Metabolites

Progressive familial intrahepatic cholestasis (PFIC) is a debilitating disease manifest by severe cholestasis, intractable pruritus and growth delay that ultimately leads to liver failure or transplantation. Maralixibat (MRX) was recently approved for the treatment of cholestatic pruritus in patients with Alagille syndrome. The aim of this study was to determine whether specific changes in the composition of the serum bile acid metabolome could predict pruritus response to treatment. Serum BAs (sBA) and 7α-hydroxy-4-cholesten-3-one (7α-C4), a surrogate marker of BA synthesis, were monitored by ultrahigh-performance liquid chromatography coupled with tandem mass spectrometry over 72 weeks in PFIC patients with mild to moderate non-truncating bile salt export pump (BSEP) mutations (n = 19) treated with MRX. The weekly itch reported outcome observer (ItchRO[Obs]) score measured pruritus severity. Linear mixed models (LMM) were applied to explore the effects of individual sBA profiles and their relationship to pruritus response. Changes in the composition of sBA correlated with pruritus improvement. Notably, the trajectory of serum total and individual BA species and 7α-C4 were significantly associated with ItchRO[Obs] score (p < 0.05). These results reveal that beyond simple total sBA concentrations, specific changes to the BA metabolome are associated with pruritus reduction in patients with BSEP deficiency, thus providing further insight into causal relationship of bile acids and pruritus. Full article

Asparagus officinalis L. is a common vegetable widely consumed due to its high consumer acceptance. In addition to its flavor, green asparagus contains a high amount of bioactive compounds with health-promoting effects. In this sense, the growing concern of the public health system to promote a diet with a higher consumption of vegetables makes research on phytochemicals from this food of interest. In order to study the content of bioactive compounds from plant matrices, the combination of advanced extraction and analytical techniques within the context of green chemistry is an indispensable working model in today’s research. In the present experimental work, the composition of the phytochemicals of green asparagus from the Protected Geographical Indication (PGI) located in Huétor Tájar, Granada (Spain), was evaluated by environmentally friendly extraction techniques. In order to carry out this work, the recovery of bioactive compounds was evaluated by pressurized liquid extraction (PLE) using GRAS (Generally Recognized As Safe) solvents (mixtures of water and ethanol). The extraction was optimized using a Response Surface Methodology (RSM) based on a 2⁴ factorial Central Composite Design (CCD). The experimental model was followed by high-performance liquid chromatography coupled to electrospray ionization time-of-flight mass spectrometry (HPLC–ESI-TOF-MS) analytical methodology for a comprehensive characterization. The optimized methodology was compared with conventional solid–liquid extraction protocols using ethanol and water. The results highlighted the potential of advanced PLE techniques compared to conventional systems for the recovery of green asparagus phytochemicals. Moreover, the analytical characterization allowed the identification and quantitation of major phenolic compounds belonging to phenolic acids and flavonoids families. Therefore, an easy, fast, and novel methodology to optimize the extraction of bioactive compounds from green asparagus has been optimized, using Green and GRAS methodology, which enables a better understanding of the bioactive composition of this widely consumed food. Full article

Chronic pain and depression affect millions of people worldwide, and their comorbidity tends to exacerbate the severity of each individual condition. Intersecting brain regions and molecular pathways could probably explain the unique yet complex bidirectional relationship between these two disorders. Recent studies have found that inflammatory reactions, frequently identified in both chronic pain and depression, stimulate certain enzymes in the kynurenine pathway, while concurrently suppressing others. Kynurenine, a major tryptophan derivative, and its metabolites have been implicated in several inflammation-associated pain syndromes and depressive mood disorders. Due to inflammation, 95% of tryptophan is metabolized via the kynurenine pathway, which drives the reaction towards the production of metabolites that have distinct roles in the pathophysiology of these disorders. Diminished levels of the neuroprotective metabolite, kynurenic acid (KYNA), and elevated levels of the neurotoxic metabolite, quinolinic acid (QUIN), have been frequently identified in human patients formally diagnosed with these disorders, as well as animal models commonly used in medical research. This review not only explores the epidemiology of comorbid chronic pain and depression, but also highlights the involvement of kynurenine and its metabolites, specifically KYNA and QUIN, in these pervasive conditions. Full article

The metabolomic and proteomic basis of mild cognitive impairment (MCI) and Alzheimer’s disease (AD) is poorly understood, and the relationships between systemic abnormalities in metabolism and AD/MCI pathogenesis is unclear. This study compared the metabolomic and proteomic signature of plasma from cognitively normal (CN) and dementia patients diagnosed with MCI or AD, to identify specific cellular pathways and new biomarkers altered with the progression of the disease. We analysed 80 plasma samples from individuals with MCI or AD, as well as age- and gender-matched CN individuals, by utilising mass spectrometry methods and data analyses that included combined pathway analysis and model predictions. Several proteins clearly identified AD from the MCI and CN groups and included plasma actins, mannan-binding lectin serine protease 1, serum amyloid A2, fibronectin and extracellular matrix protein 1 and Keratin 9. The integrated pathway analysis showed various metabolic pathways were affected in AD, such as the arginine, alanine, aspartate, glutamate and pyruvate metabolism pathways. Therefore, our multi-omics approach identified novel plasma biomarkers for the MCI and AD groups, identified changes in metabolic processes, and may form the basis of a biomarker panel for stratifying dementia participants in future clinical trials. Full article

Although exercise training is an important recommendation for the management of type 1 diabetes (T1D), most of the available research studies predominantly focus on male subjects. Given the importance of sex as a biological variable, additional studies are required to improve the knowledge gap regarding sex differences in T1D research. Therefore, the purpose of this study was to examine the role of exercise training in mediating changes in glucose homeostasis and skeletal muscle metabolism in T1D female mice. Female mice were injected with streptozotocin (STZ) to induce T1D. Two weeks after STZ injection, control (CON) and STZ mice were exercise trained on a treadmill for 4 weeks. Aerobic exercise training failed to improve glucose tolerance, prevent the decrease in body weight and adipose tissue mass, or attenuate muscle atrophy in T1D female mice. However, insulin sensitivity was improved in T1D female mice after exercise training. Aerobic exercise training maintained skeletal muscle triglyceride content but did not prevent depletion of skeletal muscle or liver glycogen in T1D mice. Gene expression analysis suggested that T1D resulted in decreased glucose transport, decreased ketone body oxidation, and increased fatty acid metabolism in the skeletal muscle, which was not altered by exercise training. These data demonstrate that 4 weeks of aerobic exercise training of a moderate intensity is insufficient to counteract the negative effects of T1D in female mice, but does lead to an improvement in insulin sensitivity. Full article

Diabetes mellitus leads to cellular damage and causes apoptosis by oxidative stress. Heartwood extract of Pterocarpus marsupium has been used in Ayurveda to treat various diseases such as leprosy, diabetes, asthma, and bronchitis. In this study, we worked out the mechanism of the antidiabetic potential of methanolic heartwood extract of Pterocarpus marsupium (MPME). First, metabolic profiling of MPME was done using gas chromatography-mass spectrometry (GCMS), ultra-performance liquid chromatography-mass spectroscopy (UPLC-MS), and high-performance thin-layer chromatography (HPTLC) to identify phenols, flavonoids, and terpenoids in MPME. Biological studies were carried out in vitro using the HepG2 cell line. Many antidiabetic compounds were identified including Quercetin. Methanolic extract of MPME (23.43 µg/mL–93.75 µg/mL) was found to be safe and effective in reducing oxyradicals in HepG2 cells. A concentration of 93.75 µg/mL improved glucose uptake efficiently. A significant decrease in oxidative stress, cell damage, and apoptosis was found in MPME-treated HepG2 cells. The study suggests that the heartwood of Pterocarpus marsupium offers good defense in HepG2 cells against oxidative stress and improves glucose uptake. The results show the significant antidiabetic potential of MPME using a HepG2 cell model. The effect seems to occur by reducing oxidative stress and sensitizing the cells towards glucose uptake, hence lowering systemic glucose levels, as well as rescuing ROS generation. Full article

Colitis-associated cancer (CAC), arising from long-lasting intestinal inflammation, is a common type of colorectal cancer. Sinomenine (SIN), the major active compound of Sinomenium acutum, displays excellent antitumor activity. In modern pharmacological research, SIN has been proved to arrest proliferation of human colon cancer cells in vitro, but its functional role and specific mechanism in CAC were still elusive. This study explored the molecular mechanism of SIN on CAC. The results showed that orally administered SIN could decrease the occurrence and development of CAC. Metabolomics results revealed SIN could reprogram metabolism in CAC mice by reversing 34 endogenous metabolites. Importantly, the most prominent metabolic alteration was lipid metabolism. Mechanistically, SIN improved lipid metabolism by enhancing the expression of CPT1A in CAC mice. Moreover, the inhibitory effect of SIN on the proliferation of human colon cancer cells was blunted via CPT1A inhibitor. The results of this study added further evidence of the molecular mechanisms that allow SIN to exert anti-CAC effect by facilitating lipid metabolism and reaffirmed its potential and distinctive role as a chemopreventive agent in CAC. Full article

Omics approaches in plant analysis find many different applications, from classification to new bioactive compounds discovery. Metabolomics seems to be one of the most informative ways of describing plants’ phenotypes, since commonly used methods such as liquid chromatography–mass spectrometry (LC-MS) and nuclear magnetic resonance spectroscopy (NMR) could provide a huge amount of information about samples. However, due to high efficiency, many disadvantages arise with the complexity of the experimental design. In the present work, we demonstrate an untargeted metabolomics pipeline with the example of a Humulus lupulus classification task. LC-MS profiling of brewing cultivars samples was carried out as a starting point. Hierarchical cluster analysis (HCA)-based classification in combination with nested feature selection was provided for sample discrimination and marker compounds discovery. Obtained metabolome-based classification showed an expected difference compared to genetic-based classification data. Nine compounds were found to have the biggest classification power during nested feature selection. Using database search and molecular network construction, five of them were identified as known hops bitter compounds. Full article

Many environmental stresses can affect the accumulation of metabolites in plants, including drought. In the present study, we found a great deal of variability in the seed metabolic profiles of the tolerant (Matterhorn, SB-DT2 and SB-DT3) common bean genotypes in comparison to the sensitive genotypes (Sawtooth, Merlot and Stampede) using ultrahigh performance liquid chromatography−tandem mass spectrometry (UPLC-MS). The genotypes were grown in the field and subjected to drought stress after flowering (terminal drought stress). We aimed to investigate the accumulation of genotype-specific metabolites and related pathways under terminal drought stress by comparing tolerant and sensitive genotypes within a race. A total of 26 potential metabolites were identified across genotype comparisons. Significant metabolic pathways, including monobactam biosynthesis, flavone and flavonol biosynthesis, pentose phosphate pathway, C5-branched dibasic acid metabolism, cysteine and methionine metabolism, vitamin B6 metabolism and flavonoid biosynthesis, were derived from the enriched metabolites. Many of these metabolic pathways were specific and varied with genotype comparisons. SB-DT2 vs. stampede revealed more significant metabolites and metabolic pathways compared to Matterhorn vs. Sawtooth and SB-DT3 vs. Merlot under terminal drought stress. Our study provides useful information regarding the metabolite profiles of seeds and their related pathways in comparisons of tolerant and sensitive common bean genotypes under terminal drought conditions. Further research, including transcriptomic and proteomic analyses, may contribute to a better understanding of molecular mechanisms and nutritional differences among seeds of common bean genotypes grown under terminal drought conditions. Full article

Radiotherapy and internal radioisotope therapy (brachytherapy) induce tumor cell death through different molecular signaling pathways. However, these therapies in cancer patients are constrained by dose-related adverse effects and local discomfort due to the prolonged exposure to the surrounding tissues. Technological advancements in nanotechnology have resulted in synthesis of high atomic elements such as nanomaterials, which can be used as radiosensitizers due to their photoelectric characteristics. The aim of this review is to elucidate the effects of novel nanomaterials in the field of radiation oncology to ameliorate dose-related toxicity through the application of ideal nanoparticle-based radiosensitizers such as Au (gold), Bi (bismuth), and Lu (Lutetium-177) for enhancing cytotoxic effects of radiotherapy via the high-Z effect. In addition, we discuss the role of nanoparticle-enhanced radiotherapy in alleviating tumor hypoxia through the nanodelivery of genes/drugs and other functional anticancer molecules. The implications of engineered nanoparticles in preclinical and clinical studies still need to be studied in order to explore potential mechanisms for radiosensitization by minimizing tumor hypoxia, operational/logistic complications and by overcoming tumor heterogeneity in radiotherapy/brachytherapy. Full article

Mass spectrometry (MS) is increasingly used in clinical studies to obtain molecular evidence of chemical exposures, such as tobacco smoke, alcohol, and drugs. This evidence can help verify clinical data retrieved through anamnesis or questionnaires and may provide insights into unreported exposures, for example those classified as the same despite small but possibly relevant chemical differences or due to contaminants in reported exposure compounds. Here, we aimed to explore the potential of untargeted SWATH metabolomics to differentiate such closely related exposures. This data-independent acquisition MS-based profiling technique was applied to urine samples of 316 liver and 570 kidney transplant recipients from the TransplantLines Biobank and Cohort Study (NCT03272841), where we focused on the immunosuppressive drug mycophenolate, which is either supplied as a morpholino-ester prodrug or as an enteric-coated product, the illicit drug cocaine, which is usually supplied as an adulterated product, and the proton pump inhibitors omeprazole and esomeprazole. Based on these examples, we found that untargeted SWATH metabolomics has considerable potential to identify different (unreported) exposure or co-exposure metabolites and may determine variations in their abundances. We also found that these signals alone may sometimes be unable to distinguish closely related exposures, and enhancement of differentiation, for example by integration with pharmacogenomics data, is needed. Full article

The regulation of DHEA-sulfate by steroid sulfotransferase (SULT) and steryl-sulfatase (STS) enzymes is a vital process for the downstream formation of many steroid hormones. DHEA-sulfate is the most abundant steroid hormone in the human body; thus, DHEA-sulfate and its hydrolyzed form, DHEA, continue to be evaluated in numerous studies, given their importance to human health. Yet, a basic question of relevance to the reproductive-age female population—whether the two steroid hormones vary across the menstrual cycle—has not been addressed. We applied a validated, multi-step protocol, involving realignment and imputation of study data to early follicular, mid-late follicular, periovulatory, and early, mid-, and late luteal subphases of the menstrual cycle, and analyzed DHEA-sulfate and DHEA serum concentrations using ultraperformance liquid chromatography tandem mass spectrometry. DHEA-sulfate levels started to decrease in the early luteal, significantly dropped in the mid-luteal, and returned to basal levels by the late luteal subphase. DHEA, however, did not vary across the menstrual cycle. The present study deep-mapped trajectories of DHEA and DHEA-sulfate across the entire menstrual cycle, demonstrating a significant decrease in DHEA-sulfate in the mid-luteal subphase. These findings are relevant to the active area of research examining associations between DHEA-sulfate levels and various disease states. Full article

The effect of glycemic stress on de novo lipogenesis (DNL) in podocytes and tubular epithelial cells is understudied. This study is aimed (A) to show the effect of glycemic stress on DNL, and (B) to assess the effect of acetyl-Co A (ACC) inhibition on halting upregulation of DNL, on the expression of other lipid regulatory genes in the DNL pathway, and on markers of fibrosis and apoptosis in podocytes and tubular epithelial cells. We used cultured mouse primary tubular epithelial cells, mouse proximal tubular (BUMPT) cells, and immortal mouse podocytes and measured their percentage of labeled ¹³C₂-palmitate as a marker of DNL after incubation with ¹³C₂ acetate in response to high glucose concentration (25 mM). We then tested the effect of ACC inhibition by complimentary strategies utilizing CRISPR/cas9 deletion or incubation with Acaca and Acacb GapmeRs or using a small molecule inhibitor on DNL under hyperglycemic concentration. Exposure to high glucose concentration (25 mM) compared to osmotic controlled low glucose concentration (5.5 mM) significantly increased labeled palmitate after 24 h up to 72 h in podocytes and primary tubular cells. Knocking out of the ACC coding Acaca and Acacb genes by CRISPR/cas9, downregulation of Acaca and Acacb by specific antisense LNA GapmeRs and inhibition of ACC by firsocostat similarly halted/mitigated upregulation of DNL and decreased markers of fibrosis and programmed cell death in podocytes and various tubular cells. ACC inhibition is a potential therapeutic target to mitigate or halt hyperglycemia-induced upregulation of DNL in podocytes and tubular cells. Full article

Irisin is an exercise-induced myokine implicated as a fundamental mediator of physical activity benefits. The aim of the present study was to investigate the role of the chronic administration model of irisin on the physiological and molecular status of skeletal muscle. A total of 20 female Sprague Dawley rats (250 ± 40 g) were implanted with an irisin-loaded osmotic pump (5 µg/kg/day) for 42 days; in addition, 3 females received a single subcutaneous injection of irisin (5 µg/kg). On a weekly basis for six weeks, animals were weighed and blood samples were collected. After 42 days, hind muscle biopsies were collected for histology and gene analysis. Serum irisin, clinical biochemistry, and histopathology were quantified and evaluated. Genes encoding for different physiological muscle activities, such as oxidative stress, fatty acid metabolism, muscle hypertrophy, mitochondrial fusion, and aging were assayed. The results showed a significant reduction in body weight percentage and creatine kinase level without affecting the morphological characteristics of skeletal muscle. Significant changes were noted in genes involved in muscle physiological activity, growth, and aging, as well as genes encoding for the antioxidant system, fatty acid oxidation processes, and mitochondrial fusion. In conclusion, exogenous irisin can induce the same physiological and molecular mechanisms that might be induced by exercise. Full article

Phloroglucinols—one of the major secondary metabolites in Dryopteris crassirhizoma—exhibit various pharmacological effects, such as antiviral, antioxidant, and antidiabetic activities. This study evaluated 30 phloroglucinols isolated from the rhizomes of D. crassirhizoma for their inhibitory activity on β-glucuronidase via in vitro assays. Among them, dimeric phloroglucinols 13–15 moderately inhibited β-glucuronidase, and trimeric phloroglucinols 26–28 showed strong inhibitory effects, with IC₅₀ values ranging from 5.6 to 8.0 μM. Enzyme kinetic analysis confirmed all six active compounds to be in a competitive mode of inhibition. Molecular docking simulations revealed the key binding interactions with the active site of β-glucuronidase protein and the binding mechanisms of these active metabolites. Our results suggest that the rhizomes of D. crassirhizoma and trimeric compounds 26–28 may serve as potential candidates for discovering and developing new β-glucuronidase inhibitors. Full article

Recently, dipeptidyl peptidase-IV (DPP-IV) has become an effective target in the management of type-2 diabetes mellitus (T2D). The study aimed to determine the efficacy of shikimate pathway-derived phenolic acids as potential DPP-IV modulators in the management of T2D. The study explored in silico (molecular docking and dynamics simulations) and in vitro (DPP-IV inhibitory and kinetics assays) approaches. Molecular docking findings revealed chlorogenic acid (CA) among the examined 22 phenolic acids with the highest negative binding energy (−9.0 kcal/mol) showing a greater affinity for DPP-IV relative to the standard, Diprotin A (−6.6 kcal/mol). The result was corroborated by MD simulation where it had a higher affinity (−27.58 kcal/mol) forming a more stable complex with DPP-IV than Diprotin A (−12.68 kcal/mol). These findings were consistent with in vitro investigation where it uncompetitively inhibited DPP-IV having a lower IC₅₀ (0.3 mg/mL) compared to Diprotin A (0.5 mg/mL). While CA showed promising results as a DPP-IV inhibitor, the findings from the study highlighted the significance of medicinal plants particularly shikimate-derived phenolic compounds as potential alternatives to synthetic drugs in the effective management of T2DM. Further studies, such as derivatisation for enhanced activity and in vivo evaluation are suggested to realize its full potential in T2D therapy. Full article

Kidney diseases encompass many pathologies, including obstructive nephropathy (ON), a common clinical condition caused by different etiologies such as urolithiasis, prostatic hyperplasia in males, tumors, congenital stenosis, and others. Unilateral ureteral obstruction (UUO) in rodents is an experimental model widely used to explore the pathophysiology of ON, replicating vascular alterations, tubular atrophy, inflammation, and fibrosis development. In addition, due to the kidney’s high energetic demand, mitochondrial function has gained great attention, as morphological and functional alterations have been demonstrated in kidney diseases. Here we explore the kidney mitochondrial proteome differences during a time course of 7, 14, and 21 days after the UUO in rats, revealing changes in proteins involved in three main metabolic pathways, oxidative phosphorylation (OXPHOS), the tricarboxylic acid cycle (TCA), and the fatty acid (FA) metabolism, all of them related to bioenergetics. Our results provide new insight into the mechanisms involved in metabolic adaptations triggered by the alterations in kidney mitochondrial proteome during the ON. Full article

The interactive mechanism of root and soil for achieving high and stable yield of maize is still unclear. Synchronizing soil nutrient supply with crop requirements by optimizing fertilization is effective cultivation measures to improve maize yield. In this study, field trials were conducted to investigate the dynamic changes of optimized fertilization on chemical and bacterial properties in rhizosphere soil, root physiological properties, and yield of fresh waxy maize. Optimized fertilization practices (one-time application of new compound fertilizer at sowing, three-, and six-leaf stages, denoted as F1, F2, and F3), local traditional fertilization (F4), and no fertilization (F0) were set up in 2-year field experiments at two sites. F3 increased the fresh ear (10.2%) and grain (9.4%) yields relative to F4. Optimized fertilization practices increased the abundance and diversity of rhizosphere soil bacterial communities at R3. The enzymatic activities of oxidoreductase, hydrolase, transferase, and lyase in rhizosphere soil under F3 were higher than those in other treatments at R1 and R3. F3 increased the contents of organic matter and total N in rhizosphere soil, as well as the root activities. These findings provide physiological information from underground on optimized fertilization types and stages in enhancing the yield of fresh waxy maize. One-time application of new compound fertilizer at six-leaf stage increased the abundance and diversity of bacterial, organic matter and total N content in rhizosphere soil, enhanced root activity at post-silking stage, and eventually improved yield of fresh waxy maize in southern China. Full article

Scopoletin, a typical example of a coumarin compound, exists in several Artemisia species and other plant genera. However, the systemic metabolic effects induced by scopoletin remain unclear. In the present study, we evaluated the metabolic profiles in scopoletin-exposed zebrafish embryos using UHPLC-Q-Obitrap-HRMS combined with multivariate analysis. Compared with the control group, 33 metabolites in scopoletin group were significantly upregulated, while 27 metabolites were significantly downregulated. Importantly, scopoletin exposure affected metabolites mainly involved in phosphonate and phosphinate metabolism, vitamin B6 metabolism, histidine metabolism, sphingolipid metabolism, and folate biosynthesis. These results suggested that scopoletin exposure to zebrafish embryos exhibited marked metabolic disturbance. This study provides a perspective of metabolic impacts and the underlying mechanism associated with scopoletin exposure. Full article