PubMed

Am J Nephrol. 2023 Oct 4. doi: 10.1159/000533537. Online ahead of print.ABSTRACTINTRODUCTION: Dysbiosis of the intestinal microbiome and related metabolites have been observed in chronic kidney disease (CKD), yet their roles in idiopathic membranous nephropathy (IMN) is poorly understood.METHODS: In this study, we describe the variation of intestinal bacteria and fecal metabolites in patients with IMN in Chinese population. Stool samples are collected from 41 IMN patients at the beginning of diagnosis confirmation and 41 gender and age matched healthy control (HC). Microbial communities are investigated by sequencing of 16S rRNA genes and functional profiles predicted using Tax4Fun, and the correlation between intestinal bacteria and IMN clinical characteristics is also analyzed. Untargeted metabolomic analysis is performed to explore the relationship between colon's microbiota and fecal metabolites.RESULTS: IMN gastrointestinal microbiota demonstrates lower richness and diversity compared to HC, and exhibits a marked taxonomic and inferred functional dysbiosis when compared to HC. Some genera are closely related to the clinical parameters, such as Citrobacter and Akkermansia. 20 characteristic microbial biomarkers are selected to establish a disease prediction model with a diagnostic accuracy of 93.53%. Fecal metabolomics shows that tryptophan metabolism is reduced in IMN patients but uremic toxin accumulation in feces is not noticeable. Fecal microbiota transplantation demonstrates that gut dysbiosis impairs gut permeability in microbiota-depleted mice and induces NOD-like receptor activation in kidneys.DISCUSSION/CONCLUSIONS: Clarifying the changes in intestinal microbiota in IMN patients will help further know the pathogenesis of this disease, and microbiota-targeted biomarkers will provide a potentially powerful tool for diagnosing and treating IMN.PMID:37793354 | DOI:10.1159/000533537

Kidney Blood Press Res. 2023 Oct 4. doi: 10.1159/000534354. Online ahead of print.ABSTRACTBACKGROUND: Hypertensive nephropathy (HN) is a high burden disorder and a leading cause of end-stage renal disorder. In spite of huge investigations, the underlying mechanisms are yet largely unknown. Systems biology is a promising approach to provide a comprehensive insight towards this complex disorder.METHODS: Protein expression profiles of kidney tubule and cortex sub-compartments were retrieved from the PRIDE database and the quality of the datasets were assessed using principal component analysis (PCA) and hierarchical clustering. Differentially expressed proteins (DEPs) were detected and their attributed metabolites were enriched and their interactions were assessed in multi-layer networks. Moreover, considering the DEPs and the predicted metabolites, key biomedical phenomena with a leading role in HN pathogenesis were proposed.RESULTS: Amino acid and purine metabolisms are the most prominent alteration in kidney cortex whereas dysregulation of energy hemostasis is a key pathogenic mechanism in tubule. Besides, actin cytoskeleton disorganization is an enriched pathway in both anatomical areas.CONCLUSION: The proteomics profiles of kidney sub-compartments were analyzed using a top-down approach to infer the main pathogenic processes. The constructed holistic map of HN can be exploited to propose novel therapeutic strategies.PMID:37793351 | DOI:10.1159/000534354

J Hazard Mater. 2023 Sep 29;461:132635. doi: 10.1016/j.jhazmat.2023.132635. Online ahead of print.ABSTRACTAlthough biological remediation of U-stressed soil has been studied for a long time, the combined effects of biochar and plant roots are rarely discussed and its influence on rhizosphere microecology are still unknown. Based on pot experiments, we explored the combined efforts of biochar addition and plant roots on U-stressed rhizosphere soil in several ways, including soil physicochemical properties, soil enzyme activities, uranium chemical speciation, bacterial community structure and metabolic pathways. Our results indicates that the content of DTPA-extractable U decreased by 49.31% after biochar and plant roots application, whereas plant roots only treatment just decreased by 25.46%. Further research has found that the pH, CEC, enzyme activities and nutritional level of rhizosphere soil were more significantly improved after biochar and plant roots application. Meanwhile, the abundance and diversity of bacterial community was also upregulated, which was also suggested by the stronger metabolisms of lipids, carbohydrate, nucleotides as well as amino acids. Correlation analyses also certified the positive associations between soil properties, bacterial communities and metabolism. We speculated that the uranium immobilization was mainly attributed to the direct fixation of biochar for its alkalinity, CEC, DOC, etc. and the joint action of biochar and plant roots for their stimulating effects on bacteria. Our findings suggested that combination of biochar and plant roots could limit bioaccessibility of U in a larger extend than plant roots only, which may be a better strategy for rapid remediation of U-streesed soil.PMID:37793252 | DOI:10.1016/j.jhazmat.2023.132635

J Agric Food Chem. 2023 Oct 4. doi: 10.1021/acs.jafc.3c04033. Online ahead of print.ABSTRACTε-Polylysine is a novel food preservative approved by the U.S. Food and Drug Administration (FDA), yet the mechanism of its effect on animal-derived foods remains unclear. Assessment of the effect of preservatives on goat meat products is necessary. Herein, metabolite accumulation and protein expression of ε-polylysine (0.025%, w/w) spiked with goat meat were investigated by nontarget metabolomics and proteomics combined with ultrahigh performance liquid chromatography quadrupole-Orbitrap high-resolution-mass spectrometry (UHPLC-Q-Orbitrap HRMS) in a simulated in vitro digestion model. The amino side chain of ε-polylysine increased the activity of glycine aminotransferase due to its nucleophilic nature, inducing a significant upregulation of l-arginine (0.43-0.72 mg kg-1) and creatine (3.98-6.89 mg kg-1), with an improvement in muscle quality of goat meat. Downregulation of enzyme phenylalanine hydroxylase expression led to upregulation of l-phenylalanine (2.26-3.25 mg kg-1) and l-tyrosine (0.98-1.29 mg kg-1). Collectively, this study first revealed the biochemical mechanism of ε-polylysine in goat meat products, which makes available new prospects for more accurate use of ε-polylysine in animal-derived foods.PMID:37793042 | DOI:10.1021/acs.jafc.3c04033

G3 (Bethesda). 2023 Oct 4:jkad228. doi: 10.1093/g3journal/jkad228. Online ahead of print.ABSTRACTPyruvate kinase (Pyk) is a rate-limiting enzyme that catalyzes the final metabolic reaction in glycolysis. The importance of this enzyme, however, extends far beyond ATP production, as Pyk is also known to regulate tissue growth, cell proliferation, and development. Studies of this enzyme in Drosophila melanogaster are complicated by the fact that the fly genome encodes six Pyk paralogs whose functions remain poorly defined. To address this issue, we used sequence distance and phylogenetic approaches to demonstrate that the gene Pyk encodes the enzyme most similar to the mammalian Pyk orthologs, while the other five Drosophila Pyk paralogs have significantly diverged from the canonical enzyme. Consistent with this observation, metabolomic studies of two different Pyk mutant strains revealed that larvae lacking Pyk exhibit a severe block in glycolysis, with a buildup of glycolytic intermediates upstream of pyruvate. However, our analysis also unexpectedly reveals that pyruvate levels are unchanged in Pyk mutants, indicating that larval metabolism maintains pyruvate pool size despite severe metabolic limitations. Consistent with our metabolomic findings, a complementary RNA-seq analysis revealed that genes involved in lipid metabolism and protease activity are elevated in Pyk mutants, again indicating that loss of this glycolytic enzyme induces compensatory changes in other aspects of metabolism. Overall, our study provides both insight into how Drosophila larval metabolism adapts to disruption of glycolytic metabolism as well as immediate clinical relevance, considering that Pyk deficiency is the most common congenital enzymatic defect in humans.PMID:37792629 | DOI:10.1093/g3journal/jkad228

Cell Rep. 2023 Oct 3;42(10):113191. doi: 10.1016/j.celrep.2023.113191. Online ahead of print.ABSTRACTIn solid tumors, drug concentrations decrease with distance from blood vessels. However, cellular adaptations accompanying the gradated exposure of cancer cells to drugs are largely unknown. Here, we modeled the spatiotemporal changes promoting chemotherapy resistance in breast cancer. Using pairwise cell competition assays at each step during the acquisition of chemoresistance, we reveal an important priming phase that renders cancer cells previously exposed to sublethal drug concentrations refractory to dose escalation. Therapy-resistant cells throughout the concentration gradient display higher expression of the solute carriers SLC38A7 and SLC46A1 and elevated intracellular concentrations of their associated metabolites. Reduced levels of SLC38A7 and SLC46A1 diminish the proliferative potential of cancer cells, and elevated expression of these SLCs in breast tumors from patients correlates with reduced survival. Our work provides mechanistic evidence to support dose-intensive treatment modalities for patients with solid tumors and reveals two members of the SLC family as potential actionable targets.PMID:37792528 | DOI:10.1016/j.celrep.2023.113191

Microb Biotechnol. 2023 Oct 4. doi: 10.1111/1751-7915.14349. Online ahead of print.ABSTRACTThe severity of heat stroke (HS) is associated with intestinal injury, which is generally considered an essential issue for HS. Heat acclimation (HA) is considered the best strategy to protect against HS. In addition, HA has a protective effect on intestinal injuries caused by HS. Considering the essential role of gut microbes in intestinal structure and function, we decided to investigate the potential protective mechanism of HA in reducing intestinal injury caused by HS. HA model was established by male C57BL/6J mice (5-6 weeks old, 17-19 g) were exposed at (34 ± 0.7)°C for 4 weeks to establish an animal HA model. The protective effect of HA on intestinal barrier injury in HS was investigated by 16S rRNA gene sequencing and nontargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics. According to the experimental results, HA can change the composition of the gut microbiota, which increases the proportion of lactobacilli, faecal bacteria, and urinobacteria but decreases the proportion of deoxycholic acid. Moreover, HA can reduce liver and kidney injury and systemic inflammation caused by HS and reduce intestinal injury by enhancing the integrity of the intestinal barrier. In addition, HA regulates inflammation by inhibiting NF-κB signalling and increasing tight junction protein expression in HS mice. HA induces changes in the gut microbiota, which may enhance tight junction protein expression, thereby reducing intestinal inflammation, promoting bile acid metabolism, and ultimately maintaining the integrity of the intestinal barrier. In conclusion, HA induced changes in the gut microbiota. Among the gut microbiota, lactobacilli may play a key role in the potential protective mechanism of HA.PMID:37792264 | DOI:10.1111/1751-7915.14349

mSphere. 2023 Oct 4:e0019423. doi: 10.1128/msphere.00194-23. Online ahead of print.ABSTRACTSore throat is one of the most common complaints encountered in the ambulatory clinical setting. Rapid, culture-independent diagnostic techniques that do not rely on pharyngeal swabs would be highly valuable as a point-of-care strategy to guide outpatient antibiotic treatment. Despite the promise of this approach, efforts to detect volatiles during oropharyngeal infection have yet been limited. In our research study, we sought to evaluate for specific bacterial volatile organic compounds (VOC) biomarkers in isolated cultures in vitro, in order to establish proof-of-concept prior to initial clinical studies of breath biomarkers. A particular challenge for the diagnosis of pharyngitis due to Streptococcus pyogenes is the likelihood that many metabolites may be shared by S. pyogenes and other related oropharyngeal colonizing bacterial species. Therefore, we evaluated whether sufficient metabolic differences are present, which distinguish the volatile metabolome of Group A streptococci from other streptococcal species that also colonize the respiratory mucosa, such as Streptococcus pneumoniae and Streptococcus intermedius. In this work, we identified 27 discriminatory VOCs (q-values < 0.05), composed of aldehydes, alcohols, nitrogen-containing compounds, hydrocarbons, ketones, aromatic compounds, esters, ethers, and carboxylic acid. From this group of volatiles, we identify candidate biomarkers that distinguish S. pyogenes from other species and establish highly produced VOCs that indicate the presence of S. pyogenes in vitro, supporting future breath-based diagnostic testing for streptococcal pharyngitis. IMPORTANCE Acute pharyngitis accounts for approximately 15 million ambulatory care visits in the United States. The most common and important bacterial cause of pharyngitis is Streptococcus pyogenesis, accounting for 15%-30% of pediatric pharyngitis. Distinguishing between bacterial and viral pharyngitis is key to management in US practice. The culture of a specimen obtained by a throat swab is the standard laboratory procedure for the microbiologic confirmation of pharyngitis; however, this method is time-consuming, which delays appropriate treatment. If left untreated, S. pyogenes pharyngitis may lead to local and distant complications. In this study, we characterized the volatile metabolomes of S. pyogenes and other related oropharyngeal colonizing bacterial species. We identify candidate biomarkers that distinguish S. pyogenes from other species and provide evidence to support future breath-based diagnostic testing for streptococcal pharyngitis.PMID:37791788 | DOI:10.1128/msphere.00194-23

J Inflamm Res. 2023 Sep 26;16:4271-4285. doi: 10.2147/JIR.S431600. eCollection 2023.ABSTRACTBACKGROUND: Rheumatoid arthritis (RA) patients are prone to developing different metabolic complications. Traditional Chinese Medicine attributes this uncertainty to varied syndrome types.METHODS AND RESULTS: We retrospectively analyzed some serological indicators of active RA patients and healthy individuals. Randomly selected RA patients were divided into three groups according to NAMPT and SIRT1 expression levels in white blood cells (WBCs). Their disease severity and metabolic status were compared. Representative blood samples were subjected to a UPLC-MS/MS-based metabolomics analysis. Different human WBCs were treated with oleic acid and palmitic acid in vitro. The results indicated that blood glucose and lipid levels were decreased in RA patients, but their decrease was not in accordance with disease severity. Nutrients in the patients highly expressing SIRT1 were well preserved, with the lowest levels of RF and β-CTX and the highest levels of adiponectin and resistin. Most of them exhibited cold symptoms. When SIRT1 deficiency was obvious, lipid depletion became evident, irrespective of expression levels of NAMPT. Simultaneous high-expression of SIRT1 and NAMPT coincided with the increase in production of lactic acid and the prevalence of hot symptoms. Despite the low levels of IL-6, joint injuries were severe. The corresponding WBCs were especially sensitive to fatty acids anti-inflammatory treatments. The levels of CCL27, CCL11, CCL5, AKP, CRP and ESR were similar among all the groups.CONCLUSION: NAMPT overexpression is a risk factor for joint injuries and nutrient depletion in RA. Supplementation with lipids would exert beneficial effects on these RA patients. Its aftermath would cause even severe inflammation. Contrarily, SIRT1 up-regulation restrains inflammation and lipid depletion.PMID:37791116 | PMC:PMC10543492 | DOI:10.2147/JIR.S431600

Front Cell Dev Biol. 2023 Sep 18;11:1255823. doi: 10.3389/fcell.2023.1255823. eCollection 2023.ABSTRACTBackground: Bone marrow stromal cells (BMSCs) are the source of multipotent stem cells, which are important for regenerative medicine and diagnostic purposes. The isolation of human BMSCs from the bone marrow (BM) cavity using BM aspiration applies the method with collection into tubes containing anticoagulants. Interactions with anticoagulants may affect the characteristics and composition of isolated BMSCs in the culture. Thus, we investigated how anticoagulants in isolation procedures and cultivation affect BMSC molecular characteristics. Methods: BM donors (age: 48-85 years) were recruited from the hematology clinic. BM aspirates were obtained from the iliac crest and divided into tubes coated with ethylenediaminetetraacetic acid (EDTA) or heparin anticoagulants. Isolated BMSCs were analyzed by flow cytometry and RNA-seq analysis. Further cellular and molecular characterizations of BMSCs including CFU, proliferation and differentiation assays, cytometry, bioenergetic assays, metabolomics, immunostaining, and RT-qPCR were performed. Results: The paired samples of isolated BMSCs obtained from the same patient showed increased cellular yield in heparin vs. EDTA samples, accompanied by the increased number of CFU colonies. However, no significant changes in molecular characteristics were found between heparin- and EDTA-isolated BMSCs. On the other hand, RNA-seq analysis revealed an increased expression of genes involved in nucleotide metabolism and cellular metabolism in cultivated vs. non-cultivated BMSCs regardless of the anticoagulant, while genes involved in inflammation and chromatin remodeling were decreased in cultivated vs. non-cultivated BMSCs. Conclusion: The type of anticoagulant in BMSC isolation did not have a significant impact on molecular characteristics and cellular composition, while in vitro cultivation caused the major change in the transcriptomics of BMSCs, which is important for future protocols using BMSCs in regenerative medicine and clinics.PMID:37791077 | PMC:PMC10544901 | DOI:10.3389/fcell.2023.1255823

Front Plant Sci. 2023 Sep 18;14:1273546. doi: 10.3389/fpls.2023.1273546. eCollection 2023.ABSTRACTINTRODUCTION: Organic soil amendments such as filter mud (FM) and biochar (BC) can potentially influence the abundance and composition of metabolites. However, our current understanding of the stimulatory effects of FM and BC's long-term impact on stress-regulating metabolites, such as abscisic acid (ABA), jasmonic acid (JA), melatonin, and phenyllactic acid (PLA), and these substrates regulatory effects on disease-causing bacteria in sugarcane ratooning field, which is susceptible to nutrients depletion, diseases, etc., remain poorly understood. Additionally, little is known about how the long-term interaction of these substrates and compounds influences sugarcane ratooning soil enzyme activities, nutrient cycling, and crop growth performance.METHODS: To answer these questions, we adopted metabolomics tools combined with high-throughput sequencing to explore the stimulatory effects of the long-term addition of FM and BC on metabolites (e.g., PLA and abscisic aldehyde) and quantify these substrates' regulatory effects on disease-causing bacteria, soil enzyme activities, nutrient cycling, and crop growth performance.RESULTS: The result revealed that ratoon crop weight, stem diameter, sugar content, as well as soil physico-chemical properties, including soil nitrate (NH3 +-N), organic matter (OM), total nitrogen (TN), total carbon (TC), and β-glucosidase, marked a significant increase under the BC and FM-amended soils. Whereas soil available potassium (AK), NO3 -N, cellulase activity, and phosphatase peaked under the BC-amended soil, primarily due to the enduring effects of these substrates and metabolites. Furthermore, BC and FM-amended soils enriched specific stress-regulating metabolites, including JA, melatonin, abscisic aldehyde, etc. The sustained effects of both BC and FM-amended soils suppressed disease-causing bacteria, eventually promoting ratooning soil growth conditions. A number of key bioactive compounds had distinct associations with several beneficial bacteria and soil physico-chemical properties.DISCUSSION: This study proves that long-term BC and FM application is one of the eco-friendly strategies to promote ratoon crop growth and soil quality through the enrichment of stress-regulating metabolites and the suppression of disease-causing bacteria.PMID:37790789 | PMC:PMC10544933 | DOI:10.3389/fpls.2023.1273546

Front Plant Sci. 2023 Sep 18;14:1267758. doi: 10.3389/fpls.2023.1267758. eCollection 2023.ABSTRACTINTRODUCTION: Jujube is an important economic forest tree whose fruit is rich in alkaloids. Chinese jujube (Ziziphus jujuba Mill.) and sour jujube (Ziziphus spinosa Hu.) are the two most important species of the jujube genus. However, the mechanisms underlying the synthesis and metabolism of alkaloids in jujube fruits remain poorly understood.METHODS: In this study, the fruits of Ziziphus jujuba 'Hupingzao' and Ziziphus spinosa 'Taigusuanzao' in different harvest stages were used as test materials, we first integrated widely targeted metabolomics and transcriptomics analyses to elucidate the metabolism of alkaloids of jujube fruits.RESULTS: In the metabolomics analysis, 44 alkaloid metabolites were identified in 4 samples, 3 of which were unique to sour jujube fruit. The differential alkaloid metabolites (DAMs) were more accumulated in sour jujube than in Chinese jujube; further, they were more accumulated in the white ripening stage than in the red stage. DAMs were annotated to 12 metabolic pathways. Additionally, transcriptomics data revealed 259 differentially expressed genes (DEGs) involved in alkaloid synthesis and metabolism. By mapping the regulatory networks of DAMs and DEGs, we screened out important metabolites and 11 candidate genes.DISCUSSION: This study preliminarily elucidated the molecular mechanism of jujube alkaloid synthesis. The candidate genes regulated the synthesis of key alkaloid metabolites, but the specific regulation mechanism is unclear. Taken together, our results provide insights into the metabolic networks of alkaloid synthesis in Chinese jujube and sour jujube fruits at different harvest stages, thereby providing a theoretical reference for further research on the regulatory mechanism of jujube alkaloids and their development and utilization.PMID:37790781 | PMC:PMC10544937 | DOI:10.3389/fpls.2023.1267758

Front Genet. 2023 Sep 18;14:1274732. doi: 10.3389/fgene.2023.1274732. eCollection 2023.ABSTRACTPlumeria rubra L. cv. Acutifolia is an ornamental tree that displays a good drought-tolerance level. However, the molecular mechanisms of P. rubra adaptation to drought stress remains unclear. Here, drought-simulating pot experiments were conducted to explore drought stress response mechanism of P. rubra. Transcriptome analysis revealed 10,967 differentially expressed genes (DEGs), 6,498 of which were increased and 4,469 decreased. Gene Ontology (GO) analysis revealed that the DEGs were enriched in binding category, in metabolic process category, and in catalytic activities category. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that 9 pathways were significantly enriched, including biosynthesis of secondary metabolites (ko01110), plant hormone signal transduction (ko04075) and so on. In addition, the transcription factor families of AP2/ERFs, bZIP, and C2H2 were significantly upregulated while the families of bHLH, MYB-related, and NAC were significantly downregulated. Moreover, the results of metabolomics analysis indicated that some compounds were accumulated under drought stress, especially flavonoids. Overall, it was speculated that under drought stress, P. rubra first activates the plant hormone signal transduction pathway to regulate hormone contents. Then osmotic regulating substances such as organic acids and amino acids are accumulated to maintain osmotic balance. Finally, flavonoid levels are increased to scavenge reactive oxygen species. These results preliminarily revealed the molecular mechanisms adopted by P. rubra in response to drought stress.PMID:37790703 | PMC:PMC10544913 | DOI:10.3389/fgene.2023.1274732

Res Sq. 2023 Sep 11:rs.3.rs-3317816. doi: 10.21203/rs.3.rs-3317816/v1. Preprint.ABSTRACTBackground: Diffuse midline gliomas (DMG), including diffuse intrinsic pontine gliomas (DIPGs), are a fatal form of brain cancer. These tumors often carry a driver mutation on histone H3 converting lysine 27 to methionine (H3K27M). DMG-H3K27M are characterized by altered metabolism and resistance to standard of care radiation (RT), but how the H3K27M mediates the metabolic response to radiation and consequent treatment resistance is uncertain. Methods: We performed metabolomics on irradiated and untreated H3K27M isogenic DMG cell lines and observed an H3K27M-specific enrichment for purine synthesis pathways. We profiled the expression of purine synthesis enzymes in publicly available patient data and in our models, quantified purine synthetic flux using stable isotope tracing, and characterized the in vitro and in vivo response to de novo and salvage purine synthesis inhibition in combination with RT. Results: DMG-H3K27M cells activate purine metabolism in an H3K27M-specific fashion. In the absence of genotoxic treatment, H3K27M-expressing cells have higher relative activity of de novo synthesis and lower activity of purine salvage due to decreased expression of the purine salvage enzymes. Inhibition of de novo synthesis radiosensitized DMG-H3K27M cells in vitro and in vivo. Irradiated H3K27M cells adaptively upregulate purine salvage enzyme expression and pathway activity. Silencing the rate limiting enzyme in purine salvage, hypoxanthine guanine phosphoribosyl transferase (HGPRT) when combined with radiation markedly suppressed DMG-H3K27M tumor growth in vivo. Conclusions: H3K27M expressing cells rely on de novo purine synthesis but adaptively upregulate purine salvage in response to RT. Inhibiting purine salvage may help overcome treatment resistance in DMG-H3K27M tumors.PMID:37790517 | PMC:PMC10543500 | DOI:10.21203/rs.3.rs-3317816/v1

Res Sq. 2023 Sep 11:rs.3.rs-3222588. doi: 10.21203/rs.3.rs-3222588/v1. Preprint.ABSTRACTCirculating metabolites act as biomarkers of dysregulated metabolism, and may inform disease pathophysiology. A portion of the inter-individual variability in circulating metabolites is influenced by common genetic variation. We evaluated whether a genetics-based "virtual" metabolomics approach can identify novel metabolite-disease associations. We examined the association between polygenic scores for 726 metabolites (derived from OMICSPRED) with 1,247 clinical phenotypes in 57,735 European ancestry and 15,754 African ancestry participants from the BioVU DNA Biobank. We probed significant relationships through Mendelian randomization (MR) using genetic instruments constructed from the METSIM Study, and validated significant MR associations using independent GWAS of candidate phenotypes. We found significant associations between 336 metabolites and 168 phenotypes in European ancestry and 107 metabolites and 56 phenotypes among African ancestry. Of these metabolite-disease pairs, MR analyses confirmed associations between 73 metabolites and 53 phenotypes in European ancestry. Of 22 metabolite-phenotype pairs evaluated for replication in independent GWAS, 16 were significant (false discovery rate p<0.05). Validated findings included the metabolites bilirubin and X-21796 with cholelithiasis, phosphatidylcholine(16:0/22:5n3,18:1/20:4) and arachidonate(20:4n6) with inflammatory bowel disease and Crohn's disease, and campesterol with coronary artery disease and myocardial infarction. These associations may represent biomarkers or potentially targetable mediators of disease risk.PMID:37790512 | PMC:PMC10543429 | DOI:10.21203/rs.3.rs-3222588/v1

Res Sq. 2023 Sep 20:rs.3.rs-3311459. doi: 10.21203/rs.3.rs-3311459/v1. Preprint.ABSTRACTCaloric restriction (CR) extends organismal lifespan and health span by improving glucose homeostasis mechanisms. How CR affects organellar structure and function of pancreatic beta cells over the lifetime of the animal remains unknown. Here, we used single nucleus transcriptomics to show that CR increases the expression of genes for beta cell identity, protein processing, and organelle homeostasis. Gene regulatory network analysis link this transcriptional phenotype to transcription factors involved in beta cell identity (Mafa) and homeostasis (Atf6). Imaging metabolomics further demonstrates that CR beta cells are more energetically competent. In fact, high-resolution light and electron microscopy indicates that CR reduces beta cell mitophagy and increases mitochondria mass, increasing mitochondrial ATP generation. Finally, we show that long-term CR delays the onset of beta cell aging and senescence to promote longevity by reducing beta cell turnover. Therefore, CR could be a feasible approach to preserve compromised beta cells during aging and diabetes.PMID:37790446 | PMC:PMC10543285 | DOI:10.21203/rs.3.rs-3311459/v1

Res Sq. 2023 Sep 22:rs.3.rs-3364037. doi: 10.21203/rs.3.rs-3364037/v1. Preprint.ABSTRACTIntrinsic metabolism shapes the immune environment associated with immune suppression and tolerance in settings such as organ transplantation and cancer. However, little is known about the metabolic activities in an immunosuppressive environment. In this study, we employed metagenomic, metabolomic, and immunological approaches to profile the early effects of the immunosuppressant drug tacrolimus, antibiotics, or both in gut lumen and circulation using a murine model. Tacrolimus induced rapid and profound alterations in metabolic activities within two days of treatment, prior to alterations in gut microbiota composition and structure. The metabolic profile and gut microbiome after seven days of treatment was distinct from that after two days of treatment, indicating continuous drug effects on both gut microbial ecosystem and host metabolism. The most affected taxonomic groups are Clostriales and Verrucomicrobiae (i.e., Akkermansia muciniphila ), and the most affected metabolic pathways included a group of interconnected amino acids, bile acid conjugation, glucose homeostasis, and energy production. Highly correlated metabolic changes were observed between lumen and serum metabolism, supporting their significant interactions. Despite a small sample size, this study explored the largely uncharacterized microbial and metabolic events in an immunosuppressed environment and demonstrated that early changes in metabolic activities can have significant implications that may serve as antecedent biomarkers of immune activation or quiescence. To understand the intricate relationships among gut microbiome, metabolic activities, and immune cells in an immune suppressed environment is a prerequisite for developing strategies to monitor and optimize alloimmune responses that determine transplant outcomes.PMID:37790403 | PMC:PMC10543476 | DOI:10.21203/rs.3.rs-3364037/v1

Res Sq. 2023 Sep 21:rs.3.rs-3127544. doi: 10.21203/rs.3.rs-3127544/v1. Preprint.ABSTRACTMajor Depressive Disorder (MDD) is an often-chronic condition with substantial molecular alterations and pathway dysregulations involved. Single metabolite, pathway and targeted metabolomics platforms have indeed revealed several metabolic alterations in depression including energy metabolism, neurotransmission and lipid metabolism. More comprehensive coverage of the metabolome is needed to further specify metabolic dysregulation in depression and reveal previously untargeted mechanisms. Here we measured 820 metabolites using the metabolome-wide Metabolon platform in 2770 subjects from a large Dutch clinical cohort with extensive depression clinical phenotyping (1101 current MDD, 868 remitted MDD, 801 healthy controls) at baseline and 1805 subjects at 6-year follow up (327 current MDD, 1045 remitted MDD, 433 healthy controls). MDD diagnosis was based on DSM-IV psychiatric interviews. Depression severity was measured with the Inventory of Depressive Symptomatology self-report. Associations between metabolites and MDD status and depression severity were assessed at baseline and at the 6-year follow-up. Metabolites consistently associated with MDD status or depression severity on both occasions were examined in Mendelian randomization (MR) analysis using metabolite (N=14,000) and MDD (N=800,000) GWAS results. At baseline, 139 and 126 metabolites were associated with current MDD status and depression severity, respectively, with 79 overlapping metabolites. Six years later, 34 out of the 79 metabolite associations were subsequently replicated. Downregulated metabolites were enriched with long-chain monounsaturated (P=6.7e-07) and saturated (P=3.2e-05) fatty acids and upregulated metabolites with lysophospholipids (P=3.4e-4). Adding BMI to the models changed results only marginally. MR analyses showed that genetically-predicted higher levels of the lysophospholipid 1-linoleoyl-GPE (18:2) were associated with greater risk of depression. The identified metabolome-wide profile of depression (severity) indicated altered lipid metabolism with downregulation of long-chain fatty acids and upregulation of lysophospholipids, for which causal involvement was suggested using genetic tools. This metabolomics signature offers a window on depression pathophysiology and a potential access point for the development of novel therapeutic approaches.PMID:37790319 | PMC:PMC10543022 | DOI:10.21203/rs.3.rs-3127544/v1

Res Sq. 2023 Sep 13:rs.3.rs-3143015. doi: 10.21203/rs.3.rs-3143015/v1. Preprint.ABSTRACTBackground : Stroke is a major cause of morbidity and mortality, and its incidence increases with age. While acute therapies for stroke are currently limited to intravenous thrombolytics and endovascular thrombectomy, recent studies have implicated an important role for the gut microbiome in post-stroke neuroinflammation. After stroke, several immuno-regulatory pathways, including the aryl hydrocarbon receptor (AHR) pathway, become activated. AHR is a master regulatory pathway that mediates neuroinflammation. Among various cell types, microglia (MG), as the resident immune cells of the brain, play a vital role in regulating post-stroke neuroinflammation and antigen presentation. Activation of AHR is dependent on a dynamic balance between host-derived and microbiota-derived ligands. While previous studies have shown that activation of MG AHR by host-derived ligands, such as kynurenine, is detrimental after stroke, the effects of post-stroke changes in microbiota-derived ligands of AHR, such as indoles, is unknown. Our study builds on the concept that differential activation of MG AHR by host-derived versus microbiome-derived metabolites affects outcomes after ischemic stroke. We examined the link between stroke-induced dysbiosis and loss of essential microbiota-derived AHR ligands. We hypothesize that restoring the balance between host-derived (kynurenine) and microbiota-derived (indoles) ligands of AHR is beneficial after stroke, offering a new potential avenue for therapeutic intervention in post-stroke neuroinflammation. Method : We performed immunohistochemical analysis of brain samples from stroke patients to assess MG AHR expression after stroke. We used metabolomics analysis of plasma samples from stroke and non-stroke control patients with matched comorbidities to determine the levels of indole-based AHR ligands after stroke. We performed transient middle cerebral artery occlusion (MCAO) in aged (18 months) wild-type (WT) and germ-free (GF) mice to investigate the effects of post-stroke treatment with microbiota-derived indoles on outcome. To generate our results, we employed a range of methodologies, including flow cytometry, metabolomics, and 16S microbiome sequencing. Results : We found that MG AHR expression is increased in human brain after stroke and after ex vivo oxygen-glucose deprivation and reperfusion (OGD/R). Microbiota-derived ligands of AHR are decreased in the human plasma at 24 hours after ischemic stroke. Kynurenine and indoles exhibited differential effects on aged WT MG survival after ex vivo OGD/R. We found that specific indole-based ligands of AHR (indole-3-propionic acid and indole-3-aldehyde) were absent in GF mice, thus their production depends on the presence of a functional gut microbiota. Additionally, a time-dependent decrease in the concentration of these indole-based AHR ligands occurred in the brain within the first 24 hours after stroke in aged WT mice. Post-stroke treatment of GF mice with a cocktail of microbiota-derived indole-based ligands of AHR regulated MG-mediated neuroinflammation and molecules involved in antigen presentation (increased CD80, MHC-II, and CD11b). Post-stroke treatment of aged WT mice with microbiota-derived indole-based ligands of AHR reduced both infarct volume and neurological deficits at 24 hours. Conclusion : Our novel findings provide compelling evidence that the restoration of a well-balanced pool of host-derived kynurenine-based and microbiota-derived indole-based ligands of AHR holds considerable therapeutic potential for the treatment of ischemic stroke.PMID:37790313 | PMC:PMC10543021 | DOI:10.21203/rs.3.rs-3143015/v1

bioRxiv. 2023 Sep 21:2023.09.21.558834. doi: 10.1101/2023.09.21.558834. Preprint.ABSTRACTThe growth of antimicrobial resistance (AMR) has highlighted an urgent need to identify bacterial pathogenic functions that may be targets for clinical intervention. Although severe bacterial infections profoundly alter host metabolism, prior studies have largely ignored alterations in microbial metabolism in this context. Performing metabolomics on patient and mouse plasma samples, we identify elevated levels of bacterially-derived N - acetylputrescine during gram-negative bloodstream infections (BSI), with higher levels associated with worse clinical outcomes. We discover that SpeG is the bacterial enzyme responsible for acetylating putrescine and show that blocking its activity reduces bacterial proliferation and slows pathogenesis. Reduction of SpeG activity enhances bacterial membrane permeability and results in increased intracellular accumulation of antibiotics, allowing us to overcome AMR of clinical isolates both in culture and in vivo. This study highlights how studying pathogen metabolism in the natural context of infection can reveal new therapeutic strategies for addressing challenging infections.PMID:37790300 | PMC:PMC10542159 | DOI:10.1101/2023.09.21.558834