PubMed

Rejuvenation Res. 2023 Jun 1. doi: 10.1089/rej.2023.0009. Online ahead of print.ABSTRACTBACKGROUND: Cerebral ischemia-reperfusion (CIR) injury occurs as a secondary injury during the treatment of ischemic stroke (IS). There is a high death rate and morbidity due to IS throughout the world. Even though Naoxintong Capsule (NXT) is effective in the treatment of CIR, its mechanisms of action are unclear.PURPOSE: The study aims to explore the clear mechanism associated with NXT therapy for CIR.METHODS: We established the model of middle cerebral artery occlusion (MCAO) to evaluate the neurological function and assess the infarct size. Brain tissue metabolomics was used to identify different metabolites, and metabolic profiling systems enriched metabolic pathways. Then, the potential targets of NXT in the treatment of CIR were explored by proteomic, transcriptomic and metabolomic methods.RESULTS: NXT improves CIR Symptoms. We found potential 11 proteins and corresponding metabolites involved in NXT treatment of CIR. Most of these metabolites are regulated to restore after treatment. According to network pharmacology, we found 6 hub genes including Glb1, Gmps, Pfas, Atic, Gaa and Acox1, and their associated core metabolites and pathways.PMID:37261991 | DOI:10.1089/rej.2023.0009

FASEB J. 2023 Jul;37(7):e23014. doi: 10.1096/fj.202300261RR.ABSTRACTParenteral nutrition, received by many patients with intestinal failure, can induce hepatobiliary complications, which is termed as parenteral nutrition-associated liver disease (PNALD). The spectrum of PNALD ranges from cholestasis and steatosis to fibrosis and cirrhosis. Although many factors contribute to the pathogenesis of PNALD, the underlying mechanisms remain unclear. In this study, we performed targeted metabolomics to characterize the metabolomic profile in neonatal piglets receiving total parenteral nutrition (TPN) or enteral nutrition (EN) for 1 or 2 weeks. Overall, the metabolomic signature of TPN groups differed from EN groups at both time points. Among the 20 acylcarnitines identified, a majority of them were significantly reduced in TPN groups. KEGG pathway analysis showed that phenylalanine metabolism-associated pathways were dysregulated accompanied by more progressive liver steatosis associated with TPN. Next, we evaluated phenylalanine catabolism and its association with fatty acid oxidation in piglets and rats with PNALD. We showed that the hepatic expression of phenylalanine-degrading enzyme phenylalanine hydroxylase (PAH) was reduced and systemic phenylalanine levels were increased in both animal models of PNALD. Moreover, carnitine palmitoyltransferase 1A, a central regulator of fatty acid oxidation, was downregulated and its expression was negatively correlated with phenylalanine levels in TPN-fed animals. To explore the effects of phenylalanine accumulation on lipid metabolism, we treated HepG2 cells with phenylalanine co-cultured with sodium palmitate or soybean oil emulsion to induce lipid accumulation. We found that phenylalanine treatment exacerbated lipid accumulation by inhibiting fatty acid oxidation without affecting fatty acid synthesis. In summary, our findings establish a pathogenic role of increased phenylalanine levels in driving liver steatosis, linking dysregulation of phenylalanine catabolism with lipid accumulation in the context of PNALD.PMID:37261736 | DOI:10.1096/fj.202300261RR

Int Microbiol. 2023 Jun 1. doi: 10.1007/s10123-023-00375-9. Online ahead of print.ABSTRACTThe compound known as effective microorganisms (EMs) is widely used in aquaculture to improve water quality, but how they affect the health of Chinese mitten crab (Eriocheir sinensis) is unclear, especially in terms of intestinal microbiota and serum metabolites. In this study, we fed juvenile crabs with an EM-containing diet to explore the effects of EM on the physiological status, intestinal microbiome, and metabolites of E. sinensis. The activities of alanine aminotransferase and alkaline phosphatase were significantly enhanced by EM, indicating that EM supplementation effectively enhanced the antioxidant capacity of E. sinensis. Proteobacteria, Tenericutes, Firmicutes, Bacteroidetes, and Actinobacteria were the main intestinal microbes in both the control and EM groups. Linear discriminant effect size analysis showed that Fusobacteriaceae, Desulfovibrio, and Morganella were biomarkers in the control group, and Exiguobacterium and Rhodobacteraceae were biomarkers in the EM group. Metabolomics analysis revealed that EM supplementation increased cellular energy sources and decreased protein consumption, and oxidative stress. Together, these results indicate that EM can optimize the intestinal microbiome and serum metabolites, thereby benefiting the health of E. sinensis.PMID:37261580 | DOI:10.1007/s10123-023-00375-9

Elife. 2023 Jun 1;12:e84508. doi: 10.7554/eLife.84508. Online ahead of print.ABSTRACTCD73 is an ectonucleotidase overexpressed on tumor cells that suppresses anti-tumor immunity. Accordingly, several CD73 inhibitors are currently being evaluated in the clinic, including in large randomized clinical trials. Yet, the tumor cell-intrinsic impact of CD73 remain largely uncharacterized. Using metabolomics, we discovered that CD73 significantly enhances tumor cell mitochondrial respiration and aspartate biosynthesis. Importantly, rescuing aspartate biosynthesis was sufficient to restore proliferation of CD73-deficient tumors in immune deficient mice. Seahorse analysis of a large panel of mouse and human tumor cells demonstrated that CD73 enhanced oxidative phosphorylation (OXPHOS) and glycolytic reserve. Targeting CD73 decreased tumor cell metabolic fitness, increased genomic instability and suppressed poly ADP ribose polymerase (PARP) activity. Our study thus uncovered an important immune-independent function for CD73 in promoting tumor cell metabolism, and provides the rationale for previously unforeseen combination therapies incorporating CD73 inhibition.PMID:37261423 | DOI:10.7554/eLife.84508

Front Oncol. 2023 May 16;13:1125855. doi: 10.3389/fonc.2023.1125855. eCollection 2023.ABSTRACTBACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with a poor patient prognosis. Remarkably, PDAC is one of the most aggressive and deadly tumor types and is notorious for its resistance to all types of treatment. PDAC resistance is frequently associated with a wide metabolic rewiring and in particular of the glycolytic branch named Hexosamine Biosynthetic Pathway (HBP).METHODS: Transcriptional and bioinformatics analysis were performed to obtain information about the effect of the HBP inhibition in two cell models of PDAC. Cell count, western blot, HPLC and metabolomics analyses were used to determine the impact of the combined treatment between an HBP's Phosphoglucomutase 3 (PGM3) enzyme inhibitor, named FR054, and erastin (ERA), a recognized ferroptosis inducer, on PDAC cell growth and survival.RESULTS: Here we show that the combined treatment applied to different PDAC cell lines induces a significant decrease in cell proliferation and a concurrent enhancement of cell death. Furthermore, we show that this combined treatment induces Unfolded Protein Response (UPR), NFE2 Like BZIP Transcription Factor 2 (NRF2) activation, a change in cellular redox state, a greater sensitivity to oxidative stress, a major dependence on glutamine metabolism, and finally ferroptosis cell death.CONCLUSION: Our study discloses that HBP inhibition enhances, via UPR activation, the ERA effect and therefore might be a novel anticancer mechanism to be exploited as PDAC therapy.PMID:37260977 | PMC:PMC10227458 | DOI:10.3389/fonc.2023.1125855

Front Plant Sci. 2023 May 16;14:1166933. doi: 10.3389/fpls.2023.1166933. eCollection 2023.ABSTRACTProgression of leaf senescence consists of both degenerative and nutrient recycling processes in crops including wheat. However, the levels of metabolites in flag leaves in spring-cultivated wheat, as well as biosynthetic pathways involved under different nitrogen fertilization regimes, are largely unknown. Therefore, the present study employed a widely untargeted metabolomic profiling strategy to identify metabolites and biosynthetic pathways that could be used in a wheat improvement program aimed at manipulating the rate and onset of senescence by handling spring wheat (Dingxi 38) flag leaves sampled from no-, low-, and high-nitrogen (N) conditions (designated Groups 1, 2, and 3, respectively) across three sampling times: anthesis, grain filling, and end grain filling stages. Through ultrahigh-performance liquid chromatography-tandem mass spectrometry, a total of 826 metabolites comprising 107 flavonoids, 51 phenol lipids, 37 fatty acyls, 37 organooxygen compounds, 31 steroids and steroid derivatives, 18 phenols, and several unknown compounds were detected. Upon the application of the stringent screening criteria for differentially accumulated metabolites (DAMs), 28 and 23 metabolites were differentially accumulated in Group 1_vs_Group 2 and Group 1_vs_Group 3, respectively. From these, 1-O-Caffeoylglucose, Rhoifolin, Eurycomalactone;Ingenol, 4-Methoxyphenyl beta-D-glucopyranoside, and Baldrinal were detected as core conserved DAMs among the three groups with all accumulated higher in Group 1 than in the other two groups. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that tropane, piperidine, and pyridine alkaloid biosynthesis; acarbose and validamycin biosynthesis; lysine degradation; and biosynthesis of alkaloids derived from ornithine, lysine, and nicotinic acid pathways were the most significantly (p < 0.05) enriched in Group 1_vs_Group 2, while flavone and flavonol as well as anthocyanins biosynthetic pathways were the most significantly (p < 0.05) enriched in Group 1_vs_Group 3. The results from this study provide a foundation for the manipulation of the onset and rate of leaf senescence and N remobilization in wheat.PMID:37260937 | PMC:PMC10227437 | DOI:10.3389/fpls.2023.1166933

Front Bioeng Biotechnol. 2023 May 16;11:1193095. doi: 10.3389/fbioe.2023.1193095. eCollection 2023.ABSTRACTFermentation is extremely important for the formation of the special flavor of Wuyi rock tea. This study determined volatile metabolite contents using GC-MS technique and futher analyzed their odor characteristics during the traditional deep fermentation technology of Wuyi rock tea. The results showed that 17 characteristic compounds significantly changed during the first stage of the preliminary processing, namely fresh leaves, withering and fermentation. The key to the formation of floral aroma lied in dihydromyrcenol, and the woody aroma derived from six terpenoids, and their synthesis depended on dihydromyrcenol content. The fruity aroma was dominated by six esters, and the fruity aroma mainly came from (Z) -3-hexen-1-yl butyrate, (E) -3-hexen-1-yl butyrate and 5-Hexenyl butyrate. This study provided an important theoretical and practical basis for improving the preliminary processing of Wuyi rock tea.PMID:37260830 | PMC:PMC10228688 | DOI:10.3389/fbioe.2023.1193095

iScience. 2023 May 13;26(6):106881. doi: 10.1016/j.isci.2023.106881. eCollection 2023 Jun 16.ABSTRACTMass spectrometry (MS)-based untargeted metabolomic and lipidomic approaches are being used increasingly in biomedical research. The adoption and integration of these data are critical to the overall multi-omic toolkit. Recently, a sample extraction method called Multi-ABLE has been developed, which enables concurrent generation of proteomic and untargeted metabolomic and lipidomic data from a small amount of tissue. The proteomics field has a well-established set of software for processing of acquired data; however, there is a lack of a unified, off-the-shelf, ready-to-use bioinformatics pipeline that can take advantage of and prepare concurrently generated metabolomic and lipidomic data for joint downstream analyses. Here we present an R pipeline called MultiABLER as a unified and simple upstream processing and analysis pipeline for both metabolomics and lipidomics datasets acquired using liquid chromatography-tandem mass spectrometry. The code is available via an open-source license at https://github.com/holab-hku/MultiABLER.PMID:37260745 | PMC:PMC10227420 | DOI:10.1016/j.isci.2023.106881

Front Cell Infect Microbiol. 2023 May 16;13:1170748. doi: 10.3389/fcimb.2023.1170748. eCollection 2023.ABSTRACTGlobally, liver cancer poses a serious threat to human health and quality of life. Despite numerous studies on the microbial composition of the gut in hepatocellular carcinoma (HCC), little is known about the interactions of the gut microbiota and metabolites and their role in HCC. This study examined the composition of the gut microbiota and serum metabolic profiles in 68 patients with HCC, 33 patients with liver cirrhosis (LC), and 34 healthy individuals (NC) using a combination of metagenome sequencing and liquid chromatography-mass spectrometry (LC-MS). The composition of the serum metabolites and the structure of the intestinal microbiota were found to be significantly altered in HCC patients compared to non-HCC patients. LEfSe and metabolic pathway enrichment analysis were used to identify two key species (Odoribacter splanchnicus and Ruminococcus bicirculans) and five key metabolites (ouabain, taurochenodeoxycholic acid, glycochenodeoxycholate, theophylline, and xanthine) associated with HCC, which then were combined to create panels for HCC diagnosis. The study discovered that the diagnostic performance of the metabolome was superior to that of the microbiome, and a panel comprised of key species and key metabolites outperformed alpha-fetoprotein (AFP) in terms of diagnostic value. Spearman's rank correlation test was used to determine the relationship between the intestinal flora and serum metabolites and their impact on hepatocarcinogenesis and progression. A random forest model was used to assess the diagnostic performance of the different histologies alone and in combination. In summary, this study describes the characteristics of HCC patients' intestinal flora and serum metabolism, demonstrates that HCC is caused by the interaction of intestinal flora and serum metabolites, and suggests that two key species and five key metabolites may be potential markers for the diagnosis of HCC.PMID:37260707 | PMC:PMC10227431 | DOI:10.3389/fcimb.2023.1170748

Front Microbiol. 2023 May 16;14:1182563. doi: 10.3389/fmicb.2023.1182563. eCollection 2023.ABSTRACTRhizobium leguminosarum bv. viciae (Rlv) UPM791 effectively nodulates pea and lentil, but bacteroids contain a number of proteins differentially expressed depending on the host. One of these host-dependent proteins (C189) is similar to a diaminobutyrate-2-oxoglutarate aminotransferase (DABA-AT). DABA-AT activity was demonstrated with cell extracts and with purified protein, so C189 was renamed as Dat. The dat gene was strongly induced in the central, active area of pea nodules, but not in lentil. Mutants defective in dat were impaired in symbiotic performance with pea plants, exhibiting reduced shoot dry weight, smaller nodules, and a lower competitiveness for nodulation. In contrast, there were no significant differences between mutant and wild-type in symbiosis with lentil plants. A comparative metabolomic approach using cell-free extracts from bacteroids induced in pea and lentil showed significant differences among the strains in pea bacteroids whereas no significant differences were found in lentil. Targeted metabolomic analysis revealed that the dat mutation abolished the presence of 2,4-diaminobutyrate (DABA) in pea nodules, indicating that DABA-AT reaction is oriented toward the production of DABA from L-aspartate semialdehyde. This analysis also showed the presence of L-homoserine, a likely source of aspartate semialdehyde, in pea bacteroids but not in those induced in lentil. The dat mutant showed impaired growth when cells were grown with L-homoserine as nitrogen source. Inclusion of DABA or L-homoserine as N source suppressed pantothenate auxotropy in Rlv UPM791, suggesting DABA as source of the pantothenate precursor β-alanine. These data indicate that Rlv UPM791 Dat enzyme is part of an adaptation mechanism of this bacterium to a homoserine-rich environment such as pea nodule and rhizosphere.PMID:37260681 | PMC:PMC10228743 | DOI:10.3389/fmicb.2023.1182563

Evid Based Complement Alternat Med. 2023 May 23;2023:2442505. doi: 10.1155/2023/2442505. eCollection 2023.ABSTRACTBACKGROUND: With the continuous advancement of clinical application and experimental research of JTP, the application prospect of JTP in nervous system diseases and metabolic diseases is becoming increasingly clear. Jiaotai Pill (JTP) is a traditional Chinese medicine formula for insomnia, consisting of Coptidis rhizoma and Cinnamomi cortex, which dates back to Han Shi Yi Tong in the Ming Dynasty of China.OBJECTIVE: Based on the brain-gut axis theory, this paper aims to explore the potential mechanism of JTP in the intervention of insomnia by using intestinal microbiome and metabolomics technology, taking the animal model of insomnia as the research object, so as to provide experimental basis for its further application and research.METHODS: The insomnia mouse model was induced by intraperitoneal injection of para-chlorophenylalanine (PCPA). The clinical equivalent dose of JTP was administered by gavage for one week. The efficacy of JTP was evaluated by behavioral tests, serum biochemical detection, and brain histomorphological observation. The contents of cecum were analyzed by microbiomics and metabolomics.RESULTS: The results show that insomnia caused by PCPA led to daytime dysfunction, higher HPA axis hormone levels, and morphologically impaired hippocampus. JTP reversed these anomalies. Omics research indicates that JTP significantly reduced gut α diversity; at the phylum level, JTP reduced the relative abundance of Firmicutes, Deferribacterota, Cyanobacteria, and Actinobacteriota and increased the relative abundance of Verrucomicrobiota, Proteobacteria, and Desulfobacterota. At the genus level, JTP reduced the relative abundance of Muribaculaceae, Lachnospiraceae_NK4A136_group, Alistipes, Colidextribacter, Muribaculum, and Mucispirillum and increased the relative abundance of Bacteroides and Akkermansia. JTP also reversed the activation of the linoleic acid metabolism pathway induced by insomnia. The combined analysis of omics suggests that JTP may play a role by regulating the inflammatory state of the body. Further gene expression analysis of brain tissue confirmed this.CONCLUSIONS: We hypothesize that JTP may achieve insomnia relief by eliminating inflammation-causing bacteria in the gut and reducing inflammation levels through the brain-gut axis, pointing to potential targets and pathways for future research on JTP.PMID:37260523 | PMC:PMC10229250 | DOI:10.1155/2023/2442505

Environ Sci Technol. 2023 Jun 1. doi: 10.1021/acs.est.2c09737. Online ahead of print.ABSTRACTOur understanding is limited concerning the interaction mechanism between widespread phthalate esters and staple crops, which have strong implications for human exposure. Therefore, this study was aimed at illuminating the transformation pathways of di-n-butyl phthalate (DnBP) in rice using an untargeted screening method. UPLC-QTOF-MS identified 16 intermediate transformation products formed through hydroxylation, hydrolysis, and oxidation in phase I metabolism and further by conjugation with amino acids, glutathione, and carbohydrates in phase II metabolism. Mono-2-hydroxy-n-butyl phthalate-l-aspartic acid (MHBP-asp) and mono-2-hydroxy-n-butyl phthalate-d-alanyl-β-d-glucoside (MHBP-ala-glu) products were observed for the first time. The proteomic analysis demonstrated that DnBP upregulated the expression of rice proteins associated with transporter activity, antioxidant synthesis, and oxidative stress response and downregulated that of proteins involved in photosynthesis, photorespiration, chlorophyll binding, and mono-oxygenase activity. Molecular docking revealed that DnBP can affect protein molecular activity via pi-sigma, pi-alkyl, and pi-pi interactions or by forming carbon-hydrogen bonds. The metabolomic analysis showed that key metabolic pathways including citrate cycle, biosynthesis of aminoacyl-tRNA, and metabolism of amino acids, sphingolipids, carbohydrates, nucleotides, and glutathione were activated in rice plants exposed to DnBP and its primary metabolite mono-n-butyl phthalate (MnBP). Furthermore, exposure to 80 ng/mL MnBP significantly perturbed the metabolic profile and molecular function in plants, with downregulation of the levels of beta-alanine (0.56-fold), cytosine (0.48-fold), thymine (0.62-fold), uracil (0.48-fold), glucose (0.59-fold), and glucose-1-phosphate (0.33-fold), as well as upregulation of the levels of l-glutamic acid (2.97-fold), l-cystine (2.69-fold), and phytosphingosine (38.38-fold). Therefore, the degradation intermediates of DnBP pose a potentially risk to plant metabolism and raise concerns for crop safety related to plasticizer pollution.PMID:37260373 | DOI:10.1021/acs.est.2c09737

Integr Zool. 2023 Jun 1. doi: 10.1111/1749-4877.12734. Online ahead of print.ABSTRACTHerbivory is common in mammals, yet our understanding of detoxification processes used by mammals to biotransform plant secondary compounds (PSCs) is limited. Specialist herbivores are thought to have evolved detoxification mechanisms that rely more heavily on energetically cheap Phase I biotransformation reactions to process high levels of PSCs in their diets. We explored this hypothesis by comparing the urinary metabolite patterns of two specialist herbivores (genus Neotoma). Neotoma stephensi is an obligate specialist on one-seeded juniper (Juniperus monosperma). Neotoma lepida is a generalist forager across its range, yet populations in the Great Basin specialize on Utah juniper (J. osteosperma). While both juniper species have high levels of terpenes, the terpene profiles and quantities differ between the two. Individuals from both woodrat species were fed diets of each juniper in a cross-over design. Urine, collected over a 24-h period, was extracted and analyzed in an untargeted metabolomics approach using both GC-MS and HPLC-MS/MS. The obligate specialist N. stephensi excreted a unique pattern of Phase I metabolites when fed its native juniper, while N. lepida excreted a unique pattern of Phase II metabolites when fed its native juniper. Both woodrat species utilized the Phase II metabolic pathway of glucuronidation more heavily when consuming the more chemically diverse J. osteosperma, and N. stephensi utilized less glucuronidation than N. lepida when consuming J. monosperma. These results are consistent with the hypothesis that obligate specialists may have evolved unique and efficient biotransformation mechanisms for dealing with PSCs in their diet.PMID:37260156 | DOI:10.1111/1749-4877.12734

Cancer Med. 2023 Jun 1. doi: 10.1002/cam4.6194. Online ahead of print.ABSTRACTBACKGROUND: Gut microbiota plays a significant role in the colorectal cancer (CRC) process. Ectopic colonization of multiple oral bacteria is reportedly associated with CRC pathogenesis and progression, but the details remain unclear.METHODS: We enrolled a cohort of 50 CRC patients and 52 healthy controls from an East China population. Taxonomic and functional analysis of the fecal microbiota were performed using 16S rDNA (50 + 52 samples) and shotgun metagenomic sequencing (8 + 6 samples), respectively, with particular attention paid to gut-colonized oral bacteria.RESULTS AND CONCLUSIONS: The results showed more detected bacterial species but lower species evenness within the samples from CRC patients. To determine the specific bacteria enriched in each group, we analyzed their possible protective, carcinogenic, or opportunistic roles in the CRC process. Among the ectopic oral bacteria, we observed a significant increase in the abundance of Fusobacterium and decreased abundance of Prevotella and Ruminococcus in the CRC group. Main differences in the functional composition of these two groups were related to energy metabolism and biosynthesis, especially the glycolytic pathway. Furthermore, we validated the colonization of Fusobacterium nucleatum subsp. animalis within CRC tissues and studied its impact on the host intestinal epithelium and tumor cells. With high selectivity for cancerous tissues, this subspecies promoted CRC cell proliferation and induced potential DNA damage.PMID:37260140 | DOI:10.1002/cam4.6194

Anal Chem. 2023 Jun 1. doi: 10.1021/acs.analchem.2c04632. Online ahead of print.ABSTRACTUntargeted metabolomics is a powerful tool for investigating chemistry of complex biological systems, but its utility is compromised by the presence of uninformative features and the limited efficiency of currently available prioritization tools. More effective filtering and prioritization tools are required to address the challenges of large untargeted metabolomics datasets. Here, we introduce Metabolomics Peak Analysis Computational Tool (MPACT), a new mass spectrometry data analysis platform employing filtering based on multiple modalities, statistical techniques incorporating multilevel replication, and interactive data visualization. We demonstrate application of MPACT to uncover hidden effects of the rare earth element cerium on tunicate-associated bacterium Streptomyces sp. PTY087I2, culminating in characterization of two thiolated compounds including a new cysteine derivative, granaticin C, and granaticin D, recently described as mycothiogranaticin A. While we demonstrate application of MPACT to microbial natural products discovery using an elicitation approach, the platform should be readily adaptable to investigation of multipartite interactions, biomarker detection, small molecules in the environment, and a wide range of other complex sample types.PMID:37260127 | DOI:10.1021/acs.analchem.2c04632

Analyst. 2023 Jun 1. doi: 10.1039/d3an00408b. Online ahead of print.ABSTRACTBacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecules in BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis sp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and that elucidating their role in complex communities should continue to be a priority.PMID:37259951 | DOI:10.1039/d3an00408b

Mol Syst Biol. 2023 Jun 1:e11267. doi: 10.15252/msb.202211267. Online ahead of print.ABSTRACTWhile cellular metabolism impacts the DNA damage response, a systematic understanding of the metabolic requirements that are crucial for DNA damage repair has yet to be achieved. Here, we investigate the metabolic enzymes and processes that are essential for the resolution of DNA damage. By integrating functional genomics with chromatin proteomics and metabolomics, we provide a detailed description of the interplay between cellular metabolism and the DNA damage response. Further analysis identified that Peroxiredoxin 1, PRDX1, contributes to the DNA damage repair. During the DNA damage response, PRDX1 translocates to the nucleus where it reduces DNA damage-induced nuclear reactive oxygen species. Moreover, PRDX1 loss lowers aspartate availability, which is required for the DNA damage-induced upregulation of de novo nucleotide synthesis. In the absence of PRDX1, cells accumulate replication stress and DNA damage, leading to proliferation defects that are exacerbated in the presence of etoposide, thus revealing a role for PRDX1 as a DNA damage surveillance factor.PMID:37259925 | DOI:10.15252/msb.202211267

J Clin Invest. 2023 Jun 1;133(11):e170195. doi: 10.1172/JCI170195.ABSTRACTFumarate hydratase-deficient (FH-deficient) renal cell carcinoma (RCC) represents a particularly aggressive form of kidney cancer. FH-deficient RCC arises in the setting of germline, or solely somatic, mutations in the FH gene, a two-hit tumor suppressor gene. Early detection can be curative, but there are no biomarkers, and in the sporadic setting, establishing a diagnosis of FH-deficient RCC is challenging. In this issue of the JCI, Zheng, Zhu, and co-authors report untargeted plasma metabolomic analyses to identify putative biomarkers. They discovered two plasma metabolites directly linked to fumarate overproduction by tumor cells, succinyl-adenosine and succinic-cysteine, which correlate with tumor burden. The identification of circulating biomarkers of FH-deficient RCC may aid in the diagnosis of FH-deficient RCC and provide a means for longitudinal follow-up.PMID:37259915 | DOI:10.1172/JCI170195

Se Pu. 2023 Jun 8;41(6):520-526. doi: 10.3724/SP.J.1123.2022.10003.ABSTRACTGas chromatography-mass spectrometry (GC-MS) detectors are widely used detection instruments owing to their distinct advantages over other analytical techniques, including lower sample consumption, higher sensitivity, faster analysis speed, and simultaneous separation and analysis. Metabolomics is an important component of system physiology that concerns systematic studies of the metabolite spectrum in one or more biological systems, such as cells, tissues, organs, body fluids, and organisms. Unfortunately, conventional GC-MS detectors also feature low scan rates, high ion loss rates, and a narrow concentration detection range, which limit their applications in the field of metabolomics. Therefore, establishing a GC-MS-based metabolomic analysis method with wide coverage is of great importance. In this research, a widely-targeted metabolomics method based on GC-MS is proposed. This method combines the universality of untargeted metabolomics with the accuracy of targeted metabolomics to realize the qualitative and semi-quantitative detection of numerous metabolites. It does not require a self-built database and exhibits high sensitivity, good repeatability, and strong support for a wide range of metabolic substances. The proposed method was used to establish the relationship between the retention time of straight-chain fatty acid methyl esters (FAMEs) and their retention index (RI) in the FiehnLib database based on the metabolite information stored in this database. We obtained a linear relationship that could be described by the equation y=40878x-47530, r2=0.9999. We then calculated the retention times of metabolites in the FiehnLib database under the experimental conditions based on their RI. In this way, the effects of significant variations in peak retention times owing to differences in the chromatographic column, temperature, carrier gas flow rate, and so on can be avoided. The retention time of a substance fluctuates within a certain threshold because of variations in instrument performance, matrix interference, and other factors. As such, the retention time threshold of the substance must be determined. In this paper, the retention time threshold was set to 0.15 min to avoid instrument fluctuations. The optimal scan interval was optimized to 0.20 s (possible values=0.10, 0.15, 0.20, 0.25, and 0.30 s) because longer sampling periods can lead to spectral data loss and reductions in the resolution of adjacent chromatographic peaks, whereas shorter sampling periods can result in deterioration of the signal-to-noise ratio of the collected signals. The metabolite quantification ions were optimized to avoid the interference of quantification ion peak accumulation in the case of similar peak times, and a selected ion monitoring (SIM) method table was constructed for 611 metabolites, covering 65% of the metabolic pathways in the KEGG (Kyoto Encyclopedia of Genes and Genomes). The developed method covered 39 pathways, including glycolysis, the tricarboxylic acid cycle, purine metabolism, pyrimidine metabolism, amino acid metabolism, and biosynthesis. Compared with the full-scan untargeted GC-MS method, the widely-targeted GC-MS method demonstrated a 20%-30% increase in the number of metabolites detected, as well as a 15%-20% increase in signal-to-noise ratio. The results of stability tests showed that 84% of the intraday relative standard deviations (RSDs) of metabolite retention times were less than 2% and 91% of that were less than 3%; moreover, 54% of the interday RSDs of metabolite retention times were less than 2% and 76% of that were less than 3%. The detection and analysis results of common biological samples confirmed that the proposed method greatly improved the quantity and signal-to-noise ratio of the detected metabolites and is applicable to substances that are thermally stable, volatile, or volatile after derivation and have relative molecular masses lower than 600. Thus, the widely-targeted GC-MS method can expand the application scope of GC-MS in metabolomics.PMID:37259877 | DOI:10.3724/SP.J.1123.2022.10003

Pharmaceuticals (Basel). 2023 Feb 6;16(2):245. doi: 10.3390/ph16020245.ABSTRACTSpiked centaury (Centaurium spicatum) is a well-known medicinal plant from the Mediterranean region with various bioactivities, but there are no studies addressing the use of different solvent systems to improve its pharmacological potential. Nine extraction procedures were adapted to study the effects of solvent composition on the content of bioactive compounds in C. spicatum extracts and on corresponding bioactivities. Targeted metabolomics was performed to obtain information on the chemical composition of extracts. Ethanol-water-based extraction procedures were the most efficient in isolating polyphenols, while less polar butanol extract contained the highest amount of iridoids. Antioxidant potential analysis revealed stronger activity in extracts with higher polyphenol content. Bacillus cereus and Staphylococus aureus were designated as the most sensitive bacterial strains to the activity of extracts, while among the micromycetes tested, Penicillium funiculosum was the most susceptible strain. Butanol extract showed antivirulence potential on Candida albicans morphological transition from yeast to hyphal form, and selected extracts were effective against biofilm formation in two Candida species. All the extracts tested in this study showed no cytotoxic activity to immortalize human skin keratinocyte cell line (HaCaT), whereas extracts obtained by ethanol-water extraction stand out for their potent wound healing effects. Moreover, the influence of the extraction solvent system on various bioactivities of C. spicatum is reported herein for the first time. Overall, the results presented in this study promote the use of C. spicatum as a source of natural products with potential antioxidant, wound healing, and antimicrobial applications that are potentially safe for human use.PMID:37259391 | DOI:10.3390/ph16020245