PubMed

Biomed Chromatogr. 2023 Aug 22:e5719. doi: 10.1002/bmc.5719. Online ahead of print.ABSTRACTLarge intestine dampness-heat syndrome (LIDHS) is a common syndrome type in animal diarrheal diseases. Yujin powder (YJP) is one of the classic prescriptions for treating damp-heat diarrhea. The aim of this study was to investigate the regulatory effects of YJP on gut microbiota and serum metabolism in LIDHS rats using 16S rRNA sequencing and nontargeted metabolomics. The LIDHS rat model was induced through a high-sugar and high-fat diet, exposure to a high-temperature and high-humidity environment, and infection with Escherichia coli. The results demonstrated that the administration of YJP resulted in a decrease in the abundance of Desulfovibrio, Parabacteroides, Bacteroides, Allobaculum, Escherichia, Butyricimonas, Parasutterella, and Blautia and an increase in Ruminococcus, Akkermansia, Roseburia, and Lachnoclostridium. A total of 25 potential biomarkers were identified in three groups of rats. These metabolites were primarily involved in glycerophospholipid metabolism, taurine and hypotaurine metabolism, glycerol ester metabolism, arachidonic acid metabolism, primary bile acid synthesis, and tryptophan metabolism. Our study demonstrated that YJP has the potential to alleviate LIDHS by modulating gut microbial and serum metabolic homeostasis. These results establish a foundation and offer valuable guidance for the utilization of YJP in the treatment of LIDHS.PMID:37605605 | DOI:10.1002/bmc.5719

Cancer Med. 2023 Aug 21. doi: 10.1002/cam4.6446. Online ahead of print.ABSTRACTBACKGROUND: Anti-folate drug pemetrexed is a vital chemotherapy medication for non-small cell lung cancer (NSCLC). Its response varies widely and often develops resistance to the treatment. Therefore, it is urgent to identify biomarkers and establish models for drug efficacy evaluation and prediction for rational drug use.METHODS: A total of 360 subjects were screened and 323 subjects were recruited. Using metabolomics in combination with machine learning methods, we are trying to select potential biomarkers to diagnose NSCLC and evaluate the efficacy of pemetrexed in treating NSCLC. Furtherly, we measured the concentration of eight metabolites in the tryptophan metabolism pathway in the validation set containing 201 subjects using a targeted metabolomics method with UPLC-MS/MS.RESULTS: In the discovery set containing 122 subjects, the metabolic profile of healthy controls (H), newly diagnosed NSCLC patients (ND), patients who responded well to pemetrexed treatment (S) and pemetrexed-resistant patients (R) differed significantly on the PLS-DA scores plot. Pathway analysis showed that glycine, serine and threonine metabolism occurred in every two group comparisons. TCA cycle, pyruvate metabolism and glycerolipid metabolism are the most significantly changed pathways between ND and H group, pyruvate metabolism was the most altered pathway between S and ND group, and tryptophan metabolism was the most changed pathway between S and R group. We found Random forest method had the maximum area under the curve (AUC) and can be easily interpreted. The AUC is 0.981 for diagnosing patients with NSCLC and 0.954 for evaluating pemetrexed efficiency.CONCLUSION: We compared eight mathematical models to evaluate pemetrexed efficiency for treating NSCLC. The Random forest model established with metabolic markers tryptophan, kynurenine and xanthurenic acidcan accurately diagnose NSCLC and evaluate the response of pemetrexed.PMID:37605514 | DOI:10.1002/cam4.6446

Anal Chem. 2023 Aug 21. doi: 10.1021/acs.analchem.3c02073. Online ahead of print.ABSTRACTResistance to clinical therapies remains a major barrier in cancer management. There is a critical need for rapid and highly sensitive diagnostic tools that enable early prediction of treatment response to allow accurate clinical decisions. Here, Raman spectroscopy was employed to monitor changes in key metabolites as early predictors of response in KRAS-mutant colorectal cancer (CRC) cells, HCT116, treated with chemotherapies. We show at the single cell level that HCT116 is resistant to cetuximab (CTX), the first-line treatment in CRC, but this resistance can be overcome with pre-sensitization of cells with oxaliplatin (OX). In combination treatment of CTX + OX, sequential delivery of OX followed by CTX rather than simultaneous administration of drugs was observed to be critical for effective therapy. Our results demonstrated that metabolic changes are well aligned to cellular mechanical changes where Young's modulus decreased after effective treatment, indicating that both changes in mechanical properties and metabolism in cells are likely responsible for cancer proliferation. Raman findings were verified with mass spectrometry (MS) metabolomics, and both platforms showed changes in lipids, nucleic acids, and amino acids as predictors of resistance/response. Finally, key metabolic pathways enriched were identified when cells are resistant to CTX but downregulated with effective treatment. This study highlights that drug-induced metabolic changes both at the single cell level (Raman) and ensemble level (MS) have the potential to identify mechanisms of response to clinical cancer therapies.PMID:37605298 | DOI:10.1021/acs.analchem.3c02073

Nat Metab. 2023 Aug 21. doi: 10.1038/s42255-023-00855-2. Online ahead of print.ABSTRACTT cell function and fate can be influenced by several metabolites: in some cases, acting through enzymatic inhibition of α-ketoglutarate-dependent dioxygenases, in others, through post-translational modification of lysines in important targets. We show here that glutarate, a product of amino acid catabolism, has the capacity to do both, and has potent effects on T cell function and differentiation. We found that glutarate exerts those effects both through α-ketoglutarate-dependent dioxygenase inhibition, and through direct regulation of T cell metabolism via glutarylation of the pyruvate dehydrogenase E2 subunit. Administration of diethyl glutarate, a cell-permeable form of glutarate, alters CD8+ T cell differentiation and increases cytotoxicity against target cells. In vivo administration of the compound is correlated with increased levels of both peripheral and intratumoural cytotoxic CD8+ T cells. These results demonstrate that glutarate is an important regulator of T cell metabolism and differentiation with a potential role in the improvement of T cell immunotherapy.PMID:37605057 | DOI:10.1038/s42255-023-00855-2

Nat Commun. 2023 Aug 21;14(1):5062. doi: 10.1038/s41467-023-40569-3.ABSTRACTWe evaluate the shared genetic regulation of mRNA molecules, proteins and metabolites derived from whole blood from 3029 human donors. We find abundant allelic heterogeneity, where multiple variants regulate a particular molecular phenotype, and pleiotropy, where a single variant associates with multiple molecular phenotypes over multiple genomic regions. The highest proportion of share genetic regulation is detected between gene expression and proteins (66.6%), with a further median shared genetic associations across 49 different tissues of 78.3% and 62.4% between plasma proteins and gene expression. We represent the genetic and molecular associations in networks including 2828 known GWAS variants, showing that GWAS variants are more often connected to gene expression in trans than other molecular phenotypes in the network. Our work provides a roadmap to understanding molecular networks and deriving the underlying mechanism of action of GWAS variants using different molecular phenotypes in an accessible tissue.PMID:37604891 | DOI:10.1038/s41467-023-40569-3

Sci Rep. 2023 Aug 21;13(1):13564. doi: 10.1038/s41598-023-40560-4.ABSTRACTOxidative stress (OS), which impacts lipid metabolic reprogramming, can affect the biological activities of cancer cells. How oxidative stress and phospholipid metabolism (OSPM) influence the prognosis of pancreatic cancer (PC) needs to be elucidated. The metabolic data of 35 pancreatic tumor samples, 34 para-carcinoma samples, and 31 normal pancreatic tissues were obtained from the previously published literature. Pan-cancer samples were obtained from The Cancer Genome Atlas (TCGA). And the Gene Expression Omnibus (GEO), International Cancer Genome Consortium (ICGC), ArrayExpress, and the Genotype-Tissue Expression (GTEx) databases were searched for more PC and normal pancreatic samples. The metabolites in PC were compared with normal and para-carcinoma tissues. The characteristics of the key OSPM genes were summarized in pan-cancer. The random survival forest analysis and multivariate Cox regression analysis were utilized to construct an OSPM-related signature. Based on this signature, PC samples were divided into high- and low-risk subgroups. The dysregulations of the tumor immune microenvironment were further investigated. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was conducted to investigate the expression of genes in the signature in PC and normal tissues. The protein levels of these genes were further demonstrated. In PC, metabolomic studies revealed the alteration of PM, while transcriptomic studies showed different expressions of OSPM-related genes. Then 930 PC samples were divided into three subtypes with different prognoses, and an OSPM-related signature including eight OSPM-related genes (i.e., SLC2A1, MMP14, TOP2A, MBOAT2, ANLN, ECT2, SLC22A3, and FGD6) was developed. High- and low-risk subgroups divided by the signature showed different prognoses, expression levels of immune checkpoint genes, immune cell infiltration, and tumor microenvironment. The risk score was negatively correlated with the proportion of TIL, pDC, Mast cell, and T cell co-stimulation. The expression levels of genes in the signature were verified in PC and normal samples. The protein levels of SLC2A1, MMP14, TOP2A, MBOAT2, ANLN, and SLC22A3 showed up-regulation in PC samples compared with normal tissues. After integrating metabolomics and transcriptomics data, the alterations in OSPM in PC were investigated, and an OSPM-related signature was developed, which was helpful for the prognostic assessment and individualized treatment for PC.PMID:37604837 | DOI:10.1038/s41598-023-40560-4

Anal Chim Acta. 2023 Oct 9;1277:341655. doi: 10.1016/j.aca.2023.341655. Epub 2023 Jul 26.ABSTRACTAlthough various metabolomic methods have been reported in recent years, simultaneous detection of hydrophilic and hydrophobic metabolites in a single analysis remains a technical challenge. In this study, based on the combination of hydrophilic interaction liquid chromatography (HILIC) and reversed phase liquid chromatography (RPLC), an online two-dimensional liquid chromatography/triple quadrupole mass spectrometry method (2D-LC/TQMS) was developed for the simultaneous analysis of hydrophilic and hydrophobic metabolites of various biological samples. The method can measure 417 biologically important metabolites (e.g., amino acids and peptides, pyrimidines, purines, monosaccharides, fatty acids and conjugates, organic dicarboxylic acids, and others) with logP values ranging from -10.3 to 21.9. The metabolites are involved in a variety of metabolic pathways (e.g., purine metabolism, pyrimidine metabolism, tyrosine metabolism, galactose metabolism, gluconeogenesis, and TCA cycle). The developed method has good intra- and inter-day reproducibility (RSD of retention time <2%, RSD of peak area <30%), good linearity (R2 > 0.9) and wide linear range (from 0.0025 μg/mL to 5 μg/mL). The applicability of the method was tested using different biological samples (i.e., plasma, serum, urine, fecal, seminal plasma and liver) and it was found that 208 (out of 417) identical metabolites were detected in all biological samples. Furthermore, the metabolomic method was applied to a case/control study of urinary of bladder cancer. Thirty differential metabolites were identified that were involved in carbohydrate and amino acid metabolism.PMID:37604610 | DOI:10.1016/j.aca.2023.341655

J Ethnopharmacol. 2023 Aug 19:117066. doi: 10.1016/j.jep.2023.117066. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Suo-Quan-Wan (SQW), a traditional Chinese prescription, has been used for hundreds of years to alleviate overactive bladder (OAB) symptoms such as frequent and nocturnal urination. However, limited modern research on OAB therapeutic targets has hindered the use and development of SQW.AIM OF THE STUDY: This study aimed to investigate the biological mechanisms and key targets of SQW on OAB in spontaneously hypertensive rats (SHR) using an integrated analysis of network pharmacology, transcriptome and metabolome.METHODS: Rats were divided into five groups: model group (SHR), control group (WKY), darifenacin group, high dose (SQWH) and low dose (SQWL) group. Urodynamic parameters and histological examination were detected. Network pharmacology, transcriptome, and metabolome were used to screen for disease gene targets, differential mRNA, and differential metabolites, respectively. The biological targets and mechanisms of SQW for OAB were analyzed. Western blotting was performed to verify the proteins of key differential targets.RESULTS: Urodynamics revealed a significant decrease in storage parameters in SHR. After SQW treatment, the inter-contraction interval, voided volume and bladder capacity increased by 2-3 times, as well as bladder compliance. Additionally, SQW improved the pathological changes in the urinary tract epithelium and the detrusor layer of the bladder in SHR. Metabolomic results showed an increase in arachidonic acid (AA) and cyclic adenosine monophosphate (cAMP) in plasma, suggesting the involvement of arachidonic acid metabolism and purine metabolism in SQW treatment. The downregulation of cytochrome P450 1B1 (CYP1B1), thromboxane-A synthase (TBXAS1), polyunsaturated fatty acid 5-lipoxygenase (ALOX5), and cAMP-specific 3',5'-cyclic phosphodiesterase 4B (PDE4B) were confirmed through topological analysis and Venn analysis of omics data and network pharmacology. These proteins affected the metabolism of AA and cAMP, respectively, and consequently affected downstream proteins, such as transient receptor potential (TRP) cation channel proteins (e.g. TRPV1, TRPA1, and TRPM8), myosin light chain kinase (MLCK), and the phosphorylation of myosin regulatory light chain (p-MLC).CONCLUSION: This study initially elucidated the importance of AA and cAMP in the treatment of SQW, indicating the AA-CYP1B1/TBXAS1/ALOX5-TRPA1/TRPV1/TRPM8 and cAMP-PDE4B-MLCK-p-MLC pathways as the important pathways in SQW-treated SHR bladder in vivo.PMID:37604331 | DOI:10.1016/j.jep.2023.117066

Adv Nutr. 2023 Aug 19:S2161-8313(23)01360-1. doi: 10.1016/j.advnut.2023.08.010. Online ahead of print.ABSTRACTBACKGROUND: Dietary metabolomics is a relatively objective approach to identifying new biomarkers of dietary intake and for use alongside traditional methods. However, methods used across dietary feeding studies vary, thus making it challenging to compare results.OBJECTIVES: To synthesize methodological components of controlled human feeding studies designed to quantify the diet-related metabolome in biospecimens, including plasma, serum, and urine following dietary interventions.METHODS: Six electronic databases were searched. Included studies were (1) conducted in healthy adults; (2) intervention studies; (3) feeding studies focusing on dietary patterns; and (4) measured the dietary metabolome.RESULTS: From 12,425 texts, 50 met all inclusion criteria. Interventions were primarily cross-over (n=25) and parallel RCTs (n=22), with between 8 to 395 participants. Seventeen different dietary patterns were tested, with the most common being "High versus Low Glycaemic Index/Load" pattern (n=11) and "Typical Country Intake" (n=11); with 32 providing all or the majority (90%) of food, 16 providing some food, and two providing no food. Metabolites were identified in urine (n=31) and plasma/serum (n=30). Metabolites were quantified using liquid chromatography, mass spectroscopy (n=31) and used untargeted metabolomics (n=37).CONCLUSIONS: There was extensive variability in the methods used in controlled human feeding studies examining the metabolome, including dietary patterns tested, biospecimen sample collection, and metabolomic analysis techniques. To improve comparability and reproducibility of controlled human feeding studies examining the metabolome, it is important to provide detailed information about the dietary interventions being tested, including information about included or restricted foods, food groups, and meal plans provided. Strategies to control for individual variability, such as a cross-over study design, statistical adjustment methods, dietary-controlled run-in periods, or providing standardized meals or test foods throughout the study should also be considered.REGISTRY NUMBER OPEN SCIENCE FRAMEWORK: The protocol for this review has been registered at Open Science Framework (https://doi.org/10.17605/OSF.IO/DAHGS).PMID:37604308 | DOI:10.1016/j.advnut.2023.08.010

Fish Shellfish Immunol. 2023 Aug 19:109012. doi: 10.1016/j.fsi.2023.109012. Online ahead of print.ABSTRACTEmerging evidence suggests that artemisinin (ART) can modulate pathogen-induced immune responses and metabolic dysregulation. However, whether this modulation is associated with metabolic pathways related to oxidative stress and inflammation remains unclear. The aim of this study was to investigate the antioxidant and anti-inflammatory effects on the ART-fed juvenile fat greenling Hexagrammos otakii and the associated metabolic pathways in response to ART administration using an integrated biochemical and metabolomic approach. Biochemical analysis and histological examination showed that ART significantly increased body weight gain and improved tissue structure. ART effectively attenuated reactive oxygen species (ROS), malondialdehyde (MDA) and inflammatory responses (NFκB, TNF-α, IL-6, and MCP-1) in the Edwardsiella tarda-induced H. otakii model. Liver metabolomics analysis revealed that twenty-nine metabolites were up-regulated and twenty-one metabolites were down-regulated after ART administration compared to those in pathogen-induced fish. Pathway analysis indicated that ART alleviated the E. tarda-induced inflammation and oxidative stress through two major pathways, namely lipid metabolism and amino acid metabolism. Taken together, ART showed great potential as a natural feed additive against pathogen-induced oxidative stress and inflammation.PMID:37604265 | DOI:10.1016/j.fsi.2023.109012

Chem Biol Interact. 2023 Aug 19:110674. doi: 10.1016/j.cbi.2023.110674. Online ahead of print.ABSTRACTHepatocellular carcinoma (HCC) is one of the most common malignant tumors with high morbidity and mortality. Targeting abnormal cholesterol metabolism is a potential therapeutic direction. Therefore, more natural drugs targeting cholesterol in HCC need to be developed. Gypenosides (Gyp), the major constituent of Gynostemma pentaphyllum, has been demonstrated to have pharmacological properties on anti-cancer, anti-obesity, and hepatoprotective. We investigated whether Gyp, isolated and purified by our lab, could inhibit HCC progression by inhibiting cholesterol synthesis. The present research showed that Gyp inhibited proliferation and migration, and induced apoptosis in Huh-7 and Hep3B cells. Metabolomics, transcriptomics, and target prediction all suggested that lipid metabolism and cholesterol biosynthesis were the mechanisms of Gyp. Gyp could limit the production of cholesterol and target HMGCS1, the cholesterol synthesis-related protein. Downregulation of HMGCS1 could suppress the progression and abnormal cholesterol metabolism of HCC. In terms of mechanism, Gyp suppressed mevalonate (MVA) pathway mediated cholesterol synthesis by inhibiting HMGCS1 transcription factor SREBP2. And the high expression of HMGCS1 in HCC human specimens was correlated with poor clinical prognosis. The data suggested that Gyp could be a promising cholesterol-lowering drug for the prevention and treatment of HCC. And targeting SREBP2-HMGCS1 axis in MVA pathway might be an effective HCC therapeutic strategy.PMID:37604220 | DOI:10.1016/j.cbi.2023.110674

Poult Sci. 2023 Jul 26;102(10):102961. doi: 10.1016/j.psj.2023.102961. Online ahead of print.ABSTRACTSkeletal characteristics are important to the growth and development of poultry. In feeding management, constant free feeding (FF) of poultry may lead to imbalance between bone development and weight gain. Feed restriction (FR), to a certain extent, is one way to solve this problem. However, the effect of feed restriction on poultry bone development needs further elucidation at the molecular level. Therefore, in the present study, we investigated the effects of different levels of feed restriction (60% FR, 70% FR, 80% FR, and FF) on the sternum development of ducks at 7 and 8 wk old. In the seventh wk, with increasing feed restriction, the values of traits including body weight, breast muscle weight, sternal weight, keel length, and calcified keel length decreased. However, in the eighth wk, the sternum weight and keel length of ducks treated with 60% FR were unexpectedly higher than those of FF individuals, indicative of catch-up growth. Then, we conducted RNA-seq and metabolomic analysis on sterna from 7- and 8-wk-old FF and 60% FR ducks. The results identified multiple differentially expressed genes (DEGs) associated with sternum development that were influenced by feed restriction. Among them, we found that the mRNA expression levels of the chondroitin sulfate synthase 3 (CHSY3) and annexin A2 (ANXA2) which are involved in glycosaminoglycan biosynthesis and bone mineralization, had smaller changes over time under FR treatment than under FF treatment, implying that the FR treatment to a certain extent prevented the premature calcification and prolonged the development time of duck sternum. In addition, the metabolomic and integrative analyses revealed that several antiaging-related metabolites and genes were associated with sternal catch-up growth. Pyrimidine metabolism was identified as the most significant pathway in which most differential metabolites (DMs) between FF and 60% FR were enriched. The results from integrative analysis revealed that the content and expression of 4-aminobutyric acid (GABA) and its related genes showed relatively higher activity in the 60% FR group than in the FF group. The present study identifies multiple biomarkers associated with duck sternum development that are influenced by feed restriction and suggests the potential mechanism of feed restriction-associated duck sternal catch-up growth.PMID:37604023 | DOI:10.1016/j.psj.2023.102961

Food Chem. 2023 Aug 17;431:137138. doi: 10.1016/j.foodchem.2023.137138. Online ahead of print.ABSTRACTThis study aimed to elucidate how the Maillard reaction (MR) affects the flavor and bioactivities of Lentinula edodes hydrolysates (LEHs). Changes in flavor were investigated using non-targeted metabolomics techniques (GC-MS and LC-MS/MS) and sensory evaluation. Simultaneously, UV absorption, fluorescence, and FT-IR spectra were used to characterize the process of MR. We also evaluated the effects of MR on the antioxidant activity, hypoglycemic activity and antimicrobial activity of LEHs in vitro. The results revealed that MR produced many volatile aldehydes and ketones and decreased the content of most amino acids, sugars and flavonoids in the LEHs while increasing the content of l-theanine and succinic acid. MRPs had a strong caramel and like-meat flavor and an obvious improvement in umami, taste continuity, and total acceptability. Furthermore, MR improved the antioxidant and antimicrobial properties of LEHs. This research establishes a theoretical foundation for MR in the deep processing of edible mushrooms.PMID:37604001 | DOI:10.1016/j.foodchem.2023.137138

Food Chem. 2023 Aug 7;431:137113. doi: 10.1016/j.foodchem.2023.137113. Online ahead of print.ABSTRACTMorus alba L. fruits are considered functional foods with an important nutritional value for their high content of polyphenols. Therefore, the type and level of phytochemicals of the soroses from 13 M. alba cultivars grown in Italy were characterized due to the lack of data available about their nutraceutical properties. Mature M. alba fruits exhibited variable polyphenol, flavonoid, anthocyanin, proanthocyanins, and 1-deoxynojirimycin contents which resulted in different antioxidant and α-glucosidase inhibitory activities. Regression models built on UHPLC-HRMS results revealed a strong correlation between the expression of quercetin derivatives, cyanidin 3-O-glucoside, caffeoyl methyl quinates, and 5,5'-dehydrodivanillic acid, and the biological activity of each fruit. On another note, principal component analysis revealed that the quantity of caffeoyl/dicaffeoyl methyl quinate, caffeoylquinic acids, and quercetin derivatives decreased during ripening. The results on the compositional and functional characterization of mature M. alba fruits might improve their consumption and economic value in Italy.PMID:37604000 | DOI:10.1016/j.foodchem.2023.137113

Plant Physiol Biochem. 2023 Aug 11;202:107955. doi: 10.1016/j.plaphy.2023.107955. Online ahead of print.ABSTRACTSweetness is an important attribute of fruit quality, which directly affects consumers' preference for fresh fruit and is mostly determined by carbohydrate composition. 'Fengtang' plum (Prunus salicina Lindl.) is recognized for its high soluble sugar content, but the sugar composition and the molecular mechanisms underlying sugar overproduction are not fully understood. In this work, the sugar components were analyzed using gas chromatography-mass spectrometry combined with transcription profiles from RNA-sequencing and Quantitative Real-time PCR during fruit development. The target metabolic group showed that sucrose was the dominant sugar component in mature fruit, followed by glucose, fructose, and sorbitol. Based on the transcriptome data and qRT-PCR validation, we identified 12 key structural genes that significantly responded to corresponding component accumulation: sucrose synthase (PsSUS4), sucrose phosphate synthase (PsSPS2), neutral invertase (PsNINV1/3/4), phosphoglucomutase (PsPGM1), UTP-glucose-1-phosphate uridylyl transferase (PsUGP1/2), hexose kinase (PsHXK1/3), sugar transport protein (PsSTP1), and Sugars Will Eventually be Exported Transporter (PsSWEET4). In which PsSUS4 and PsSPS2, whose encoding proteins immediately catalyze sucrose synthesis, were selected to be silenced using the virus-induced gene silencing technology. Silencing of PsSUS4 or PsSPS2 resulted in decreased sucrose content by 27.6% and 8%, respectively, compared with the control, verifying their important roles in sucrose accumulation. Subsequently, sugar metabolism networks in this high-sugar plum were constructed with 12 key structural genes, 72 putative transcription factors, and 4 major sugar components. These results might facilitate a better understanding of the molecular mechanisms of sugar accumulation in 'Fengtang' plum and provide a framework for future fruit quality improvement.PMID:37603969 | DOI:10.1016/j.plaphy.2023.107955

Int Immunopharmacol. 2023 Aug 19;124(Pt A):110776. doi: 10.1016/j.intimp.2023.110776. Online ahead of print.ABSTRACTIrritable bowel syndrome (IBS) is one of the most common functional gastrointestinal disorders worldwide, characterized by chronic abdominal pain or discomfort and altered bowel habits. To date, the exact pathogenesis of IBS remains elusive, but is clearly multifactorial, including environmental and host factors. However, the management of patients with IBS is challenging and the current diagnostic and therapeutic modalities have unsatisfactory outcomes. Therefore, it is important to develop more effective methods to diagnose IBS early. Metabolomics studies the metabolites most closely related to patient characteristics, which can provide useful clinical biomarkers that can be applied to IBS and may open up new diagnostic approaches. Traditional Chinese medicine (TCM) can play a role in improving symptoms and protecting target organs, but its mechanism needs to be studied in depth. In this review, based on PubMed/MEDLINE and other databases, we searched metabolomics studies related to IBS in the past 5 years, including those related to clinical studies and animal studies, as well as literatures on TCM interventions in IBS, to provide an updated overview of the application of metabolomics to the diagnosis and treatment of IBS and the improvement of IBS by TCM.PMID:37603947 | DOI:10.1016/j.intimp.2023.110776

Theriogenology. 2023 Aug 16;211:84-96. doi: 10.1016/j.theriogenology.2023.08.010. Online ahead of print.ABSTRACTThe canine mammary tumor is the most common tumor type in female dogs and seriously threatens their life. Currently, no effective treatments are available for this condition. Hence, it is essential to identify biomarkers that positively influence the early diagnosis and treatment and prognosis of this disease. To provide a basis for early diagnosis of canine breast tumors, in this study, 23 dogs with mammary tumors were identified via histopathological examination combined with ancillary diagnoses via blood examinations and diagnostic imaging. The canine mammary tumor and tumor-adjacent healthy tissues were collected, and their metabolites were identified utilizing a UHPLC-qTOF-MS-based untargeted metabolomics approach. The metabolic results revealed a total of 979 ion features in the positive polarity mode and 371 ion features in the negative polarity mode in the tissues of two groups; among them, 536 differential metabolites (385 in the positive and 151 in the negative polarity mode) were analyzed by PCA and PLS-DA. Subsequently, the enrichment pathways purine metabolism, alpha-linolenic acid metabolism, vitamin B6 metabolism, and fatty acid biosynthesis were analyzed using Metaboanalyst 4.0, which suggested that these pathways were valuable diagnostic and therapeutic targets. Moreover, the receiver operating characteristic curves further confirmed 13Z,16Z-docosadienoic acid, 23-nordeoxycholic acid, and (±)12(13)-DiHOME as expected candidate biomarkers of canine mammary tumors. In conclusion, the discovery of tumor biomarkers based on untargeted metabolomics is informative for pathological mechanism studies and facilitates the early diagnosis of canine mammary tumors.PMID:37603937 | DOI:10.1016/j.theriogenology.2023.08.010

Proc Natl Acad Sci U S A. 2023 Aug 29;120(35):e2302147120. doi: 10.1073/pnas.2302147120. Epub 2023 Aug 21.ABSTRACTMetabolite levels shape cellular physiology and disease susceptibility, yet the general principles governing metabolome evolution are largely unknown. Here, we introduce a measure of conservation of individual metabolite levels among related species. By analyzing multispecies tissue metabolome datasets in phylogenetically diverse mammals and fruit flies, we show that conservation varies extensively across metabolites. Three major functional properties, metabolite abundance, essentiality, and association with human diseases predict conservation, highlighting a striking parallel between the evolutionary forces driving metabolome and protein sequence conservation. Metabolic network simulations recapitulated these general patterns and revealed that abundant metabolites are highly conserved due to their strong coupling to key metabolic fluxes in the network. Finally, we show that biomarkers of metabolic diseases can be distinguished from other metabolites simply based on evolutionary conservation, without requiring any prior clinical knowledge. Overall, this study uncovers simple rules that govern metabolic evolution in animals and implies that most tissue metabolome differences between species are permitted, rather than favored by natural selection. More broadly, our work paves the way toward using evolutionary information to identify biomarkers, as well as to detect pathogenic metabolome alterations in individual patients.PMID:37603743 | DOI:10.1073/pnas.2302147120

Anal Chem. 2023 Aug 21. doi: 10.1021/acs.analchem.3c00736. Online ahead of print.ABSTRACTThe purity of tandem mass spectrometry (MS/MS) is essential to MS/MS-based metabolite annotation and unknown exploration. This work presents a de novo approach to cleaning chimeric MS/MS spectra generated in liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics. The assumption is that true fragments and their precursors are well correlated across the samples in a study, while false or contamination fragments are rather independent. Using data simulation, this work starts with an investigation of the negative effects of chimeric MS/MS spectra on spectral similarity analysis and molecular networking. Next, the characteristics of true and false fragments in chimeric MS/MS spectra were investigated using MS/MS of chemical standards. We recognized three fragment peak attributes indicative of whether a peak is a false fragment, including (1) intensity ratio fluctuation, (2) appearance rate, and (3) relative intensity. Using these attributes, we tested three machine learning models and identified XGBoost as the best model to achieve an area under the precision-recall curve of 0.98 for a clear separation between true and false fragments. Based on the trained model, we constructed an automated bioinformatic platform, DNMS2Purifier (short for de novo MS2Purifier), for metabolic features from metabolomics studies. DNMS2Purifier recognizes and processes chimeric MS/MS spectra without additional sample analysis or library confirmation. DNMS2Purifer was evaluated on a metabolomics data set generated with different MS/MS precursor isolation windows. It successfully captured the increase in the number of false fragments from the increased isolation window. DNMS2Purifier was also compared to MS2Purifier, an existing MS/MS spectral cleaning tool based on the addition of data-independent acquisition (DIA) analysis. Results indicated that DNMS2Purifier uniquely recognizes false fragments, which complements the previous DIA-based approach. Finally, DNMS2Purifier was demonstrated using a real experimental metabolomics study, showing improved MS/MS spectral quality and leading to an improved spectral match ratio and molecular networking outcome.PMID:37603462 | DOI:10.1021/acs.analchem.3c00736

Endocr Rev. 2023 Aug 21:bnad029. doi: 10.1210/endrev/bnad029. Online ahead of print.ABSTRACTThe decline in cognitive function and the prevalence of neurodegenerative disorders are among the most serious threats to health in old age. The prevalence of dementia has reached 50 million people worldwide and has become one of the major public health problems. The causes of age-related cognitive impairment are multiple, complex, and difficult to determine. However, type 2 diabetes (T2D) is linked to an enhanced risk of cognitive impairment and dementia. Human studies have shown that patients with T2D exhibit dysbiosis of the gut microbiota. This dysbiosis may contribute to the development of insulin resistance and increased plasma lipopolysaccharide concentrations. Metformin medication mimics some of the benefits of calorie restriction and physical activity, such as greater insulin sensitivity and decreased cholesterol levels, and hence may also have a positive impact on aging in humans. According to recent human investigations, metformin might partially restore gut dysbiosis related to T2D. Likewise, some studies showed that metformin reduced the risk of dementia and improved cognition, although not all studies are concordant. Therefore, this review focused on those human studies describing the effects of metformin on the gut microbiome (specifically the changes in taxonomy, function, and circulating metabolomics), the changes in cognitive function and their possible bidirectional implications.PMID:37603460 | DOI:10.1210/endrev/bnad029