PubMed

bioRxiv. 2023 May 8:2023.05.06.539713. doi: 10.1101/2023.05.06.539713. Preprint.ABSTRACTMost Americans (∼90%) are deficient in dietary choline, an essential nutrient. Associations between circulating choline and pathological progression in Alzheimer's disease (AD) remain unknown. Here, we examined these associations and performed a metabolomic analysis in blood serum from severe AD, moderate AD, and healthy controls. Additionally, to gain mechanistic insight, we assessed the effects of dietary choline deficiency (Ch-) in 3xTg-AD mice and choline supplementation (Ch+) in APP/PS1 mice. In humans, we found AD-associated reductions in choline, it's derivative acetylcholine (ACh), and elevated pro-inflammatory cytokine TNFα. Choline and ACh were negatively correlated with Plaque density, Braak stage, and TNFα, but positively correlated with MMSE and brain weight. Metabolites L-Valine, 4-Hydroxyphenylpyruvic, Methylmalonic, and Ferulic acids were associated with choline levels. In mice, Ch-paralleled AD severe, but Ch+ was protective. In conclusion, low circulating choline is associated with AD-neuropathological progression, illustrating the importance of dietary choline consumption to offset disease.PMID:37214864 | PMC:PMC10197582 | DOI:10.1101/2023.05.06.539713

bioRxiv. 2023 May 9:2023.05.07.539744. doi: 10.1101/2023.05.07.539744. Preprint.ABSTRACTTumor angiogenesis is a cancer hallmark, and its therapeutic inhibition has provided meaningful, albeit limited, clinical benefit. While anti-angiogenesis inhibitors deprive the tumor of oxygen and essential nutrients, cancer cells activate metabolic adaptations to diminish therapeutic response. Despite these adaptations, angiogenesis inhibition incurs extensive metabolic stress, prompting us to consider such metabolic stress as an induced vulnerability to therapies targeting cancer metabolism. Metabolomic profiling of angiogenesis-inhibited intracranial xenografts showed universal decrease in tricarboxylic acid cycle intermediates, corroborating a state of anaplerotic nutrient deficit or stress. Accordingly, we show strong synergy between angiogenesis inhibitors (Avastin, Tivozanib) and inhibitors of glycolysis or oxidative phosphorylation through exacerbation of anaplerotic nutrient stress in intracranial orthotopic xenografted gliomas. Our findings were recapitulated in GBM xenografts that do not have genetically predisposed metabolic vulnerabilities at baseline. Thus, our findings cement the central importance of the tricarboxylic acid cycle as the nexus of metabolic vulnerabilities and suggest clinical path hypothesis combining angiogenesis inhibitors with pharmacological cancer interventions targeting tumor metabolism for GBM tumors.PMID:37214825 | PMC:PMC10197573 | DOI:10.1101/2023.05.07.539744

Res Sq. 2023 May 9:rs.3.rs-2883555. doi: 10.21203/rs.3.rs-2883555/v1. Preprint.ABSTRACTAnimals rely on volatile chemical compounds for their communication and behavior. Many of these compounds are sequestered in endocrine and exocrine glands and are synthesized by anaerobic microbes. While the volatile organic compound (VOC) or microbiome composition of glandular secretions has been investigated in several mammalian species, few have linked specific bacterial taxa to the production of volatiles or to specific microbial gene pathways. Here, we use metagenomic sequencing, mass-spectrometry based metabolomics, and culturing to profile the microbial and volatile chemical constituents of anal gland secretions in twenty-three domestic cats ( Felis catus ), in attempts to identify organisms potentially involved in host odor production. We found that the anal gland microbiome was dominated by bacteria in the genera Corynebacterium , Bacteroides , Proteus , Lactobacillus , and Streptococcus , and showed striking variation among individual cats. Microbiome profiles also varied with host age and obesity. Metabolites such as fatty-acids, ketones, aldehydes and alcohols were detected in glandular secretions. Overall, microbiome and metabolome profiles were modestly correlated (r=0.17), indicating that a relationship exists between the bacteria in the gland and the metabolites produced in the gland. Functional analyses revealed the presence of genes predicted to code for enzymes involved in VOC metabolism such as dehydrogenases, reductases, and decarboxylases. From metagenomic data, we generated 85 high-quality metagenome assembled genomes (MAGs). Of these, four were inferred to have high relative abundance in metagenome profiles and had close relatives that were recovered as cultured isolates. These four MAGs were classified as Corynebacterium frankenforstense , Proteus mirabilis , Lactobacillus johnsonii , and Bacteroides fragilis . They represent strong candidates for further investigation of the mechanisms of volatile synthesis and scent production in the mammalian anal gland.PMID:37214811 | PMC:PMC10197813 | DOI:10.21203/rs.3.rs-2883555/v1

Front Pharmacol. 2023 May 5;14:1155271. doi: 10.3389/fphar.2023.1155271. eCollection 2023.ABSTRACTDrug hepatotoxicity assessment is a relevant issue both in the course of drug development as well as in the post marketing phase. The use of human relevant in vitro models in combination with powerful analytical methods (metabolomic analysis) is a promising approach to anticipate, as well as to understand and investigate the effects and mechanisms of drug hepatotoxicity in man. The metabolic profile analysis of biological liver models treated with hepatotoxins, as compared to that of those treated with non-hepatotoxic compounds, provides useful information for identifying disturbed cellular metabolic reactions, pathways, and networks. This can later be used to anticipate, as well to assess, the potential hepatotoxicity of new compounds. However, the applicability of the metabolomic analysis to assess the hepatotoxicity of drugs is complex and requires careful and systematic work, precise controls, wise data preprocessing and appropriate biological interpretation to make meaningful interpretations and/or predictions of drug hepatotoxicity. This review provides an updated look at recent in vitro studies which used principally mass spectrometry-based metabolomics to evaluate the hepatotoxicity of drugs. It also analyzes the principal drawbacks that still limit its general applicability in safety assessment screenings. We discuss the analytical workflow, essential factors that need to be considered and suggestions to overcome these drawbacks, as well as recent advancements made in this rapidly growing field of research.PMID:37214440 | PMC:PMC10196061 | DOI:10.3389/fphar.2023.1155271

Front Pharmacol. 2023 May 5;14:1135264. doi: 10.3389/fphar.2023.1135264. eCollection 2023.ABSTRACTIntroduction: Chuanxiong, a traditional Chinese medicine, has been proved to treat a variety of cardiovascular and cerebrovascular diseases by promoting angiogenesis. However, the mechanisms of Chuanxiong's pro-angiogenesis is currently unknown. This study aimed to uncover the effect and mechanisms of Chuanxiong promoting angiogenesis in vivo and in vitro. Methods: First, potential targets were predicted by network pharmacology analysis, and PPI network was established and the pathways were enriched. Then, the chorioallantoic membrane test on quails was applied to assess the proangiogenic effects in vivo. As well, to evaluate the effects in vitro, real-time PCR, western blot analysis, the scratch test, and the tube formation experiment were used. Subsequently, the major metabolic pathways were analyzed using non-targeted metabolomics. Results: As a result of network pharmacological analysis, 51 collective targets of Chuanxiong and angiogenesis were identified, which are mainly associated with PI3K/AKT/Ras/MAPK pathway. And the biological verification results showed that Chuanxiong could increase the vessel numbers and vessel area in qCAM models. Meanwhile, Chuanxiong contributed to HUVEC proliferation, tube formation, migration, by encouraging scratch healing rates and boosting tube branch points. In addition, the levels of VEGFR2, MAPK and PI3K were elevated compared to the control group. The western blot analysis also confirmed Chuanxiong could promote an increase in AKT, FOXO1 and Ras. Furtheremore, metabolomic results showed that the proangiogenic effect of Chuanxiong is associated with glycine, serine and threonine metabolism. Discussion: In conclusion, this study clarified that Chuanxiong could promote angiogenesis in vivo and in vitro via regulating PI3K/AKT/Ras/MAPK pathway.PMID:37214436 | PMC:PMC10196038 | DOI:10.3389/fphar.2023.1135264

Front Mol Biosci. 2023 May 4;10:1180537. doi: 10.3389/fmolb.2023.1180537. eCollection 2023.ABSTRACTKawasaki disease (KD) is a childhood vasculitis disease that is difficult to diagnose, and there is an urgent need for the identification of accurate and specific biomarkers. Here, we aimed to investigate metabolic alterations in patients with KD to determine novel diagnostic and prognostic biomarkers for KD. To this end, we performed untargeted metabolomics and found that several metabolic pathways were significantly enriched, including amino acid, lipid, and tryptophan metabolism, the latter of which we focused on particularly. Tryptophan-targeted metabolomics was conducted to explore the role of tryptophan metabolism in KD. The results showed that Trp and indole acetic acid (IAA) levels markedly decreased, and that l-kynurenine (Kyn) and kynurenic acid (Kyna) levels were considerably higher in patients with KD than in healthy controls. Changes in Trp, IAA, Kyn, and Kyna levels in a KD coronary arteritis mouse model were consistent with those in patients with KD. We further analyzed public single-cell RNA sequencing data of patients with KD and revealed that their peripheral blood mononuclear cells showed Aryl hydrocarbon receptor expression that was remarkably higher than that of healthy children. These results suggest that the Trp metabolic pathway is significantly altered in KD and that metabolic indicators may serve as novel diagnostic and therapeutic biomarkers for KD.PMID:37214338 | PMC:PMC10192854 | DOI:10.3389/fmolb.2023.1180537

Anim Nutr. 2023 Apr 7;13:401-410. doi: 10.1016/j.aninu.2023.01.012. eCollection 2023 Jun.ABSTRACTChromium yeast (CY) supplementation has the potential to alleviate the negative effects of heat stress in dairy cows, but the mechanism remains elusive. We aimed to identify the metabolic mechanisms whereby CY supplementation alleviates the negative effects of heat stress in mid-lactation dairy cows. Twelve Holstein dairy cows with similar milk yield (24.6 ± 1.5 kg/d), parity (2 or 3) and days in milk (125 ± 8 d) were fed the same basal diet containing 0.09 mg of Cr/kg DM. They were allocated randomly to 2 groups: a control group (CON, without CY supplementation) and a CY group (CY, administered 0.36 mg Cr/kg DM). The experiment was performed over 8 weeks during a hot summer, in which the mean temperature-humidity index was 79.0 ± 3.13 (>72), indicating that the dairy cows were exposed to heat stress. Chromium yeast supplementation reduced rectal temperature (P = 0.032), and increased the lactation performance by increasing the yield of milk (+2.6 kg/d), protein, lactose and total solid, and protein and lactose percentages in the milk of the heat-stressed dairy cows (P < 0.05). Supplementation with CY increased the serum glucose and thyroxine concentrations, but reduced the urea nitrogen, insulin, and triiodothyronine concentrations on d 56 (P < 0.05). Furthermore, plasma metabolomic analysis was performed using liquid chromatography tandem-mass spectrometry, which identified 385 metabolites in the two groups. Subsequently, 16 significantly different metabolites in the plasma, were significantly higher in the CY group (variable importance for the projection >1.0, P < 0.05), and found to be involved in 6 Kyoto Encyclopedia of Genes and Genomes pathways, including those involved in nicotinate and nicotinamide metabolism. Specifically, plasma concentration of nicotinamide was higher after CY supplementation, which might also contribute to the reduction of rectal temperature, the regulation of glucose homeostasis, and an improvement in the lactation performance of heat-stressed dairy cows. In conclusion, CY supplementation reduces rectal temperature, influences metabolism by reducing serum insulin concentration and increasing serum glucose and plasma nicotinamide concentrations, and finally increases lactation performance of heat-stressed dairy cows.PMID:37214216 | PMC:PMC10196334 | DOI:10.1016/j.aninu.2023.01.012

Anim Nutr. 2023 Apr 7;13:386-400. doi: 10.1016/j.aninu.2023.03.007. eCollection 2023 Jun.ABSTRACTThe objectives of this study were to determine the effects of dietary supplementation with citrus flavonoid extracts (CFE) on milk performance, serum biochemistry parameters, fecal volatile fatty acids, fecal microbial community, and fecal metabolites in dairy cows. Eight multiparous lactating Holstein cows were used in a replicated 4 × 4 Latin square design (21-day period). Cows were fed a basal diet without addition (CON) or basal diet with added CFE at 50 (CFE50), 100 (CFE10), and 150 g/d (CFE150). Feeding CFE up to 150 g/d increased milk yield and milk lactose percentage. Supplementary CFE linearly decreased milk somatic cell count. Serum cytokines interleukin-1β (IL-1β), IL-2, IL-6, and tumor necrosis factor-α (TNF-α) concentrations decreased linearly as the levels of CFE increased. Cows in CFE150 had lower serum lipopolysaccharide and lipopolysaccharide binding protein compared with CON. These results indicate feeding CFE decreased systemic inflammation and endotoxin levels in dairy cows. Furthermore, feeding CFE linearly increased the concentrations of total volatile fatty acids, acetate, and butyrate in feces. The relative abundances of beneficial bacteria Bifidobacterium spp., Clostridium coccoides-Eubacterium rectale group, and Faecalibacterium prausnitzii in feces increased linearly with increasing CFE supplementation. The diversity and community structure of fecal microbiota were unaffected by CFE supplementation. However, supplementing CFE reduced the relative abundances of genera Ruminococcus_torques_group, Roseburia, and Lachnospira, but increased genera Bacteroides and Phascolarctobacterium. Metabolomics analysis showed that supplementary CFE resulted in a significant modification in the fecal metabolites profile. Compared with CON, fecal naringenin, hesperetin, hippuric acid, and sphingosine concentrations were greater in CFE150 cows, while fecal GlcCer(d18:1/20:0), Cer(d18:0/24:0), Cer(d18:0/22:0), sphinganine, and deoxycholic acid concentrations were less in CFE150 cows. Predicted pathway analysis suggested that "sphingolipid metabolism" was significantly enriched. Overall, these results indicate that citrus flavonoids could exert health-promoting effects by modulating hindgut microbiome and metabolism in lactating cows.PMID:37214215 | PMC:PMC10196341 | DOI:10.1016/j.aninu.2023.03.007

World Allergy Organ J. 2023 May 15;16(5):100777. doi: 10.1016/j.waojou.2023.100777. eCollection 2023 May.ABSTRACTThe prevalence of food allergy (FA) among children is increasing, affecting nearly 8% of children, and FA is the most common cause of anaphylaxis and anaphylaxis-related emergency department visits in children. Importantly, FA is a complex, multi-system, multifactorial disease mediated by food-specific immunoglobulin E (IgE) and type 2 immune responses and involving environmental and genetic factors and gene-environment interactions. Early exposure to external and internal environmental factors largely influences the development of immune responses to allergens. Genetic factors and gene-environment interactions have established roles in the FA pathophysiology. To improve diagnosis and identification of FA therapeutic targets, high-throughput omics approaches have emerged and been applied over the past decades to screen for potential FA biomarkers, such as genes, transcripts, proteins, and metabolites. In this article, we provide an overview of the current status of FA omics studies, namely genomic, transcriptomic, epigenomic, proteomic, exposomic, and metabolomic. The current development of multi-omics integration of FA studies is also briefly discussed. As individual omics technologies only provide limited information on the multi-system biological processes of FA, integration of population-based multi-omics data and clinical data may lead to robust biomarker discovery that could translate into advances in disease management and clinical care and ultimately lead to precision medicine approaches.PMID:37214173 | PMC:PMC10199264 | DOI:10.1016/j.waojou.2023.100777

Hortic Res. 2023 Mar 15;10(5):uhad047. doi: 10.1093/hr/uhad047. eCollection 2023 May.ABSTRACTFallopia multiflora (Thunb.) Harald, a vine belonging to the Polygonaceae family, is used in traditional medicine. The stilbenes contained in it have significant pharmacological activities in anti-oxidation and anti-aging. This study describes the assembly of the F. multiflora genome and presents its chromosome-level genome sequence containing 1.46 gigabases of data (with a contig N50 of 1.97 megabases), 1.44 gigabases of which was assigned to 11 pseudochromosomes. Comparative genomics confirmed that F. multiflora shared a whole-genome duplication event with Tartary buckwheat and then underwent different transposon evolution after separation. Combining genomics, transcriptomics, and metabolomics data to map a network of associated genes and metabolites, we identified two FmRS genes responsible for the catalysis of one molecule of p-coumaroyl-CoA and three molecules of malonyl-CoA to resveratrol in F. multiflora. These findings not only serve as the basis for revealing the stilbene biosynthetic pathway but will also contribute to the development of tools for increasing the production of bioactive stilbenes through molecular breeding in plants or metabolic engineering in microbes. Moreover, the reference genome of F. multiflora is a useful addition to the genomes of the Polygonaceae family.PMID:37213683 | PMC:PMC10194901 | DOI:10.1093/hr/uhad047

Front Microbiol. 2023 May 5;14:1124454. doi: 10.3389/fmicb.2023.1124454. eCollection 2023.ABSTRACTINTRODUCTION: Psychological stress can induce affective disorders. Gut microbiota plays a vital role in emotional function regulation; however, the association between gut microbiota and psychological stress is poorly understood. We investigated effects of psychological stress on the gut microbiome and fecal metabolites and assessed the relationship between affective disorder behavior and altered fecal microbiota.METHODS: A psychological stress model was established in C57BL/6J mice using a communication box. Sucrose preference test, forced swim test, and open field test helped assess anxiety- and depression-like behaviors. Fecal microbiota transplantation (FMT) was conducted using fecal samples from stressed and non-stressed mice. Moreover, 16S rRNA gene sequencing and untargeted metabolomics were performed.RESULTS: After stress exposure for 14 days, a significant increase in anxiety- and depression-like behaviors was observed. FMT of "affective disorder microbiota" from psychologically stressed mice increased stress sensitivity relative to FMT of "normal microbiota" from non-stressed mice. 16S rRNA gene sequencing revealed decreased abundance of Bacteroides, Alistipes, and Lactobacillus and increased abundance of Parasutterella and Rikenellaceae_RC9_gut_group in stressed mice; furthermore, stressed mice showed differential metabolite profiles. KEGG pathway analysis indicated that differential metabolites were chiefly involved in the downregulated pathways of α-linolenic acid metabolism, taste transduction, and galactose metabolism. Alistipes and Bacteroides were mainly positively correlated and Parasutterella was mainly negatively correlated with diverse metabolites.DISCUSSION: Our findings suggest that gut microbiome dysbiosis contributes to affective disorder development in response to psychological stress.PMID:37213506 | PMC:PMC10196128 | DOI:10.3389/fmicb.2023.1124454

Front Microbiol. 2023 May 4;14:1187321. doi: 10.3389/fmicb.2023.1187321. eCollection 2023.ABSTRACTINTRODUCTION: Phytopathogenic fungi are a considerable concern for agriculture, as they can threaten the productivity of several crops worldwide. Meanwhile, natural microbial products are acknowledged to play an important role in modern agriculture as they comprehend a safer alternative to synthetic pesticides. Bacterial strains from underexplored environments are a promising source of bioactive metabolites.METHODS: We applied the OSMAC (One Strain, Many Compounds) cultivation approach, in vitro bioassays, and metabolo-genomics analyses to investigate the biochemical potential of Pseudomonas sp. So3.2b, a strain isolated from Antarctica. Crude extracts from OSMAC were analyzed through HPLC-QTOF-MS/MS, molecular networking, and annotation. The antifungal potential of the extracts was confirmed against Rhizoctonia solani strains. Moreover, the whole-genome sequence was studied for biosynthetic gene clusters (BGCs) identification and phylogenetic comparison.RESULTS AND DISCUSSION: Molecular networking revealed that metabolite synthesis has growth media specificity, and it was reflected in bioassays results against R. solani. Bananamides, rhamnolipids, and butenolides-like molecules were annotated from the metabolome, and chemical novelty was also suggested by several unidentified compounds. Additionally, genome mining confirmed a wide variety of BGCs present in this strain, with low to no similarity with known molecules. An NRPS-encoding BGC was identified as responsible for producing the banamides-like molecules, while phylogenetic analysis demonstrated a close relationship with other rhizosphere bacteria. Therefore, by combining -omics approaches and in vitro bioassays, our study demonstrates that Pseudomonas sp. So3.2b has potential application to agriculture as a source of bioactive metabolites.PMID:37213498 | PMC:PMC10192879 | DOI:10.3389/fmicb.2023.1187321

Front Oncol. 2023 May 5;13:1169369. doi: 10.3389/fonc.2023.1169369. eCollection 2023.ABSTRACTAIMS: We conducted bibliometric and visualization analyses to evaluate the current research status, hotspots, and trends related to the human microbiota markers in colorectal cancer screening.METHODS: The related studies were acquired from the Web of Science Core Collection (WoSCC) database on 5 January 2023. Analyses of the co-occurrence and cooperation relationships between the cited authors, institutions, countries/regions, cited journals, cited articles, and keywords in the studies were carried out using CiteSpace 5.8.R3 software and the Online Analysis platform of Literature Metrology. Additionally, relevant knowledge graphs were drawn to perform visualization analyses; a keywords cluster analysis and a burst analysis were also conducted.RESULTS: After analyzing 700 relevant articles, this bibliometric analysis found that the annual publications showed an increasing trend from 1992 to 2022. Yu Jun from the Chinese University of Hong Kong had the highest cumulative number of publications, whereas Shanghai Jiao Tong University was the most productive institution. China and the USA have contributed the largest number of studies. The keywords frequency analysis demonstrated that "colorectal cancer," "gut microbiota," "Fusobacterium nucleatum," "risk," and "microbiota" were the most frequent keywords, and the keywords cluster analysis found that the current hotspots were as follows: (a) the precancerous lesions of colorectal cancer (CRC) that need to be screened, such as inflammatory bowel disease (IBD) and advanced adenoma, (b) the gut-derived microbiome for CRC screening, and (c) the early detection of CRC. The burst analysis further showed that the combination of microbiomics with metabolomics might be the future research trend in the field of CRC screening.CONCLUSION: The findings of the current bibliometric analysis firstly provide an insight into the current research status, hotspots, and future trends in the field of CRC screening based on the microbiome; the research in this field is becoming more in-depth and diversified. Some human microbiota markers, especially "Fusobacterium nucleatum," are promising biomarkers in CRC screening, and a future hotspot might be the combined analysis of microbiomics and metabolomics for CRC risk screening.PMID:37213286 | PMC:PMC10196493 | DOI:10.3389/fonc.2023.1169369

iScience. 2023 May 4;26(6):106777. doi: 10.1016/j.isci.2023.106777. eCollection 2023 Jun 16.ABSTRACTThe retina is a notable tissue with high metabolic needs which relies on specialized vascular networks to protect the neural retina while maintaining constant supplies of oxygen, nutrients, and dietary essential fatty acids. Here we analyzed the lipidome of the mouse retina under healthy and pathological angiogenesis using the oxygen-induced retinopathy model. By matching lipid profiles to changes in mRNA transcriptome, we identified a lipid signature showing that pathological angiogenesis leads to intense lipid remodeling favoring pathways for neutral lipid synthesis, cholesterol import/export, and lipid droplet formation. Noteworthy, it also shows profound changes in pathways for long-chain fatty acid production, vital for retina homeostasis. The net result is accumulation of large quantities of mead acid, a marker of essential fatty acid deficiency, and a potential marker for retinopathy severity. Thus, our lipid signature might contribute to better understand diseases of the retina that lead to vision impairment or blindness.PMID:37213234 | PMC:PMC10199268 | DOI:10.1016/j.isci.2023.106777

iScience. 2023 May 4;26(6):106812. doi: 10.1016/j.isci.2023.106812. eCollection 2023 Jun 16.ABSTRACTBacterial transformation and processing of diatom-derived organic matter (OM) is extremely important for the cycling of production and energy in marine ecosystems; this process contributes to the production of microbial food webs. In this study, a cultivable bacterium (Roseobacter sp. SD-R1) from the marine diatom Skeletonema dohrnii were isolated and identified. A combined Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS)/untargeted metabolomics approach was used to synthesize the results of bacterial transformation with dissolved OM (DOM) and lysate OM (LOM) under warming and acidification through laboratory experiments. Roseobacter sp. SD-R1 had different preferences for the conversion of molecules in S. dohrnii-derived DOM and LOM treatments. The effects of warming and acidification contribute to the increased number and complexity of molecules of carbon, hydrogen, oxygen, nitrogen, and sulfur after the bacterial transformation of OM. The chemical complexity generated by bacterial metabolism provides new insights into the mechanisms that shape OM complexity.PMID:37213222 | PMC:PMC10197009 | DOI:10.1016/j.isci.2023.106812

Anal Bioanal Chem. 2023 May 22. doi: 10.1007/s00216-023-04724-5. Online ahead of print.ABSTRACTIdentifying metabolites in model organisms is critical for many areas of biology, including unravelling disease aetiology or elucidating functions of putative enzymes. Even now, hundreds of predicted metabolic genes in Saccharomyces cerevisiae remain uncharacterized, indicating that our understanding of metabolism is far from complete even in well-characterized organisms. While untargeted high-resolution mass spectrometry (HRMS) enables the detection of thousands of features per analysis, many of these have a non-biological origin. Stable isotope labelling (SIL) approaches can serve as credentialing strategies to distinguish biologically relevant features from background signals, but implementing these experiments at large scale remains challenging. Here, we developed a SIL-based approach for high-throughput untargeted metabolomics in S. cerevisiae, including deep-48 well format-based cultivation and metabolite extraction, building on the peak annotation and verification engine (PAVE) tool. Aqueous and nonpolar extracts were analysed using HILIC and RP liquid chromatography, respectively, coupled to Orbitrap Q Exactive HF mass spectrometry. Of the approximately 37,000 total detected features, only 3-7% of the features were credentialed and used for data analysis with open-source software such as MS-DIAL, MetFrag, Shinyscreen, SIRIUS CSI:FingerID, and MetaboAnalyst, leading to the successful annotation of 198 metabolites using MS2 database matching. Comparable metabolic profiles were observed for wild-type and sdh1Δ yeast strains grown in deep-48 well plates versus the classical shake flask format, including the expected increase in intracellular succinate concentration in the sdh1Δ strain. The described approach enables high-throughput yeast cultivation and credentialing-based untargeted metabolomics, providing a means to efficiently perform molecular phenotypic screens and help complete metabolic networks.PMID:37212869 | DOI:10.1007/s00216-023-04724-5

Radiat Res. 2023 May 22. doi: 10.1667/RADE-22-00211.1. Online ahead of print.ABSTRACTNovel biodosimetry assays for use in preparedness and response to potential malicious attacks or nuclear accidents would ideally provide accurate dose reconstruction independent of the idiosyncrasies of a complex exposure to ionizing radiation. Complex exposures will consist of dose rates spanning the low dose rates (LDR) to very high-dose rates (VHDR) that need to be tested for assay validation. Here, we investigate how a range of relevant dose rates affect metabolomic dose reconstruction at potentially lethal radiation exposures (8 Gy in mice) from an initial blast or subsequent fallout exposures compared to zero or sublethal exposures (0 or 3 Gy in mice) in the first 2 days, which corresponds to an integral time individuals will reach medical facilities after a radiological emergency. Biofluids (urine and serum) were collected from both male and female 9-10-week-old C57BL/6 mice at 1 and 2 days postirradiation (total doses of 0, 3 or 8 Gy) after a VHDR of 7 Gy/s. Additionally, samples were collected after a 2-day exposure consisting of a declining dose rate (1 to 0.004 Gy/min) recapitulating the 7:10 rule-of-thumb time dependency of nuclear fallout. Overall similar perturbations were observed in both urine and serum metabolite concentrations irrespective of sex or dose rate, with the exception of xanthurenic acid in urine (female specific) and taurine in serum (VHDR specific). In urine, we developed identical multiplex metabolite panels (N6,N6,N6-trimethyllysine, carnitine, propionylcarnitine, hexosamine-valine-isoleucine, and taurine) that could identify individuals receiving potentially lethal levels of radiation from the zero or sublethal cohorts with excellent sensitivity and specificity, with creatine increasing model performance at day 1. In serum, individuals receiving a 3 or 8 Gy exposure could be identified from their pre-irradiation samples with excellent sensitivity and specificity, however, due to a lower dose response the 3 vs. 8 Gy groups could not be distinguished from each other. Together with previous results, these data indicate that dose-rate-independent small molecule fingerprints have potential in novel biodosimetry assays.PMID:37212727 | DOI:10.1667/RADE-22-00211.1

Epigenomics. 2023 May 22. doi: 10.2217/epi-2023-0078. Online ahead of print.ABSTRACTNicotinamide metabolism is important in carcinogenesis. Nicotinamide affects the cellular methyl pool, thus affecting DNA and histone methylation and gene expression. Cancer cells have increased expression of nicotinamide N-methyl transferase (NNMT), the key enzyme in nicotinamide metabolism. NNMT contributes to tumor angiogenesis. Overexpression of NNMT is associated with poorer prognosis in cancers. Additionally, NNMT can contribute to cancer-associated morbidities, such as cancer-associated thrombosis. 1-methylnicotinamide (1-MNA), a metabolite of nicotinamide, has anti-inflammatory and antithrombotic effects. Therefore, targeting NNMT can affect both carcinogenesis and cancer-associated morbidities. Several antitumor drugs have been shown to inhibit NNMT expression in cancer cells. Implementing these drugs to reverse NNMT effects in addition to 1-MNA supplementation has the potential to prevent cancer-associated thrombosis through various mechanisms.PMID:37212051 | DOI:10.2217/epi-2023-0078

J Invest Dermatol. 2023 Jun;143(6):893-912. doi: 10.1016/j.jid.2023.02.019.ABSTRACTAlthough the application of stem cells to chronic wounds emerged as a candidate therapy in the previous century, the mechanism of action remains unclear. Recent evidence has implicated secreted paracrine factors in the regenerative properties of cell-based therapies. In the last two decades, considerable research advances involving the therapeutic potential of stem cell secretomes have expanded the scope of secretome-based therapies beyond stem cell populations. In this study, we review the modes of action of cell secretomes in wound healing, important preconditioning strategies for enhancing their therapeutic efficacy, and clinical trials on secretome-based wound healing.PMID:37211377 | DOI:10.1016/j.jid.2023.02.019

Sci Total Environ. 2023 May 19:164147. doi: 10.1016/j.scitotenv.2023.164147. Online ahead of print.ABSTRACTBacterial interactions occurring on and around seeds are integral to plant fitness, health and productivity. Although seed- and plant-associated bacteria are sensitive to environmental stress, the effects of microgravity, as present during plant cultivation in space, on microbial assembly during seed germination are not clear. Here, we characterized the bacterial microbiome assembly process and mechanisms during seed germination of two wheat varieties under simulated microgravity by 16S rRNA gene amplicon sequencing and metabolome analysis. We found that the bacterial community diversity, and network complexity and stability were significantly decreased under simulated microgravity. In addition, the effects of simulated microgravity on the plant bacteriome of the two wheat varieties tended to be consistent in seedlings. At this stage, the relative abundance of Oxalobacteraceae, Paenibacillaceae, Xanthomonadaceae, Lachnospiraceae, Sphingomonadaceae and Ruminococcaceae decreased, while the relative abundance of Enterobacteriales increased under simulated microgravity. Analysis of predicted microbial function revealed that simulated microgravity exposure leads to lower sphingolipid signaling and calcium signaling pathways. We also found that simulated microgravity drove the strengthening of deterministic processes in microbial community assembly. Importantly, some specific metabolites exhibited significant changes under simulated microgravity, suggesting that bacteriome assembly is mediated, at least in part, by metabolites altered by microgravity. The data we present here moves us closer to a holistic understanding of the plant bacteriome under microgravity stress at plant emergence, and provides a theoretical basis for the precise utilization of microorganisms in microgravity to improve plant adaptation to the challenge of cultivation in space.PMID:37211108 | DOI:10.1016/j.scitotenv.2023.164147