, insight into understanding disease pathology and identifying potential targets. Metabolomics technology is crucial for discovering targets of small-molecule metabolites involved in disease phenotype. Mass spectrometry-based metabolomics has implemented in applications in various fields including target discovery, explanation of disease mechanisms and compound screening. It is used to analyze the physiological or pathological states of the organism by investigating the changes in endogenous small-molecule metabolites and associated metabolism from complex metabolic pathways in biological samples. The present review provides a critical update of high-throughput functional metabolomics techniques and diverse applications, and recommends the use of mass spectrometry-based metabolomics for discovering small-molecule metabolite signatures that provide valuable insights into metabolic targets. We also recommend using mass spectrometry-based metabolomics as a powerful tool for identifying and understanding metabolic patterns, metabolic targets and for efficacy evaluation of herbal medicine.

Spotting of Volatile Signatures through GC-MS Analysis of Bacterial and Fungal Infections in Stored Potatoes (Solanum tuberosum L.)

Potatoes inoculated with Pectobacterium carotovorum spp., Aspergillus flavus and Aspergillus niger, along with healthy (control) samples, were stored at different storage temperatures (4 ± 1 °C, 8 ± 1 °C, 25 ± 1 °C) for three weeks. Volatile organic compounds (VOCs) were mapped using the headspace gas analysis through solid phase micro extraction-gas chromatography-mass spectroscopy every week. The VOC data were arranged into different groups and classified using principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) models. Based on a variable importance in projection (VIP) score > 2 and the heat map, prominent VOCs were identified as 1-butanol and 1-hexanol, which can act as biomarkers for Pectobacter related bacterial spoilage during storage of potatoes in different conditions. Meanwhile, hexadecanoic acid and acetic acid were signature VOCs for A. flavus, and hexadecane, undecane, tetracosane, octadecanoic acid, tridecene and undecene were associated with A. niger. The PLS-DA model performed better at classifying the VOCs of the three different species of infection and the control sample compared to PCA, with high values of R² (96-99%) and Q² (0.18-0.65). The model was also found to be reliable for predictability during random permutation test-based validation. This approach can be adopted for fast and accurate diagnosis of pathogenic invasion of potatoes during storage.

Anti-inflammatory peptides and metabolomics-driven biomarkers discovery from sea cucumber protein hydrolysates

The hydrolysates from Apostichopus japonicus sea cucumber are an important source of nitrogen that may be added to foods. We evaluated the effect of A. japonicus hydrolysates on inflammation-associated leukocyte recruitment. The results revealed that leukocyte migration to the site of injury was significantly blocked by AJH-1 (<10 kDa), suggesting a protective effect against CuSO₄ -induced neuromast damage in a zebrafish model. Based on liquid chromatography/time-of-flight/mass spectrometry, and metabolomic analysis, the nine biomarker candidates in AJH-1 were Val, Ala-Pro-Arg, Gly-Lys, Asp propyl ester, Glu methyl ester, His butyl ester, Ile-Ala-Ala-Lys, Tyr-Lys, and Asn-Pro-Gly-Lys. We used molecular docking to predict the binding affinity and docked position of the peptides onto the angiotensin converting enzyme (ACE). All the identified peptides had adequate binding affinity toward ACE, especially peptides Ala-Pro-Arg and Gly-Lys. These peptides may be used in the development of therapeutic foods. PRACTICAL APPLICATION: The study revealed the anti-inflammatory properties of the fractionated sea cucumber protein hydrolysate (<10 kDa). The characteristic peptides may be used as functional ingredients in nutraceutical foods and beverages.

Serum metabolic signature of binge-like palatable food consumption in female rats by nuclear magnetic resonance spectroscopy

Maladaptive eating behavior is a growing public health problem and compulsively eating excessive food in a short time, or binge eating, is a key symptom of many eating disorders. In order to investigate the binge-like eating behavior in female rats, induced by intermittent food restrictions/refeeding and frustration stress, we analyzed for the first time the metabolic profile obtained from serum of rats, through nuclear magnetic resonance (NMR) spectroscopy. In this experimental protocol, rats were exposed to chow food restricting/refeeding and frustration stress manipulation. This stress procedure consists of 15 min exposure to the odor and sight of a familiar chocolate paste, without access to it, just before offering the palatable food. In this model, a "binge-eating episode" was considered the significantly higher palatable food consumption within 2 h in restricted and stressed rats (R + S) than in the other three experimental groups: rats with no food restriction and no stress (NR + NS), only stressed rats (NR + S) or only restricted rats (R + NS). Serum samples from these four different rat groups were collected. The statistical analysis of the ¹ H NMR spectral profiles of the four sets of samples pointed to O- and N-acetyl glycoproteins as the main biomarkers for the discrimination of restriction effects. Other metabolites, such as threonine, glycine, glutamine, acetate, pyruvate and lactate, showed trends that may be useful to understand metabolic pathways involved in eating disorders. This study suggested that NMR-based metabolomics is a suitable approach to detect biomarkers related to binge-eating behavior.

Proteomics and metabolomics analysis reveal potential mechanism of extended-spectrum β-lactamase production in Escherichia coli

In this study, ten clinical susceptible strains and ten clinical ESBL-EC (extended-spectrum β-lactamase-producing Escherichia coli) were screened and obtained by microbial identification using ITEK® 2 Compact. TMT (Tandem Mass Tag) proteomics analysis discovered 1553 DEPs (differentially expressed proteins) between ESBL-EC and non-ESBL-EC. In addition, an untargeted metabolomics assay by using UHPLC-MS (ultra-high-performance liquid chromatography-mass spectrometry) was applied to compare the differential profiles of metabolites between β-lactam antibiotic-sensitive E. coli and multidrug-resistant ESBL-producing E. coli strains. The PCA (principal component analysis) score plots and OPLS-DA (orthogonal projections to latent structures discriminant analysis) plots clearly discriminated ESBL-EC and non-ESBL-EC, and volcano analysis presented 606 and 459 altered metabolites between ESBL-EC vs. non-ESBL-EC in positive and negative ion modes, respectively. Interestingly, the bioinformatics analysis demonstrated that the purine metabolism pathway was enriched in ESBL-EC. These results suggest that the existence of extended-spectrum β-lactamase affects the metabolite and protein profiles of E. coli. The correlation analysis of metabolomics and proteomics data established a correlation between DEPs and differential metabolites in the purine metabolism pathway. Moreover, three metabolite candidates in the purine metabolism pathway were validated by the UPLC-MRM-MS (ultra-performance liquid chromatography multiple reaction monitoring mass spectrometry) method. Our data suggest that these DEPs and differential metabolites may play important roles in the antibiotic resistance of ESBL-EC. Our study can provide scientific data for the mechanism study of antibiotic resistance of ESBL-EC at the metabolite and protein levels and targeting modulators to these pathways may be effective for treatment of ESBL-EC strains.

Proteomic and metabolomics revealed the underlying mechanism of extended-spectrum β-lactamase production in Escherichia coli.