PubMed

Adv Exp Med Biol. 2023;1426:215-235. doi: 10.1007/978-3-031-32259-4_10.ABSTRACTThe application of mathematical and computational analysis, together with the modelling of biological and physiological processes, is transforming our understanding of the pathophysiology of complex diseases. This systems biology approach incorporates large amounts of genomic, transcriptomic, proteomic, metabolomic, breathomic, metagenomic and imaging data from disease sites together with deep clinical phenotyping, including patient-reported outcomes. Integration of these datasets will provide a greater understanding of the molecular pathways associated with severe asthma in each individual patient and determine their personalised treatment regime. This chapter describes some of the data integration methods used to combine data sets and gives examples of the results obtained using single datasets and merging of multiple datasets (data fusion and data combination) from several consortia including the severe asthma research programme (SARP) and the Unbiased Biomarkers Predictive of Respiratory Disease Outcomes (U-BIOPRED) consortia. These results highlight the involvement of several different immune and inflammatory pathways and factors in distinct subsets of patients with severe asthma. These pathways often overlap in patients with distinct clinical features of asthma, which may explain the incomplete or no response in patients undergoing specific targeted therapy. Collaboration between groups will improve the predictions obtained using a systems medicine approach in severe asthma.PMID:37464123 | DOI:10.1007/978-3-031-32259-4_10

Sci Rep. 2023 Jul 18;13(1):11583. doi: 10.1038/s41598-023-38571-2.ABSTRACTIn grafted apple, rootstock-derived signals influence scion cold tolerance by initiating physiological changes to survive over the winter. To understand the underlying molecular interactions between scion and rootstock responsive to cold, we developed transcriptomics and metabolomics data in the stems of two scion/rootstock combinations, 'Gala'/'G202' (cold resistant rootstock) and 'Gala'/'M9' (cold susceptible rootstock). Outer layers of scion and rootstock stem, including vascular tissues, were collected from the field-grown grafted apple during the winter. The clustering of differentially expressed genes (DEGs) and gene ontology enrichment indicated distinct expression dynamics in the two graft combinations, which supports the dependency of scion cold tolerance on the rootstock genotypes. We identified 544 potentially mobile mRNAs of DEGs showing highly-correlated seasonal dynamics between scion and rootstock. The mobility of a subset of 544 mRNAs was validated by translocated genome-wide variants and the measurements of selected RNA mobility in tobacco and Arabidopsis. We detected orthologous genes of potentially mobile mRNAs in Arabidopsis thaliana, which belong to cold regulatory networks with RNA mobility. Together, our study provides a comprehensive insight into gene interactions and signal exchange between scion and rootstock responsive to cold. This will serve for future research to enhance cold tolerance of grafted tree crops.PMID:37463950 | DOI:10.1038/s41598-023-38571-2

Cancer Biol Ther. 2023 Dec 31;24(1):2237200. doi: 10.1080/15384047.2023.2237200.ABSTRACTCancer cells show enhanced nucleotide biosynthesis, which is essential for their unlimited proliferation, but the underlying mechanisms are not entirely clear. Ubiquitin specific peptidase 29 (USP29) was reported to sustain neuroblastoma progression by promoting glycolysis and glutamine catabolism; however, its potential role in regulating nucleotide biosynthesis in tumor cells remains unknown. In this study, we depleted endogenous USP29 in MYCN-amplified neuroblastoma SK-N-BE2 cells by sgRNAs and conducted metabolomic analysis in cells with or without USP29 depletion, we found that USP29 deficiency caused a disorder of intermediates involved in glycolysis and nucleotide biosynthesis. De novo nucleotide biosynthesis was analyzed using 13C6 glucose as a tracer under normoxia and hypoxia. The results indicated that USP29-depleted cells showed inhibition of nucleotide anabolic intermediates derived from glucose, and this inhibition was more significant under hypoxic conditions. Analysis of RNA sequencing data in SK-N-BE2 cells demonstrated that USP29 promoted the gene expression of metabolic enzymes involved in nucleotide anabolism, probably by regulating MYC and E2F downstream pathways. These findings indicated that USP29 is a key regulator of nucleotide biosynthesis in tumor cells.PMID:37463886 | DOI:10.1080/15384047.2023.2237200

FEBS Lett. 2023 Jul 18. doi: 10.1002/1873-3468.14698. Online ahead of print.ABSTRACTThe nicotinamide adenine dinucleotide (NAD+ ) precursor nicotinamide mononucleotide (NMN) is a proposed therapy for age-related disease, whereby it is assumed that NMN is incorporated into NAD+ through the canonical recycling pathway. During oral delivery, NMN is exposed to the gut microbiome, which could modify the NAD+ metabolome through enzyme activities not present in the mammalian host. We show that orally delivered NMN can undergo deamidation and incorporation in mammalian tissue via the de novo pathway, which is reduced in animals treated with antibiotics to ablate the gut microbiome. Antibiotics increased the availability of NAD+ metabolites, suggesting the microbiome could be in competition with the host for dietary NAD+ precursors. These findings highlight new interactions between NMN and the gut microbiome.PMID:37463842 | DOI:10.1002/1873-3468.14698

J Affect Disord. 2023 Jul 16:S0165-0327(23)00940-0. doi: 10.1016/j.jad.2023.07.089. Online ahead of print.ABSTRACTPrenatal stress (PS) increases offspring susceptibility to depression, but the underlying mechanism remains unclear. Our previous results showed that PS can affect depression-like behavior in offspring through neurotransmitters and neuroinflammatory substances in the hippocampus and frontal cortex. In recent years there has been increasing evidence for a role of the gut microbiome in depression. The brain-gut axis theory suggests there is a need to further explore the mechanism involving the gut microbiome in the susceptibility of offspring to depression caused by PS. In the present study we used a stress model relevant to depression in which pregnant female rats undergo prenatal restraint stress and the offspring show susceptibility to depression. High-resolution gene sequencing for 16S ribosomal RNA markers and non-targeted metabolomic analysis were used to evaluate the fecal microbiome and the availability of metabolites, respectively. PS was found to induce depressive-like behavior in susceptible offspring (PS-S), as detected by the sucrose preference and forced swimming tests, as well as altering Alpha and Beta diversity. The different microbiota between the PS-S and control groups were mainly involved in membrane transport, carbohydrate metabolism, amino acid metabolism, and replication and repair pathways. In total, 237 and 136 important differential metabolites with significant influence on modeling analysis were obtained under positive and negative modes, respectively. The main canonical pathways found to be altered were glycerophospholipid metabolism and glycerolipid metabolism. These results suggest that gut microbiota might contribute to the onset of PS-induced depression-like behavior by affecting the glycerophospholipid and glycerolipid metabolic pathways.PMID:37463643 | DOI:10.1016/j.jad.2023.07.089

Cell Host Microbe. 2023 Jul 10:S1931-3128(23)00260-3. doi: 10.1016/j.chom.2023.06.009. Online ahead of print.ABSTRACTEarly administration of azithromycin after allogeneic hematopoietic stem cell transplantation was shown to increase the relapse of hematological malignancies. To determine the impact of azithromycin on the post-transplant gut ecosystem and its influence on relapse, we characterized overtime gut bacteriome, virome, and metabolome of 55 patients treated with azithromycin or a placebo. We describe four enterotypes and the network of associated bacteriophage species and metabolic pathways. One enterotype associates with sustained remission. One taxon from Bacteroides specifically associates with relapse, while two from Bacteroides and Prevotella correlate with complete remission. These taxa are associated with lipid, pentose, and branched-chain amino acid metabolic pathways and several bacteriophage species. Enterotypes and taxa associate with exhausted T cells and the functional status of circulating immune cells. These results illustrate how an antibiotic influences a complex network of gut bacteria, viruses, and metabolites and may promote cancer relapse through modifications of immune cells.PMID:37463582 | DOI:10.1016/j.chom.2023.06.009

Food Chem. 2023 Jul 13;429:136859. doi: 10.1016/j.foodchem.2023.136859. Online ahead of print.ABSTRACTThis study hypothesized the existence of cultivar-associated correlations between grape berry metabolites and its microbial residents, in Douro wine region. Integrated metabolomics with metabarcoding showed that the microbial biodiversity is not associated to berry sugar concentration, but closely connected to the profile of amino acids, flavonoids and wax compounds, which drove cultivar differentiation together with the prevalence of pathogenic fungi, yeasts and bacteria, mainly Dothideomycetes and Gammaproteobacteria. Over 7000 metabolite-microbiota correlations with ρ >|0.99| exposed a core of 15 metabolites linked to 11 microbial taxa. Serine, oxalate, cyanidin-3-O-glucoside, petunidin-3-O-glucoside, gallic acid, germanicol, sitosterol and erythrodiol correlated negatively to the abundance of most taxa, including Alternaria, Aureobasidium, Pseudopithomyces, Pseudomonas and Sphingomonas. In contrast, phenylalanine, asparagine, alanine, (epi)gallocatechin and procyanidin gallate mediated positive metabolite-OTU correlations. E. necator and A. carbonarius correlated negatively with stigmasterol and amyrin. Complex fungi-bacteria relationships ruled by Dothideomycetes and Alphaproteobacteria further suggest tight host-microbe interactions at the carposphere.PMID:37463536 | DOI:10.1016/j.foodchem.2023.136859

J Gerontol A Biol Sci Med Sci. 2023 Jul 18:glad171. doi: 10.1093/gerona/glad171. Online ahead of print.ABSTRACTBACKGROUND: Lower urinary tract syndrome (LUTS) is a group of urinary tract symptoms and signs which can include urinary incontinence. Advancing age is a major risk factors for LUTS; however the underlying biochemical mechanisms of age-related LUTS remain unknown. HX (hypoxanthine) is a purine metabolite associated with generation of tissue damaging reactive oxygen species (ROS). This study tested the hypothesis that exposure of the adult bladder to HX-ROS over time damages key LUT elements, mimicking qualitatively some of the changes observed with aging.METHODS: Adult 3-month-old female Fischer 344 (F344) rats were treated with vehicle or HX (10 mg/kg/day; 3 weeks) administered in drinking water. Targeted purine metabolomics and molecular approaches were used to assess purine metabolites and biomarkers for oxidative stress and cellular damage. Biomechanical approaches assessed LUT structure and measurements of LUT function (using custom-metabolic cages and cystometry) were also employed.RESULTS: HX exposure increased biomarkers indicative of oxidative stress, pathophysiological ROS production and depletion of cellular energy with declines in NAD + levels. Moreover, HX treatment caused bladder remodeling and decreased the intercontraction interval and leak point pressure (surrogate measure to assess stress urinary incontinence).CONCLUSIONS: These studies provide evidence that in adult rats chronic exposure to HX causes changes in voiding behavior and in bladder structure resembling alterations observed with aging. These results suggest that increased levels of uro-damaging HX were associated with ROS/oxidative stress-associated cellular damage which may be central to age-associated development of LUTS, opening up potential opportunities for geroscience-guided interventions.PMID:37463319 | DOI:10.1093/gerona/glad171

Cancer Res. 2023 Jul 18:CAN-22-3481. doi: 10.1158/0008-5472.CAN-22-3481. Online ahead of print.ABSTRACTMultiple myeloma (MM) cells undergo metabolic reprogramming in response to the hypoxic and nutrient-deprived bone marrow microenvironment. Primary oncogenes in recurrent translocations might be able to drive metabolic heterogeneity to survive the microenvironment that can present new vulnerabilities for therapeutic targeting. t(4;14) translocation leads to the universal overexpression of histone methyltransferase NSD2 that promotes plasma cell transformation through a global increase in H3K36me2. Here, we identified PKCα as an epigenetic target that contributes to the oncogenic potential of NSD2. RNA-sequencing of t(4;14) MM cell lines revealed a significant enrichment in the regulation of metabolic processes by PKCα, and the glycolytic gene, hexokinase 2 (HK2), was transcriptionally regulated by PKCα in a PI3K/Akt-dependent manner. Loss of PKCα displaced mitochondria-bound HK2 and reversed sensitivity to the glycolytic inhibitor 3-bromopyruvate. Additionally, the perturbation of glycolytic flux led to a metabolic shift to a less energetic state and decreased ATP production. Metabolomics analysis indicated lactate as a differential metabolite associated with PKCα. As a result, PKCα conferred resistance to the immunomodulatory drugs (IMiD) lenalidomide in a cereblon-independent manner and could be phenocopied by either overexpression of HK2 or direct supplementation of lactate. Clinically, t(4;14) MM patients had elevated plasma lactate levels and did not benefit from lenalidomide-based regimens. Altogether, this study provides insights into the epigenetic-metabolism crosstalk in MM and highlights the opportunity for therapeutic intervention that leverages the distinct metabolic program in t(4;14) myeloma.PMID:37463241 | DOI:10.1158/0008-5472.CAN-22-3481

Food Funct. 2023 Jul 18. doi: 10.1039/d3fo01659e. Online ahead of print.ABSTRACTPremature ovarian insufficiency (POI) has become one of the greatest health threats to the reproduction of women during their fertile age. Lycium barbarum polysaccharides (LBPs) are known for anti-aging and reproductive protective functions. Here, we investigated the protective effect of LBP on POI mice and revealed its possible mechanism by a combination of 16S rRNA sequencing and metabolomics analysis. In the current study, female C57BL/6J mice treated with D-galactose were used as a model to investigate the reversal effect of LBP on the degenerative ovarian function. The ameliorative effect of LBP on POI was evaluated from the estrous cycle, ovarian reserve, serum sex hormone levels, and fertility testing. Additionally, 16S rRNA gene sequencing and untargeted metabolomics were integrated to analyze the effects of LBP on the gut microbiota and fecal metabolic profile in the POI mice. The results showed that LBP administration significantly increased the total number of follicles and the number of follicles at different developmental stages in the POI mice. In addition, LBP was effective in reducing the serum levels of follicle-stimulating hormone (FSH) and luteinizing hormone (LH), regularizing the disordered estrous cycle, and increasing the number of offspring of the POI mice. The results from 16S rRNA sequencing showed that LBP had beneficial effects on the composition and structure of the gut microbiota in the POI mice. In a metabolomics study, a total of 23 metabolites were finally identified as potential biomarkers of POI, and multiple pathways were regulated after the treatment of LBP, especially the arginine biosynthesis, glycerophospholipid metabolism and steroid hormone biosynthesis pathways. Pearson's correlation analysis showed that the regulation effect of LBP on metabolites was closely related to Faecalibaculum, Bilophila and Anaerofustis in the gut microbiota. In summary, the results demonstrated that LBP could improve the ovarian reserve and provides evidence both on the gut microbiota and metabolism, which provide beneficial support for the applications of LBP in female ovarian function degeneration.PMID:37463025 | DOI:10.1039/d3fo01659e

Int J Phytoremediation. 2023 Jul 18:1-9. doi: 10.1080/15226514.2023.2232874. Online ahead of print.ABSTRACTPer- and polyfluoroalkyl substances (PFAS) constitute a large class of toxic manmade compounds that have been used in many industrial and household products. Dispersion of PFAS in the environment has raised concerns because of their persistence and toxicity for living organisms. Both terrestrial and aquatic plants have been shown to take up PFAS from contaminated soil and groundwater, and to accumulate these compounds inside their tissues. Although PFAS generally exert a low toxicity on plants at environmentally relevant concentrations, they frequently impact biomass growth and photosynthetic activity at higher levels. Uptake, translocation, and toxicity of PFAS in plants have been well covered in literature. Although less attention has been given to the molecular mechanisms underlying the plant response to PFAS, recent studies based on -omics approaches indicate that PFAS affects the plant metabolism even a low concentration. The objective of this review is to summarize the current knowledge about the effects of PFAS on plants at the molecular level. Results from recent transcriptomics, proteomics, and metabolomics studies show that low levels of PFAS induce oxidative stress and affect multiple plant functions and processes, including photosynthesis and energy metabolism. These potentially harmful effects trigger activation of defense mechanisms.PMID:37462666 | DOI:10.1080/15226514.2023.2232874

Food Funct. 2023 Jul 18. doi: 10.1039/d3fo01771k. Online ahead of print.ABSTRACTDiets rich in various active ingredients may be an effective intervention strategy for non-alcoholic fatty liver disease (NAFLD). The green pea hull (GPH) is a processing by-product of green peas rich in dietary fiber and polyphenols. Here, a mouse model of NAFLD induced by DSS + high-fat diet (HFD) was established to explore the intervention effect of the GPH. The results showed that dietary supplements with the GPH can inhibit obesity and reduce lipid accumulation in the mouse liver to prevent liver fibrosis. GPH intervention can improve liver antioxidant capacity, reduce blood lipid deposition and maintain glucose homeostasis. DSS-induced disruption of the intestinal barrier aggravates NAFLD, which may be caused by the influx of large amounts of LPS. A multi-omics approach combining metabolomics and transcriptomic analysis indicated that glycine was the key target and its content was decreased in the liver after GPH intervention, and that dietary supplements with the GPH can relieve NAFLD via the SHMT2/glycine/mTOR/PPAR-γ signaling pathway, which was further supported by liver-associated protein expression. In conclusion, our study demonstrated that dietary GPH can significantly ameliorate NAFLD, and the future development of related food products can enhance the economic value of the GPH.PMID:37462466 | DOI:10.1039/d3fo01771k

Leuk Lymphoma. 2023 Jul 18:1-11. doi: 10.1080/10428194.2023.2234523. Online ahead of print.ABSTRACTAltered metabolic fingerprints of Diffuse large B-cell lymphoma, not otherwise specified (DLBCL NOS) may offer novel opportunities to identify new biomarkers and improve the understanding of its pathogenesis. This study aimed to investigate the modified metabolic pathways in extranodal, germinal center B-cell (GCB) and non-GCB DLBCL NOS from the head and neck. Formalin-fixed paraffin-embedded (FFPE) tissues from eleven DLBCL NOS classified according to Hans' algorithm using immunohistochemistry, and five normal lymphoid tissues (LT) were analyzed by high-performance liquid chromatography-mass spectrometry-based untargeted metabolomics. Partial Least Squares Discriminant Analysis showed that GCB and non-GCB DLBCL NOS have a distinct metabolomics profile, being the former more similar to normal lymphoid tissues. Metabolite pathway enrichment analysis indicated the following altered pathways: arachidonic acid, tyrosine, xenobiotics, vitamin E metabolism, and vitamin A. Our findings support that GCB and non-GCB DLBCL NOS has a distinct metabolomic profile, in which GCB possibly shares more metabolic similarities with LT than non-GCB DLBCL NOS.PMID:37462418 | DOI:10.1080/10428194.2023.2234523

Res Sq. 2023 Jun 30:rs.3.rs-3069713. doi: 10.21203/rs.3.rs-3069713/v1. Preprint.ABSTRACTPro-longevity dietary interventions such as caloric restriction (CR)1 and methionine restriction2 (MR) are associated with 'browning' of white adipose tissue in rodents, an adaptive response that increases heat production to maintain core-body temperature for the survival of homeotherms3,4. Here, the analysis of metabolome and transcriptome of adipose tissue of healthy humans5 identified that sustained caloric restriction (CR) decreases methionine cycle and lowers cysteine levels despite elevated expression of enzyme cystathionine γ-lyase (CTH), which catalyzes the synthesis of cysteine in the transsulfuration (TSP) pathway6,7. Cysteine starvation of global, but not adipocyte- or hepatocyte-specific Cth deficient mice, triggered lethal thermogenesis through conversion of white adipose tissue into uncoupled "brown"-like adipocytes. This manifests as depletion of energy reserves and drastic weight-loss. Mechanistically, cysteine starvation-induced thermogenesis and energy expenditure increases adipose noradrenaline bioavailability and induces a UCP1-independent response that partially requires FGF21. Therapeutically, reduction of cysteine reversed obesity by increasing thermogenesis and lowering inflammation. These findings establish that adaptation to dietary restriction requires activation of TSP to defend organismal cysteine levels that serves as a thermogenic checkpoint for regulation of core-body temperature and conservation of energy.PMID:37461682 | PMC:PMC10350108 | DOI:10.21203/rs.3.rs-3069713/v1

bioRxiv. 2023 Jul 11:2023.07.07.548031. doi: 10.1101/2023.07.07.548031. Preprint.ABSTRACTINTRODUCTION: KDM2B encodes a JmjC domain-containing histone lysine demethylase, which functions as an oncogene in several types of tumors, including TNBC. This study was initiated to address the cancer relevance of the results of our earlier work, which had shown that overexpression of KDM2B renders mouse embryonic fibroblasts (MEFs) resistant to oxidative stress by regulating antioxidant mechanisms.METHODS: We mainly employed a multi-omics strategy consisting of RNA-Seq, quantitative TMT proteomics, Mass-spectrometry-based global metabolomics, ATAC-Seq and ChIP-seq, to explore the role of KDM2B in the resistance to oxidative stress and intermediary metabolism. These data and data from existing patient datasets were analyzed using bioinformatic tools, including exon-intron-split analysis (EISA), FLUFF and clustering analyses. The main genetic strategy we employed was gene silencing with shRNAs. ROS were measured by flow cytometry, following staining with CellROX and various metabolites were measured with biochemical assays, using commercially available kits. Gene expression was monitored with qRT-PCR and immunoblotting, as indicated.RESULTS: The knockdown of KDM2B in basal-like breast cancer cell lines lowers the levels of GSH and sensitizes the cells to ROS inducers, GSH targeting molecules, and DUB inhibitors. To address the mechanism of GSH regulation, we knocked down KDM2B in MDA-MB-231 cells and we examined the effects of the knockdown, using a multi-omics strategy. The results showed that KDM2B, functioning in the context of ncPRC1.1, regulates a network of epigenetic and transcription factors, which control a host of metabolic enzymes, including those involved in the SGOC, glutamate, and GSH metabolism. They also showed that KDM2B enhances the chromatin accessibility and expression of MYC and ATF4, and that it binds in concert with MYC and ATF4, the promoters of a large number of transcriptionally active genes, including many, encoding metabolic enzymes. Additionally, MYC and ATF4 binding sites were enriched in genes whose accessibility depends on KDM2B, and analysis of a cohort of TNBCs expressing high or low levels of KDM2B, but similar levels of MYC and ATF4 identified a subset of MYC targets, whose expression correlates with the expression of KDM2B. Further analyses of basal-like TNBCs in the same cohort, revealed that tumors expressing high levels of all three regulators exhibit a distinct metabolic signature that carries a poor prognosis.CONCLUSIONS: The present study links KDM2B, ATF4, and MYC in a transcriptional network that regulates the expression of multiple metabolic enzymes, including those that control the interconnected SGOC, glutamate, and GSH metabolic pathways. The co-occupancy of the promoters of many transcriptionally active genes, by all three factors, the enrichment of MYC binding sites in genes whose chromatin accessibility depends on KDM2B, and the correlation of the levels of KDM2B with the expression of a subset of MYC target genes in tumors that express similar levels of MYC, suggest that KDM2B regulates both the expression and the transcriptional activity of MYC. Importantly, the concerted expression of all three factors also defines a distinct metabolic subset of TNBCs with poor prognosis. Overall, this study identifies novel mechanisms of SGOC regulation, suggests novel KDM2B-dependent metabolic vulnerabilities in TNBC, and provides new insights into the role of KDM2B in the epigenetic regulation of transcription.HIGHLIGHTS: The knockdown of KDM2B in basal-like breast cancer cell lines lowers the levels of GSH and sensitizes the cells to ROS inducers, GSH targeting molecules, and DUB inhibitors.KDM2B regulates intermediary metabolism by targeting the expression of a host of metabolic enzymes, including those in the SGOC, glutamate, and GSH metabolism.KDM2B enhances chromatin accessibility of MYC and ATF4 and promotes their expression.MYC and ATF4 binding sites are enriched in the promoters of genes whose accessibility depends on KDM2B.KDM2B functioning in the context of ncPRC1.1, binds the promoters of transcriptionally active genes, including those encoding KDM2B-regulated metabolic enzymes, in concert with MYC and ATF4.Basal-like TNBCs expressing high levels of all three regulators, exhibit a distinct metabolic signature that is associated with poor prognosis.PMID:37461630 | PMC:PMC10350079 | DOI:10.1101/2023.07.07.548031

bioRxiv. 2023 Jul 9:2023.07.07.548174. doi: 10.1101/2023.07.07.548174. Preprint.ABSTRACTMolecular understanding of the vertebrate Organizer, a tissue center critical for inductive signaling during gastrulation, has so far been limited to transcripts and some proteins due to limitations in detection and sensitivity. The Spemann-Mangold Organizer (SMO) in the South African Clawed Frog ( X. laevis ), a popular model of development, has long been discovered to induce the patterning of the central nervous system. Molecular screens on the tissue have identified several genes, such as goosecoid, chordin, and noggin, with independent ability to establish a body axis. A comprehensive study of proteins and metabolites produced in the SMO and their functional roles has been lacking. Here, we pioneer a deep discovery proteomic and targeted metabolomic screen of the SMO in comparison to the rest of the embryo using liquid chromatography high-resolution mass spectrometry (HRMS). Quantification of ∼4,600 proteins and a panel of metabolites documented differential expression for ∼450 proteins and multiple intermediates of energy metabolism in the SMO. Upregulation of oxidative phosphorylation (OXPHOS) and redox regulatory proteins gave rise to elevated oxidative stress and an accumulation of reactive oxygen species in the Organizer. Imaging experiments corroborated these findings, discovering enrichment of hydrogen peroxide in the SMO tissue. Chemical perturbation of the redox gradient affected mesoderm involution during early tissue movements of gastrulation. HRMS expands the bioanalytical toolbox of cell and developmental biology, providing previously unavailable information on molecular classes to challenge and refine our classical understanding of the Organizer and its function during early patterning of the embryo.PMID:37461553 | PMC:PMC10350060 | DOI:10.1101/2023.07.07.548174

bioRxiv. 2023 Jul 4:2023.07.03.547607. doi: 10.1101/2023.07.03.547607. Preprint.ABSTRACTMachine learning (ML) has become a widespread strategy for studying complex microbiome signatures associated with disease. To this end, metagenomics data are often processed into a single "view" of the microbiome, such as its taxonomic (species) or functional (gene) composition, which in turn serves as input to such ML models. When further omics are available, such as metabolomics, these can be analyzed as additional complementary views. Following training and evaluation, the resulting model can be explored to identify informative features, generating hypotheses regarding underlying mechanisms. Importantly, however, using a single view generally offers relatively limited hypotheses, failing to capture simultaneous shifts or dependencies across multiple microbiome layers that likely play a role in microbiome-host interactions. In this work, inspired by the broad domain of multi-view learning , we constructed an integrated ML analysis pipeline using multiple microbiome views. We specifically aimed to investigate the impact of various integration approaches on the ability to predict disease state based on multiple microbiome-related views, and to generate biological insights. Applying this pipeline to data from 25 case-control metagenomics studies, we found that multi-view models typically result in performances that are comparable to the best-performing single view, yet, provide a mixed set of informative features from different views, while accounting for dependencies and links between them. To further enhance such models, we developed a new framework termed MintTea, based on sparse generalized canonical correlation analysis, to identify multi-view modules of features, highlighting shared trends in the data expressed by the different views. We showed that this framework identified multiple modules that were both highly predictive of the disease state, and exhibited strong within-module associations between features from different views. We accordingly advocate for using multi-view models to capture multifaceted microbiome signatures that likely better reflect the complex mechanisms underlying microbiome-disease associations.PMID:37461534 | PMC:PMC10349976 | DOI:10.1101/2023.07.03.547607

Res Sq. 2023 Jul 6:rs.3.rs-3112286. doi: 10.21203/rs.3.rs-3112286/v1. Preprint.ABSTRACTNutrient handling is an essential function of the gastrointestinal tract. Most nutrient absorption occurs in the small intestine and is coordinated by hormone-producing intestinal epithelial cells known as enteroendocrine cells (EECs). In contrast, the colon mostly reclaims water and electrolytes, and handles the influx of microbially-derived metabolites, including short chain fatty acids (SCFA). Hormonal responses of small intestinal EECs have been extensively studied but much less in known about the role of colonic EECs in metabolic regulation. To address this core question, we investigated a mouse model deficient in colonic EECs. We found that colonic EEC deficiency leads to hyperphagia and obesity. Surprisingly, colonic EEC deficiency results in altered microbiota composition and metabolism, which we found through antibiotic treatment and transfer to germ free recipients, to be both necessary and sufficient for the development of obesity. Moreover, studying stool and blood metabolomes, we found that differential glutamate production by intestinal microbiota corresponds to increase appetite due to EEC loss. Finally, we show that colonic glutamate administration can directly increase food intake and activate appetite centers in the central nervous system. These observations shed light on an unanticipated host-microbiota axis in the colon, part of a larger gut-brain axis, that regulates host metabolism and body weight.PMID:37461519 | PMC:PMC10350199 | DOI:10.21203/rs.3.rs-3112286/v1

Comb Chem High Throughput Screen. 2023 Jul 17. doi: 10.2174/1386207326666230717094936. Online ahead of print.ABSTRACTBACKGROUND: Liver cirrhosis is one of the leading causes of decreased life expectancy worldwide. However, the molecular mechanisms underlying liver cirrhosis remain unclear. In this study, we performed a comprehensive analysis using transcriptome and metabolome sequencing to explore the genes, pathways, and interactions associated with liver cirrhosis.METHODS: We performed transcriptome and metabolome sequencing of blood samples from patients with cirrhosis and healthy controls (1:1 matched for sex and age). We validated the differentially expressed microRNA (miRNA) and mRNAs using real-time quantitative polymerase chain reaction.RESULTS: For transcriptome analysis, we screened for differentially expressed miRNAs and mRNAs, analyzed mRNAs to identify possible core genes and pathways, and performed co-analysis of miRNA and mRNA sequencing results. In terms of the metabolome, we screened five pathways that were substantially enriched in the differential metabolites. Next, we identified the metabolites with the most pronounced differences among these five metabolic pathways. We performed receiver operating characteristic (ROC) curve analysis of these five metabolites to determine their diagnostic efficacy for cirrhosis. Finally, we explored possible links between the transcriptome and metabolome.CONCLUSION: Based on sequencing and bioinformatics, we identified miRNAs and genes that were differentially expressed in the blood of patients with liver cirrhosis. By exploring pathways and disease-specific networks, we identified unique biological mechanisms. In terms of metabolomes, we identified novel biomarkers and explored their diagnostic efficacy. We identified possible common pathways in the transcriptome and metabolome that could serve as candidates for further studies.PMID:37461343 | DOI:10.2174/1386207326666230717094936

J Mass Spectrom. 2023 Jul 17:e4961. doi: 10.1002/jms.4961. Online ahead of print.ABSTRACTA breeding program to produce new grape varieties tolerant to main vine fungal pathogens (Plasmopara viticola and Erysiphe necator) is carrying out by crossing Vitis vinifera cv. "Glera" with resistant genotypes such as "Solaris," "Bronner," and "Kunleany." Firstly, resistance gene-based markers analyses allowed the identification of five genotypes, which have inherited the resistance loci against mildews. To select those that also inherited the phenotype as close as possible to 'Glera' suitable to be introduced in the Prosecco wine production protocols, the grape glycosidic derivatives were studied by UHPLC/QTOF mass spectrometry. Targeted identification of the metabolites was performed using a database expressly constructed by including the glycosidic volatile precursors previously identified in grape and wine. A total of 77 glycosidic derivatives including many aroma precursors and some variety markers, were identified. Original resistant genotypes had distinct metabolomic profiles and different to 'Glera', while the crossings showed varying similarity degrees to V. vinifera parent. Findings demonstrated the Glera × Bronner and Glera × Solaris crossings are more suitable to produce high-sustainable Prosecco wines. Coupling of glycosidic volatile precursors profiling to multivariate statistical analysis was effective for phenotypic characterization of grapes and to evaluate their enological potential.PMID:37461255 | DOI:10.1002/jms.4961