Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

Combining 16S rRNA Sequencing and Metabolomics Data to Decipher the Interactions between Gut Microbiota, Host Immunity, and Metabolites in Diarrheic Young Small Ruminants

Sat, 29/07/2023 - 12:00
Int J Mol Sci. 2023 Jul 13;24(14):11423. doi: 10.3390/ijms241411423.ABSTRACTDiarrhea is associated with gut microbiota, immunity, and metabolic alterations in goat kids and lambs. This study used 28 lambs (11 healthy and 17 diarrheic) and 20 goat kids (10 healthy and 10 diarrheic) to investigate the association between diarrhea occurrence and changes in gut microbiota, metabolism, and immunity in goat kids and lambs. The results revealed that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in goat kids and lambs. In addition, Enterobacteriaceae and Lachnospiraceae families were identified in both diarrheic goat kids and lambs. Furthermore, functional prediction of microbiota showed that it was involved in cell motility and cancer pathways. The identified differential metabolites were implicated in the bile secretion pathway. Lambs had significant differences in immunoglobulin G (IgG), immunoglobulin M (IgM), interleukin-1β (IL-1β), and tumor necrosis factor-alpha (TNF-α) compared to goat kids. IgG and IL-1β were positively correlated to Patescibacteria, Clostridiaceae, and unclassified_Muribaculaceae in both diarrheic goat kids and lambs. In addition, weighted gene co-expression network analysis (WGCNA) revealed that the MEgreen module was positively associated with IgG, IgM, IL-1β, TNF-α, and triglyceride (TG). In conclusion, our results characterized the gut microbiota, metabolism, and immune status of lambs and goat kids suffering from diarrhea.PMID:37511183 | PMC:PMC10380214 | DOI:10.3390/ijms241411423

Exploring Metabolomic Patterns in Type 2 Diabetes Mellitus and Response to Glucose-Lowering Medications-Review

Sat, 29/07/2023 - 12:00
Genes (Basel). 2023 Jul 18;14(7):1464. doi: 10.3390/genes14071464.ABSTRACTThe spectrum of information related to precision medicine in diabetes generally includes clinical data, genetics, and omics-based biomarkers that can guide personalized decisions on diabetes care. Given the remarkable progress in patient risk characterization, there is particular interest in using molecular biomarkers to guide diabetes management. Metabolomics is an emerging molecular approach that helps better understand the etiology and promises the identification of novel biomarkers for complex diseases. Both targeted or untargeted metabolites extracted from cells, biofluids, or tissues can be investigated by established high-throughput platforms, like nuclear magnetic resonance (NMR) and mass spectrometry (MS) techniques. Metabolomics is proposed as a valuable tool in precision diabetes medicine to discover biomarkers for diagnosis, prognosis, and management of the progress of diabetes through personalized phenotyping and individualized drug-response monitoring. This review offers an overview of metabolomics knowledge as potential biomarkers in type 2 diabetes mellitus (T2D) diagnosis and the response to glucose-lowering medications.PMID:37510368 | PMC:PMC10379356 | DOI:10.3390/genes14071464

Quantitative, Targeted Analysis of Gut Microbiota Derived Metabolites Provides Novel Biomarkers of Early Diabetic Kidney Disease in Type 2 Diabetes Mellitus Patients

Sat, 29/07/2023 - 12:00
Biomolecules. 2023 Jul 7;13(7):1086. doi: 10.3390/biom13071086.ABSTRACTDiabetic kidney disease (DKD) is one of the most debilitating complications of type 2 diabetes mellitus (T2DM), as it progresses silently to end-stage renal disease (ESRD). The discovery of novel biomarkers of early DKD becomes acute, as its incidence is reaching catastrophic proportions. Our study aimed to quantify previously identified metabolites from serum and urine through untargeted ultra-high-performance liquid chromatography coupled with electrospray ionization-quadrupole-time of flight-mass spectrometry (UHPLC-QTOF-ESI+-MS) techniques, such as the following: arginine, dimethylarginine, hippuric acid, indoxyl sulfate, p-cresyl sulfate, L-acetylcarnitine, butenoylcarnitine and sorbitol. The study concept was based on the targeted analysis of selected metabolites, using the serum and urine of 20 healthy subjects and 90 T2DM patients with DKD in different stages (normoalbuminuria-uACR < 30 mg/g; microalbuminuria-uACR 30-300 mg/g; macroalbuminuria-uACR > 300 mg/g). The quantitative evaluation of metabolites was performed with pure standards, followed by the validation methods such as the limit of detection (LOD) and the limit of quantification (LOQ). The following metabolites from this study resulted as possible biomarkers of early DKD: in serum-arginine, dimethylarginine, hippuric acid, indoxyl sulfate, butenoylcarnitine and sorbitol and in urine-p-cresyl sulfate.PMID:37509122 | PMC:PMC10377254 | DOI:10.3390/biom13071086

The Effects of Natural Epigenetic Therapies in 3D Ovarian Cancer and Patient-Derived Tumor Explants: New Avenues in Regulating the Cancer Secretome

Sat, 29/07/2023 - 12:00
Biomolecules. 2023 Jul 1;13(7):1066. doi: 10.3390/biom13071066.ABSTRACTHigh mortality rates in ovarian cancer have been linked to recurrence, metastasis, and chemoresistant disease, which are known to involve not only genetic changes but also epigenetic aberrations. In ovarian cancer, adipose-derived stem cells from the omentum (O-ASCs) play a crucial role in supporting the tumor and its tumorigenic microenvironment, further propagating epigenetic abnormalities and dissemination of the disease. Epigallocatechin gallate (EGCG), a DNA methyltransferase inhibitor derived from green tea, and Indole-3-carbinol (I3C), a histone deacetylase inhibitor from cruciferous vegetables, carry promising effects in reprograming aberrant epigenetic modifications in cancer. Therefore, we demonstrate the action of these diet-derived compounds in suppressing the growth of 3D ovarian cancer spheroids or organoids as well as post-treatment cancer recovery through proliferation, migration, invasion, and colony formation assays when compared to the synthetic epigenetic compound Panobinostat with or without standard chemotherapy. Finally, given the regulatory role of the secretome in growth, metastasis, chemoresistance, and relapse of disease, we demonstrate that natural epigenetic compounds can regulate the secretion of protumorigenic growth factors, cytokines, extracellular matrix components, and immunoregulatory markers in human ovarian cancer specimens. While further studies are needed, our results suggest that these treatments could be considered in the future as adjuncts to standard chemotherapy, improving efficiency and patient outcomes.PMID:37509102 | PMC:PMC10377145 | DOI:10.3390/biom13071066

Nutritional lipidomics for the characterization of lipids in food

Sat, 29/07/2023 - 12:00
Adv Food Nutr Res. 2023;105:97-172. doi: 10.1016/bs.afnr.2022.12.002. Epub 2023 Jan 20.ABSTRACTLipids represent one out of three major macronutrient classes in the human diet. It is estimated to account for about 15-20% of the total dietary intake. Triacylglycerides comprise the majority of them, estimated 90-95%. Other lipid classes include free fatty acids, phospholipids, cholesterol, and plant sterols as minor components. Various methods are used for the characterization of nutritional lipids, however, lipidomics approaches become increasingly attractive for this purpose due to their wide coverage, comprehensiveness and holistic view on composition. In this chapter, analytical methodologies and workflows utilized for lipidomics profiling of food samples are outlined with focus on mass spectrometry-based assays. The chapter describes common lipid extraction protocols, the distinct instrumental mass-spectrometry based analytical platforms for data acquisition, chromatographic and ion-mobility spectrometry methods for lipid separation, briefly mentions alternative methods such as gas chromatography for fatty acid profiling and mass spectrometry imaging. Critical issues of important steps of lipidomics workflows such as structural annotation and identification, quantification and quality assurance are discussed as well. Applications reported over the period of the last 5years are summarized covering the discovery of new lipids in foodstuff, differential profiling approaches for comparing samples from different origin, species, varieties, cultivars and breeds, and for food processing quality control. Lipidomics as a powerful tool for personalized nutrition and nutritional intervention studies is briefly discussed as well. It is expected that this field is significantly growing in the near future and this chapter gives a short insight into the power of nutritional lipidomics approaches.PMID:37516469 | DOI:10.1016/bs.afnr.2022.12.002

Blood metabolomics reveals the therapeutic effect of Pueraria polysaccharide on calf diarrhea

Sat, 29/07/2023 - 12:00
BMC Vet Res. 2023 Jul 29;19(1):98. doi: 10.1186/s12917-023-03662-9.ABSTRACTBACKGROUND: Neonatal calf diarrhea (NCD) is typically treated with antibiotics, while long-term application of antibiotics induces drug resistance and antibiotic residues, ultimately decreasing feed efficiency. Pueraria polysaccharide (PPL) is a versatile antimicrobial, immunomodulatory, and antioxidative compound. This study aimed to compare the therapeutic efficacy of different doses of PPL (0.2, 0.4, 0.8 g/kg body weight (BW)) and explore the effect of plasma metabolites in diarrheal calves by the best dose of PPL.RESULTS: PPL could effectively improve the daily weight gain, fecal score, and dehydration score, and the dosage of 0.4 g/kg BW could reach curative efficacy against calf diarrhea (with effective rates 100.00%). Metabolomic analysis suggested that diarrhea mainly affect the levels of taurocholate, DL-lactate, LysoPCs, and intestinal flora-related metabolites, trimethylamine N-oxide; however, PPL improved liver function and intestinal barrier integrity by modulating the levels of DL-lactate, LysoPC (18:0/0:0) and bilirubin, which eventually attenuated neonatal calf diarrhea. It also suggested that the therapeutic effect of PPL is related to those differential metabolites in diarrheal calves.CONCLUSIONS: The results showed that 0.4 g/kg BW PPL could restore the clinical score of diarrhea calves by improving the blood indexes, biochemical indexes, and blood metabolites. And it is a potential medicine for the treatment of calf diarrhea.PMID:37516856 | DOI:10.1186/s12917-023-03662-9

The changes in metabolomics profile induced by intermittent theta burst stimulation in major depressive disorder: an exploratory study

Sat, 29/07/2023 - 12:00
BMC Psychiatry. 2023 Jul 29;23(1):550. doi: 10.1186/s12888-023-05044-9.ABSTRACTBACKGROUND: Recently, there has been an ongoing interest in the mechanism of intermittent theta burst stimulation (iTBS) in major depressive disorder. Studying the metabolite changes induced by iTBS may help to understand the mechanism.METHODS: Eleven participants with major depressive disorder received 10 days iTBS treatment. Magnetic resonance imaging (MRI) was used to target the region of the left dorsolateral prefrontal cortex (DLPFC) in each participant. We analyzed the effects of iTBS on metabolites using high-throughput profiling and assessed its impact on depressive symptoms. These analyses were considered exploratory, and no correction for multiple comparisons was applied.RESULTS: Among the 318 measured metabolites, a significant increase in cystine, asymmetric dimethylarginine (ADMA), 1-methylhistidine, indoleacetic acid (IAA), diethanolamine (DEA), dopa, riboflavin-5'-monophosphate (FMN), and a significant decrease in alphalinolenic acid (ALA), gamma-linolenic acid (GLA), serotonin, linoleic acid (LA) (p < 0.05) were detected in the patients after iTBS treatment. In Pearson correlation analysis, the plasma levels of LA, FMN and ADMA at baseline were significantly related to the reduction rate of the 17-item Hamilton Depression Rating Scale and the Patient Health Questionnaire-9 scores (p < 0.05).CONCLUSIONS: Our study highlights that LA, FMN, ADMA and their relationship with oxidative stress, may be key factors in the antidepressant efficacy of iTBS.PMID:37516823 | DOI:10.1186/s12888-023-05044-9

An iPSC-derived astrocyte model of fragile X syndrome exhibits dysregulated cholesterol homeostasis

Sat, 29/07/2023 - 12:00
Commun Biol. 2023 Jul 29;6(1):789. doi: 10.1038/s42003-023-05147-9.ABSTRACTCholesterol is an essential membrane structural component and steroid hormone precursor, and is involved in numerous signaling processes. Astrocytes regulate brain cholesterol homeostasis and they supply cholesterol to the needs of neurons. ATP-binding cassette transporter A1 (ABCA1) is the main cholesterol efflux transporter in astrocytes. Here we show dysregulated cholesterol homeostasis in astrocytes generated from human induced pluripotent stem cells (iPSCs) derived from males with fragile X syndrome (FXS), which is the most common cause of inherited intellectual disability. ABCA1 levels are reduced in FXS human and mouse astrocytes when compared with controls. Accumulation of cholesterol associates with increased desmosterol and polyunsaturated phospholipids in the lipidome of FXS mouse astrocytes. Abnormal astrocytic responses to cytokine exposure together with altered anti-inflammatory and cytokine profiles of human FXS astrocyte secretome suggest contribution of inflammatory factors to altered cholesterol homeostasis. Our results demonstrate changes of astrocytic lipid metabolism, which can critically regulate membrane properties and affect cholesterol transport in FXS astrocytes, providing target for therapy in FXS.PMID:37516746 | DOI:10.1038/s42003-023-05147-9

Integrated analysis of proteomics, epigenomics and metabolomics data revealed divergent pathway activation patterns in the recent versus chronic post-traumatic stress disorder

Sat, 29/07/2023 - 12:00
Brain Behav Immun. 2023 Jul 27:S0889-1591(23)00208-8. doi: 10.1016/j.bbi.2023.07.015. Online ahead of print.ABSTRACTMetabolomics, proteomics and DNA methylome assays, when done in tandem from the same blood sample and analyzed together, offer an opportunity to evaluate the molecular basis of post-traumatic stress disorder (PTSD) course and pathogenesis. We performed separate metabolomics, proteomics, and DNA methylome assays on blood samples from two well-characterized cohorts of 159 active duty male participants with relatively recent onset PTSD (<1.5 years) and 300 male veterans with chronic PTSD (>7 years). Analyses of the multi-omics datasets from these two independent cohorts were used to identify convergent and distinct molecular profiles that might constitute potential signatures of severity and progression of PTSD and its comorbid conditions. Molecular signatures indicative of homeostatic processes such as signaling and metabolic pathways involved in cellular remodeling, neurogenesis, molecular safeguards against oxidative stress, metabolism of polyunsaturated fatty acids, regulation of normal immune response, post-transcriptional regulation, cellular maintenance and markers of longevity were significantly activated in the active duty participants with recent PTSD. In contrast, we observed significantly altered multimodal molecular signatures associated with chronic inflammation, neurodegeneration, cardiovascular and metabolic disorders, and cellular attritions in the veterans with chronic PTSD. Activation status of signaling and metabolic pathways at the early and late timepoints of PTSD demonstrated the differential molecular changes related to homeostatic processes at its recent and multi-system syndromes at its chronic phase. Molecular alterations in the recent PTSD seem to indicate some sort of recalibration or compensatory response, possibly directed in mitigating the pathological trajectory of the disorder.PMID:37516387 | DOI:10.1016/j.bbi.2023.07.015

Quantitative Analysis of Soluble Costimulatory Molecules as Potential Diagnostic Biomarkers for Rheumatoid Arthritis using LC-MS/MS in MRM Mode

Sat, 29/07/2023 - 12:00
Clin Chim Acta. 2023 Jul 27:117501. doi: 10.1016/j.cca.2023.117501. Online ahead of print.ABSTRACTBACKGROUND AND AIMS: Rheumatoid arthritis (RA) is a chronic autoimmune disease. RA-induced immunological responses are coordinated by T-cell stimulation. The costimulatory signal CD28-B7 is essential for T-cell activation by interacting CD28 with CD80 and CD86 costimulatory proteins. CTLA4 is another costimulatory protein that binds to CD80 and CD86 to inhibit T-cell activity. The soluble costimulatory proteins: sCD80, sCD86, sCD28, and sCTLA-4 were detected and quantified in human plasma and correlated with RA development. As potential diagnostic biomarkers for RA, developing a sensitive, specific, and reproducible method for quantifying these costimulatory molecules in human plasma and establishing quantitative ranges for each protein in healthy and RA patients' plasma is essential for advancing the clinical diagnostic and health outcomes.MATERIALS AND METHODS: A novel quantitative liquid chromatography-tandem spectrometry (LC-MS/MS) technique using multiple reaction monitoring (MRM) modes was developed and validated to measure soluble costimulatory molecules sCTLA4, sCD28, sCD80, and sCD86 in human plasma samples. Furthermore, the method was applied to determine sCTLA4, sCD28, sCD80, and sCD86 levels in plasma samples from RA patients (n= 23) and healthy controls (n=21).RESULTS: The method was successfully developed and validated according to international inter- and intra-assay precision and accuracy guidelines. The linearity of the method was achieved between 0.5 nM to 100 nM for each protein with a correlation coefficient of > 0.998. The plasma level of sCTLA4, sCD80, and sCD86 in RA patients was significantly elevated compared to controls. RA patients had 63.32 ± 17.63 nM sCTLA4 and controls 36.05 ± 18.83 nM; p<0.0001. The performance of the four proteins was determined using ROC curves, where sCTLA4 showed the highest diagnostic and clinical performance compared to the others.CONCLUSIONS: This study reports the first use of LC-MS/MS in MRM mode to accurately quantify soluble costimulatory molecules in plasma samples as potential RA diagnostic biomarkers. Determination of the reference range for each protein with high selectivity and sensitivity increases the potential for utilizing this method as a clinical diagnostic.PMID:37516334 | DOI:10.1016/j.cca.2023.117501

Analysis of the effects of sulfamethoxazole on the secondary metabolites and antioxidants in oilseed rape (Brassica napus L.) and the underlying mechanisms

Sat, 29/07/2023 - 12:00
Sci Total Environ. 2023 Jul 27:165768. doi: 10.1016/j.scitotenv.2023.165768. Online ahead of print.ABSTRACTThe secondary metabolism of plants is key for mediating responses to environmental stress, but few studies have examined how the relationship between secondary metabolism and the stress response of plants is affected by exposure to antibiotics. Here, we studied the effects of sulfamethoxazole (SMZ) on the secondary metabolism and antioxidant activity of oilseed rape (Brassica napus L.). SMZ significantly affected the growth of rape seedlings. Low and high concentrations of SMZ induced the production of a large number of reactive oxygen species (ROS) in rape seedlings, which damaged cells. SMZ stress altered the activity of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), as well as the content of malondialdehyde (MDA). SMZ promoted the activities of phenylalanine ammonia lyase (PAL), tyrosine ammonia lyase (TAL), cinnamic acid-4-hydroxylase (C4H), and 4-coumaric acid: coenzyme A ligase (4CL) by activating the phenylpropanoid pathway. The content of secondary metabolites changed. The content of phenolic acids and flavonoids increased, and the content of sinapine and anthocyanins was altered to cope with the oxidative damage induced by antibiotics. Transcriptomic and metabolomic analysis showed that differentially expressed genes and differentially expressed metabolites were mainly involved in Phenylpropanoid biosynthesis. SMZ alters the secondary metabolites of rapeseed, which mitigates the deleterious effects of stress, by modulating upstream secondary metabolism pathways and the production of plant hormones involved in signal transduction. In sum, these results provide a new perspective on the effects of SMZ on plants relative to secondary metabolites and improve our understanding of the toxicity of SMZ.PMID:37516166 | DOI:10.1016/j.scitotenv.2023.165768

Mume Fructus (Prunus mume Sieb. et Zucc.) extract accelerates colonic mucosal healing of mice with colitis induced by dextran sulfate sodium through potentiation of cPLA2-mediated lysophosphatidylcholine synthesis

Sat, 29/07/2023 - 12:00
Phytomedicine. 2023 Jul 20;119:154985. doi: 10.1016/j.phymed.2023.154985. Online ahead of print.ABSTRACTBACKGROUND: Mume Fructus (MF) is the fruit of Prunus mume Sieb. et Zucc, a plant of Rosaceae family. Previous studies demonstrated that MF was capable of ameliorating ulcerative colitis (UC) in mice, its action mechanism needs to be clarified.PURPOSE: This study deciphered whether and how MF extract accelerates colonic mucosal healing, the therapeutic endpoint of UC.METHODS: Biochemical, histopathological and qRT-PCR analyses were utilized to define the therapeutic efficacy of MF on dextran sulfate sodium (DSS)-induced colitis in mice. UHPLC-QTOF-MS/MS-based metabolomics technique was adopted to explore the changes of endogenous metabolites associated with UC and responses to MF intervention. qRT-PCR analysis was performed to confirm the molecular pathway in vivo. The effects of MF and lysophosphatidylcholine (LPC) on cell viability, wound healing, proliferation, and migration were examined through a series of in vitro experiments. Moreover, the effects of different subtypes of phospholipase A2 (PLA2) inhibitors on MF-treated colonic epithelial cells were detected by wound healing test and transwell assay.RESULTS: Orally administered MF could alleviate colitis in mice mainly by accelerating the healing of colonic mucosa. Guided by an unbiased metabolomics screen, we identified LPC synthesis as a major modifying pathway in colitis mice after MF treatment. Notably, MF facilitated the synthesis of LPC by enhancing the expression of PLA2 in colitis mice. Mechanistically, MF and LPC accelerated wound closure by promoting cell migration. Moreover, the promotion of MF on wound healing and migration of colonic epithelial cells was blunted by a cytosolic phospholipase A2 (cPLA2) inhibitor.CONCLUSION: MF can facilitate colonic mucosal healing of mice with colitis through cPLA2-mediated intestinal LPC synthesis, which may become a novel therapeutic agent of UC.PMID:37516090 | DOI:10.1016/j.phymed.2023.154985

Ameliorative effects of the Coptis inflorescence extract against lung injury in diabetic mice by regulating AMPK/NEU1 signaling

Sat, 29/07/2023 - 12:00
Phytomedicine. 2023 Jul 16;118:154963. doi: 10.1016/j.phymed.2023.154963. Online ahead of print.ABSTRACTBACKGROUND: In diabetic patients, complications are the leading cause of death and disability, while diabetic lung damage has received little research. The Coptis inflorescence extract (CE) has hypoglycemic properties, but the mechanism of its protective role on diabetic lung injury is understood.PURPOSE: This study aims to explore the protective actions and molecular mechanism of CE and its active ingredients in diabetic lung disease.METHOD: Twenty-nine metabolites were identified in the metabolomic profile of CE using HPLC-ESI/MS, and high-content substances of berberine (BBR) and linarin (LIN) were isolated from CE using column chromatography. The potential targets and molecular mechanisms of CE against diabetic lung damage were systematically investigated by network pharmacology and in vitro experimental validation.RESULTS: CE significantly improved lung function and pathology. CE (360 mg/kg) or metformin treatment significantly improved lipid metabolism disorders, including decreased HDL-C and elevated serum TG, TC, and LDL-C levels. Furthermore, CE's chemical composition was determined using the HPLC-QTOF-MS method. CE identified five compounds as candidate active compounds (Berberine, Linarin, Palmatine, Worenine, and Coptisine). Network pharmacology analysis predicted CE contained five active compounds and target proteins, that AMPK, TGFβ1, and Smad might be the key targets in treating diabetic lung injury. Then we investigated the therapeutic effect of bioactive compounds of CE on diabetic lung damage through in vivo and in vitro experiments. Intragastric administration with BBR (50 mg/kg) or LIN (20 mg/kg) suppressed weight loss, hyperglycemia, and dyslipidemia, significantly alleviating lung inflammation in diabetic mice. Further mechanism research revealed that LIN or BBR inhibited alveolar epithelial-mesenchymal transition induced by high glucose by regulating AMPK/NEU-mediated signaling pathway.CONCLUSION: In conclusion, the administration of CE can effectively alleviate diabetic lung damage, providing a scientific basis for lowering blood sugar to moisturize lung function. BBR and LIN, the main components of CE, can effectively alleviate diabetic lung damage by regulating AMPK/NEU1 Signaling and inhibiting the TGF-β1 level, which may be a critical mechanism of its effects.PMID:37516057 | DOI:10.1016/j.phymed.2023.154963

Multi-omics in vitro study of the salivary modulation of the goat rumen microbiome

Sat, 29/07/2023 - 12:00
Animal. 2023 Jul 4;17(8):100895. doi: 10.1016/j.animal.2023.100895. Online ahead of print.ABSTRACTRuminants are able to produce large quantities of saliva which enter into the rumen and salivary components exert different physiological functions. Although previous research has indicated that salivary immunoglobulins can partially modulate the rumen microbial activity, the role of the salivary components other than ions on the rumen microbial ecosystem has not been thoroughly investigated in ruminants. To investigate this modulatory activity, a total of 16 semi-continuous in vitro cultures with oats hay and concentrate were used to incubate rumen fluid from four donor goats with autoclaved saliva (AUT) as negative control, saliva from the same rumen fluid donor (OWN) as positive control, and either goat (GOAT) or sheep (SHEEP) saliva as experimental interventions. Fermentation was monitored throughout 7 days of incubation and the microbiome and metabolome were analysed at the end of this incubation by Next-Generation sequencing and liquid chromatography coupled with mass spectrometry, respectively. Characterisation of the proteome and metabolome of the different salivas used for the incubation showed a high inter-animal variability in terms of metabolites and proteins, including immunoglobulins. Incubation with AUT saliva promoted lower fermentative activity in terms of gas production (-9.4%) and highly divergent prokaryotic community in comparison with other treatments (OWN, GOAT and SHEEP) suggesting a modulatory effect derived from the presence of bioactive salivary components. Microbial alpha-diversity at amplicon sequence variant (ASV) level was unaffected by treatment. However, some differences were found in the microbial communities across treatments, which were mostly caused by a greater abundance of Proteobacteria and Rikenellacea in the AUT treatment and lower of Prevotellaceae. These bacteria, which are key in the rumen metabolism, had greater abundances in GOAT and SHEEP treatments. Incubation with GOAT saliva led to a lower protozoal concentration and propionate molar proportion indicating a capacity to modulate the rumen microbial ecosystem. The metabolomics analysis showed that the AUT samples were clustered apart from the rest indicating different metabolic pathways were promoted in this treatment. These results suggest that specific salivary components contribute to host-associated role in selecting the rumen commensal microbiota and its activity. These findings could open the possibility of developing new strategies to modulate the saliva composition as a way to manipulate the rumen function and activity.PMID:37515965 | DOI:10.1016/j.animal.2023.100895

Microbial single-cell mass spectrometry: status, challenges, and prospects

Sat, 29/07/2023 - 12:00
Curr Opin Biotechnol. 2023 Jul 27;83:102977. doi: 10.1016/j.copbio.2023.102977. Online ahead of print.ABSTRACTSingle-cell analysis uncovers phenotypic differences between cells in a population and dissects their individual physiological states and differences on all omics levels from genome to phenome. Spectrometric observation allows label-free analysis of the metabolome and proteome of individual cells, but is still mainly limited to the analysis of mammalian single cells. Recent progress in mass spectrometry approaches now enables the analysis of microbial single cells - mainly by miniaturizing cell handling, incubation, and improving chip-coupling concepts for analyte ionization by interfacing microfluidic chips and mass spectrometers. This review aims at distilling the enabling principles behind microbial single-cell mass spectrometry and puts them into perspective for the future of the field.PMID:37515936 | DOI:10.1016/j.copbio.2023.102977

Comparison of two different integrated method of pharmacokinetics by the integrated pharmacokinetic research of fangji huangqi decoction

Sat, 29/07/2023 - 12:00
J Chromatogr B Analyt Technol Biomed Life Sci. 2023 Jul 17;1228:123831. doi: 10.1016/j.jchromb.2023.123831. Online ahead of print.ABSTRACTTraditional Chinese medicine (TCM) is characterized by its multiple components. The utilization of mathematical statistical methods to integrate the pharmacokinetics of monomer components can provide a comprehensive understanding of the holistic pharmacokinetic process of TCM. Two distinct integrated methods, namely the correlation coefficient method and the AUC-based weight coefficient method, were employed in this study to elucidate and compare their differences in the integrated pharmacokinetic research of Fangji Huangqi decoction (FHD). FHD is commonly used in clinical practice to treat the nephrotic syndrome. Firstly, one-dose FHD was given to doxorubicin-induced nephropathy (DN) rats, and the prototype compounds of FHD and their metabolites in plasma were qualitatively and semi-quantitatively analyzed by UHPLC-MS/MS. Secondly, the efficacy of FHD was quantitatively characterized by the relative distance method based on metabolomics. The correlation coefficients were obtained by analyzing the correlation between efficacy (relative distance values) and the content of compound, and they were subsequently used for the model integration (correlation coefficient method). Thirdly, the effective compounds of FHD treating DN were screened by integrating network pharmacology and molecular docking, and they were used for another integrated pharmacokinetic model by AUD-based weight coefficient method. Finally, the 2 integrated methods and the 2 integrated pharmacokinetic models were compared. In this study, 30 prototype compounds and 41 metabolites of FHD in plasma were identified, and the pharmacokinetic curve of 18 prototype compounds were built. The efficacy of FHD in the treatment of DN has been relatively quantitation. The 2 established integrated pharmacokinetic models of FHD indicated that the correlation coefficient method was the optimal approach for conducting the integrated pharmacokinetic research on the TCM with unknown effective compounds, whereas the AUC-based coefficient method was suitable for the TCM with the clear effective compounds. The integrated pharmacokinetic models indicated that FHD had high bioavailability and an absorption peak at about 6 h after administration, indicating that the 6 h after administration was the critical period of FHD treating DN. This research would be helpful for the pharmacological and pharmacokinetic research of FHD, and provide a method reference for the integrated pharmacokinetic research of TCM.PMID:37515912 | DOI:10.1016/j.jchromb.2023.123831

Precise prediction of metabolites patterns using machine learning approaches in distinguishing honey and sugar diets fed to mice

Sat, 29/07/2023 - 12:00
Food Chem. 2023 Jul 17;430:136915. doi: 10.1016/j.foodchem.2023.136915. Online ahead of print.ABSTRACTAs a natural sweetener produced by honey bees, honey was recognized as being healthier for consumption than table sugar. Our previous study also indicated thatmetaboliteprofiles in mice fed honey and mixedsugardiets aredifferent. However, it is still noteworthy about the batch-to-batch consistency of the metabolic differences between two diet types. Here, the machine learning (ML) algorithms were applied to complement and calibrate HPLC-QTOF/MS-based untargeted metabolomics data. Data were generated from three batches of mice that had the same treatment, which can further mine the metabolite biomarkers. Random Forest and Extra-Trees models could better discriminate between honey and mixed sugar dietary patterns under five-fold cross-validation. Finally, SHapley Additive exPlanations tool identified phosphatidylethanolamine and phosphatidylcholine as reliable metabolic biomarkers to discriminate the honey diet from the mixed sugar diet. This study provides us new ideas for metabolomic analysis of larger data sets.PMID:37515908 | DOI:10.1016/j.foodchem.2023.136915

Knockdown of SDC-1 Gene Alleviates the Metabolic Pathway for the Development of MODS

Sat, 29/07/2023 - 12:00
Mol Biotechnol. 2023 Jul 29. doi: 10.1007/s12033-023-00809-9. Online ahead of print.ABSTRACTThis study aims to reveal the metabolic differences between SDC-1 knockout mice and wild-type mice and the metabolic differences caused by shock in SDC-1 knockout mice by integrating transcriptomics and metabolomics. A total of 1009 differential metabolites were differentially expressed based on untargeted metabolomics and high-resolution mass spectrometry detection techniques. According to Kyoto Encyclopedia of Genes and Genomes enrichment, SDC-1 knockout significantly altered fat digestion and absorption, GnRH signaling pathway, fructose and mannose metabolism, and some other amino-related metabolic pathways and significantly modulated positively regulated longevity regulatory pathways, longevity regulatory pathways-worm, nicotinamide and niacinamide metabolism, and vitamin digestion and absorption pathways after its shock. Our findings indicate that SDC-1 knockout may have potential therapeutic effects in hemorrhagic shock by increasing nicotinamide metabolism.PMID:37515659 | DOI:10.1007/s12033-023-00809-9

Metabolomic Characterization of <em>Phoradendron brachystachyum</em> Mistletoe and In-Silico and In-Vitro Investigation of Its Therapeutic Potential in Metabolic Disorders

Sat, 29/07/2023 - 12:00
Plants (Basel). 2023 Jul 22;12(14):2729. doi: 10.3390/plants12142729.ABSTRACTPlants of the Phoradendron genus have been traditionally used for their lipid- and glucose-lowering effects. However, the compounds responsible for these effects and the overall chemical profile of these plants have not been thoroughly investigated. We aimed to characterize the metabolome of leaves, stems, and aerial parts of the Phoradendron brachystachyum plant. We used mass spectrometry and colorimetric screening techniques (with various solvents) to identify and characterize the metabolites present. We also evaluated the antioxidant (FRAP, ORAC, TEAC, and DPPH assays) and inhibitory effects on pancreatic lipase and α-glucosidase enzymes of hydrophilic extracts. Furthermore, we compared the molecular fingerprints between the identified metabolites and FDA-approved drugs to gain insights into the metabolites that might be responsible for the observed effects on enzymes. Our findings revealed the presence of 59 putative metabolites, primarily flavonoids. However, we also hint at the presence of peptide and carbohydrate derivatives. The leaf extracts demonstrated the most promising metrics across all assays, exhibiting strong antioxidant and enzyme inhibitory effects as well as high levels of phenolic compounds, flavonoids, and tannins. Fingerprint analysis suggested potential peptide and carbohydrate metabolites as pancreatic lipase and α-glucosidase inhibitors. Overall, our study provides evidence on specific metabolites in Phoradendron brachystachyum that could be responsible for the therapeutic effects noted in obese and type 2 diabetes subjects.PMID:37514343 | DOI:10.3390/plants12142729

Analysis of Hormone Regulation on Seed Germination of Coix Based on Muli-Omics Analysis

Sat, 29/07/2023 - 12:00
Plants (Basel). 2023 Jul 20;12(14):2700. doi: 10.3390/plants12142700.ABSTRACTSeed germination is an important stage of growth and reproduction and plays an important role in the life cycle of spermatophyte. It is co-determined by both genetic and environmental factors, and plant hormone regulation may be a highly conservative mechanism. Coix lachryrma-jobi (coix) is a grain with balanced nutrition for medicine and food and has substantial production value. It is an important part of agricultural production, and the efficiency of seed germination after sowing is a key link. In this study, coix species "small white shell Xingren" was used as the experimental material, and changes in gene expression levels and metabolite enrichment in seeds were identified by transcriptome and metabonomic analysis before and after seed germination. A total of 599 metabolites, including those from amino acid metabolism, sugar metabolism, and fatty acid metabolism, were significantly increased in germinating coix. Simultaneously, 10,929 differentially expressed genes (DEGs) were identified, and functional clusters of genes were also significantly clustered in hormone-signaling and glucose and fatty acid metabolism. In addition, this study found that a considerable number of hormone-signaling genes were significantly up-regulated during seed germination, activating multiple metabolic processes. The results of our conjoint analysis of multi omics showed that glucose and fatty acid metabolism played an important role in seed germination under hormone regulation.PMID:37514314 | DOI:10.3390/plants12142700

Pages