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

Dual Fragmentation Isobaric Tags for Metabolomics

Mon, 10/07/2023 - 12:00
J Am Soc Mass Spectrom. 2023 Jul 10. doi: 10.1021/jasms.3c00171. Online ahead of print.ABSTRACTIsobaric tags typically leverage an a1 type fragmentation to produce constant mass reporter ions. While this motif allows for efficient reporter formation, isobaric tags lack structural diversity, which limits the number and type of isotopes that are synthetically available. Presented here are two examples of dual fragmentation isobaric tagging. The first example mimics the typical isobaric tag structure through trimethylamine neutral loss and cyclization. Subsequent fragmentation releases a constant mass reporter with high efficiency. This provides a route to create a variety of isobaric tags with regard to both the reporter and the balancer mass. The second example is a set of six-plex isobaric, thiol-reactive tags that produce constant mass reporters by a similar sequential fragmentation mechanism. A trimethylamine neutral loss allows for the incorporation of up to 13 total isotopes in the balancer region, while minimizing deuterium retention time shifts. A subsequent C-S bond cleavage produces a constant mass reporter in the low-mass region. The thiols investigated produced an average RSD of 14% and R2 of 0.98 when analyzed as a six-plex injection. Thiol metabolism was disrupted using the glutamyl-cysteine synthetase inhibitor buthionine sulfoximine (BSO). Endothelial cells were incubated with BSO and showed significant decreases in glutathione and cysteinyl-glycine compared to control. Overall, a new method to generate constant mass reporters using a dual fragmentation scheme is presented.PMID:37427806 | DOI:10.1021/jasms.3c00171

Natural variation of warm temperature-induced raffinose accumulation identifies TREHALOSE-6-PHOSPHATE SYNTHASE 1 as a modulator of thermotolerance

Mon, 10/07/2023 - 12:00
Plant Cell Environ. 2023 Jul 10. doi: 10.1111/pce.14664. Online ahead of print.ABSTRACTHigh-temperature stress limits plant growth and reproduction. Exposure to high temperature, however, also elicits a physiological response, which protects plants from the damage evoked by heat. This response involves a partial reconfiguration of the metabolome including the accumulation of the trisaccharide raffinose. In this study, we explored the intraspecific variation of warm temperature-induced raffinose accumulation as a metabolic marker for temperature responsiveness with the aim to identify genes that contribute to thermotolerance. By combining raffinose measurements in 250 Arabidopsis thaliana accessions following a mild heat treatment with genome-wide association studies, we identified five genomic regions that were associated with the observed trait variation. Subsequent functional analyses confirmed a causal relationship between TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) and warm temperature-dependent raffinose synthesis. Moreover, complementation of the tps1-1 null mutant with functionally distinct TPS1 isoforms differentially affected carbohydrate metabolism under more severe heat stress. While higher TPS1 activity was associated with reduced endogenous sucrose levels and thermotolerance, disruption of trehalose 6-phosphate signalling resulted in higher accumulation of transitory starch and sucrose and was associated with enhanced heat resistance. Taken together, our findings suggest a role of trehalose 6-phosphate in thermotolerance, most likely through its regulatory function in carbon partitioning and sucrose homoeostasis.PMID:37427798 | DOI:10.1111/pce.14664

1st International Conference on Biomedical Sciences, Dow University of Health Sciences, Karachi Pakistan

Mon, 10/07/2023 - 12:00
J Pak Med Assoc. 2023 Jun;73(6):1349-1352. doi: 10.47391/JPMA.23-47.ABSTRACTInstitute of Biomedical Sciences (IBMS) at Dow University of Health Sciences (DUHS), organised a two day's conference on Biomedical Sciences. IBMS being the part of one of the largest public sector health universities of Pakistan, is now transforming the research trends to be effectively translated at the community level. Currently with a strong PhD faculty line in basic and clinical sciences, DUHS has a significant contribution in research output of the country. The scientific data however represents a small population per scientific study and the generalization of results may not be inferred. It must be extended through translational research for effectiveness. The conference was planned with a theme to bridge the gap between basic and translational research. The two day's conference conducted in second week of March 2023 at Dow International Medical College Ojha Campus DUHS was able to attract more than 300 participants. The scientific sessions encompassed a vast variety of health issues and their proposed solutions including neurosciences, virtual biopsies, metabolomics, medical writings and incorporation of engineering and artificial intelligence to facilitate detection and prognosis of disease. The conference was able to conclude that the multidisciplinary research studies with collaboration of two or more institutes/organizations are the need of time. Young researchers need an effective platform to showcase their research and make collaborations. Moreover, the incorporation of artificial intelligence would enhance patient care within health systems.PMID:37427652 | DOI:10.47391/JPMA.23-47

Rapid and non-invasive diagnostic techniques for embryonic developmental potential: a metabolomic analysis based on Raman spectroscopy to identify the pregnancy outcomes of IVF-ET

Mon, 10/07/2023 - 12:00
Front Cell Dev Biol. 2023 Jun 23;11:1164757. doi: 10.3389/fcell.2023.1164757. eCollection 2023.ABSTRACTThe non-invasive and rapid assessment of the developmental potential of embryos is of great clinical importance in assisted reproductive technology (ART). In this retrospective study, we analyzed the metabolomics of 107 samples provided by volunteers and utilized Raman spectroscopy to detect the substance composition in the discarded culture medium of 53 embryos resulting in successful pregnancies and 54 embryos that did not result in pregnancy after implantation. The culture medium from D3 cleavage-stage embryos was collected after transplantation and a total of 535 (107 × 5) original Raman spectra were obtained. By combining several machine learning methods, we predicted the developmental potential of embryos, and the principal component analysis-convolutional neural network (PCA-CNN) model achieved an accuracy rate of 71.5%. Furthermore, the chemometric algorithm was used to analyze seven amino acid metabolites in the culture medium, and the data showed significant differences in tyrosine, tryptophan, and serine between the pregnancy and non-pregnancy groups. The results suggest that Raman spectroscopy, as a non-invasive and rapid molecular fingerprint detection technology, shows potential for clinical application in assisted reproduction.PMID:37427383 | PMC:PMC10326628 | DOI:10.3389/fcell.2023.1164757

Integrated gut microbiota and metabolome analysis reveals the mechanism of Xiaoai Jiedu recipe in ameliorating colorectal cancer

Mon, 10/07/2023 - 12:00
Front Oncol. 2023 Jun 22;13:1184786. doi: 10.3389/fonc.2023.1184786. eCollection 2023.ABSTRACTINTRODUCTION: Xiaoai Jiedu recipe (XJR), a classical prescription of traditional Chinese medicine (TCM), has been clinically proven to be effective in ameliorating colorectal cancer (CRC). However, its exact mechanism of action is still elusive, limiting its clinical application and promotion to a certain extent. This study aims to evaluate the effect of XJR on CRC and further illustrate mechanism underlying its action.METHODS: We investigated the anti-tumor efficacy of XJR in vitro and vivo experiments. An integrated 16S rRNA gene sequencing and UPLC-MS based metabolomics approach were performed to explore possible mechanism of XJR anti-CRC on the gut microbiota and serum metabolic profiles. The correlation between altered gut microbiota and disturbed serum metabolites was investigated using Pearson's correlation analysis.RESULTS: XJR effectively displayed anti-CRC effect both in vitro and in vivo. The abundance of aggressive bacteria such as Bacteroidetes, Bacteroides, and Prevotellaceae decreased, while the levels of beneficial bacteria increased (Firmicutes, Roseburia, and Actinobacteria). Metabolomics analysis identified 12 potential metabolic pathways and 50 serum metabolites with different abundances possibly affected by XJR. Correlation analysis showed that the relative abundance of aggressive bacteria was positively correlated with the levels of Arachidonic acid, Adrenic acid, 15(S)-HpETE, DL-Arginine, and Lysopc 18:2, which was different from the beneficial bacteria.DISCUSSION: The regulation of gut microbiota and related metabolites may be potential breakthrough point to elucidate the mechanism of XJR in the treatment of the CRC. The strategy employed would provide theoretical basis for clinical application of TCM.PMID:37427121 | PMC:PMC10325652 | DOI:10.3389/fonc.2023.1184786

Urine metabolites and viral pneumonia among children: a case-control study in China

Mon, 10/07/2023 - 12:00
Transl Pediatr. 2023 Jun 30;12(6):1192-1203. doi: 10.21037/tp-23-199. Epub 2023 Jun 28.ABSTRACTBACKGROUND: Viral pneumonia in children is common and has grave consequences. The study aims to better understand the pathophysiological processes involved in the onset and progression of viral pneumonia and identify common effects or biomarkers across different viruses.METHODS: This study collected urine samples from 96 patients with viral pneumonia including respiratory syncytial virus (RSV) (n=30), influenza virus (IV) (n=23), parainfluenza virus (PIV) (n=24), and adenovirus (ADV) (n=19), and 31 age- and sex-matched normal control (NC) subjects. The samples were analyzed using liquid chromatography coupled with mass spectrometry (LC-MS) to identify endogenous substances. The XCMS Online platform was utilized for data processing and analysis , including feature detection, retention time correction, alignment, annotation, and statistical analysis for difference between groups and biomarker identification.RESULTS: A total of 948 typical metabolites were identified using the XCMS Online platform with the Mummichog technique. After analyzing the data, 24 metabolites were selected as potential biomarkers for viral pneumonia, of which 16 were aspartate and asparagine metabolites, byproducts of alanine, leucine, and isoleucine degradation, and butanoate metabolites.CONCLUSIONS: This study specific metabolites and altered pathways in children with viral pneumonia and propose that these findings could contribute to the discovery of new treatments and the development of antiviral drugs.PMID:37427067 | PMC:PMC10326753 | DOI:10.21037/tp-23-199

4-methylumbelliferone (4-MU) enhances drought tolerance of apple by regulating rhizosphere microbial diversity and root architecture

Mon, 10/07/2023 - 12:00
Hortic Res. 2023 May 19;10(6):uhad099. doi: 10.1093/hr/uhad099. eCollection 2023 Jun.ABSTRACTThe dwarfing rootstocks-mediated high-density apple orchard is becoming the main practice management. Currently, dwarfing rootstocks are widely used worldwide, but their shallow root system and drought sensitivity necessitate high irrigation requirements. Here, the root transcriptome and metabolome of dwarfing (M9-T337, a drought-sensitive rootstock) and vigorous rootstocks (Malus sieversii, a drought-tolerant species, is commonly used as a rootstock) showed that a coumarin derivative, 4-Methylumbelliferon (4-MU), was found to accumulate significantly in the roots of vigorous rootstock under drought condition. When exogenous 4-MU was applied to the roots of dwarfing rootstock under drought treatment, the plants displayed increased root biomass, higher root-to-shoot ratio, greater photosynthesis, and elevated water use efficiency. In addition, diversity and structure analysis of the rhizosphere soil microbial community demonstrated that 4-MU treatment increased the relative abundance of putatively beneficial bacteria and fungi. Of these, Pseudomonas, Bacillus, Streptomyces, and Chryseolinea bacterial strains and Acremonium, Trichoderma, and Phoma fungal strains known for root growth, or systemic resistance against drought stress, were significantly accumulated in the roots of dwarfing rootstock after 4-MU treatment under drought stress condition. Taken together, we identified a promising compound-4-MU, as a useful tool, to strengthen the drought tolerance of apple dwarfing rootstock.PMID:37427035 | PMC:PMC10327542 | DOI:10.1093/hr/uhad099

Editorial: A large-scale biology view of crop-environment interaction: the influence of water and temperature stresses on the development of cereal and horticultural crops

Mon, 10/07/2023 - 12:00
Front Plant Sci. 2023 Jun 22;14:1235466. doi: 10.3389/fpls.2023.1235466. eCollection 2023.NO ABSTRACTPMID:37426989 | PMC:PMC10325649 | DOI:10.3389/fpls.2023.1235466

Integrated transcriptomics and metabolomics analysis provide insight into the resistance response of rice against brown planthopper

Mon, 10/07/2023 - 12:00
Front Plant Sci. 2023 Jun 20;14:1213257. doi: 10.3389/fpls.2023.1213257. eCollection 2023.ABSTRACTINTRODUCTION: The brown planthopper (Nilaparvata lugens Stål, BPH) is one of the most economically significant pests of rice. The Bph30 gene has been successfully cloned and conferred rice with broad-spectrum resistance to BPH. However, the molecular mechanisms by which Bph30 enhances resistance to BPH remain poorly understood.METHODS: Here, we conducted a transcriptomic and metabolomic analysis of Bph30-transgenic (BPH30T) and BPH-susceptible Nipponbare plants to elucidate the response of Bph30 to BPH infestation.RESULTS: Transcriptomic analyses revealed that the pathway of plant hormone signal transduction enriched exclusively in Nipponbare, and the greatest number of differentially expressed genes (DEGs) were involved in indole 3-acetic acid (IAA) signal transduction. Analysis of differentially accumulated metabolites (DAMs) revealed that DAMs involved in the amino acids and derivatives category were down-regulated in BPH30T plants following BPH feeding, and the great majority of DAMs in flavonoids category displayed the trend of increasing in BPH30T plants; the opposite pattern was observed in Nipponbare plants. Combined transcriptomics and metabolomics analysis revealed that the pathways of amino acids biosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis and flavonoid biosynthesis were enriched. The content of IAA significantly decreased in BPH30T plants following BPH feeding, and the content of IAA remained unchanged in Nipponbare. The exogenous application of IAA weakened the BPH resistance conferred by Bph30.DISCUSSION: Our results indicated that Bph30 might coordinate the movement of primary and secondary metabolites and hormones in plants via the shikimate pathway to enhance the resistance of rice to BPH. Our results have important reference significance for the resistance mechanisms analysis and the efficient utilization of major BPH-resistance genes.PMID:37426975 | PMC:PMC10327896 | DOI:10.3389/fpls.2023.1213257

Impact of dehydration on the physiochemical properties of <em>Nostoc calcicola</em> BOT1 and its untargeted metabolic profiling through UHPLC-HRMS

Mon, 10/07/2023 - 12:00
Front Plant Sci. 2023 Jun 23;14:1147390. doi: 10.3389/fpls.2023.1147390. eCollection 2023.ABSTRACTThe global population growth has led to a higher demand for food production, necessitating improvements in agricultural productivity. However, abiotic and biotic stresses pose significant challenges, reducing crop yields and impacting economic and social welfare. Drought, in particular, severely constrains agriculture, resulting in unproductive soil, reduced farmland, and jeopardized food security. Recently, the role of cyanobacteria from soil biocrusts in rehabilitating degraded land has gained attention due to their ability to enhance soil fertility and prevent erosion. The present study focused on Nostoc calcicola BOT1, an aquatic, diazotrophic cyanobacterial strain collected from an agricultural field at Banaras Hindu University, Varanasi, India. The aim was to investigate the effects of different dehydration treatments, specifically air drying (AD) and desiccator drying (DD) at various time intervals, on the physicochemical properties of N. calcicola BOT1. The impact of dehydration was assessed by analyzing the photosynthetic efficiency, pigments, biomolecules (carbohydrates, lipids, proteins, osmoprotectants), stress biomarkers, and non-enzymatic antioxidants. Furthermore, an analysis of the metabolic profiles of 96-hour DD and control mats was conducted using UHPLC-HRMS. Notably, there was a significant decrease in amino acid levels, while phenolic content, fatty acids, and lipids increased. These changes in metabolic activity during dehydration highlighted the presence of metabolite pools that contribute to the physiological and biochemical adjustments of N. calcicola BOT1, mitigating the impact of dehydration to some extent. Overall, present study demonstrated the accumulation of biochemical and non-enzymatic antioxidants in dehydrated mats, which could be utilized to stabilize unfavorable environmental conditions. Additionally, the strain N. calcicola BOT1 holds promise as a biofertilizer for semi-arid regions.PMID:37426961 | PMC:PMC10327440 | DOI:10.3389/fpls.2023.1147390

Identification and characterization of CYP71 subclade cytochrome P450 enzymes involved in the biosynthesis of bitterness compounds in <em>Cichorium intybus</em>

Mon, 10/07/2023 - 12:00
Front Plant Sci. 2023 Jun 22;14:1200253. doi: 10.3389/fpls.2023.1200253. eCollection 2023.ABSTRACTIndustrial chicory (Cichorium intybus var. sativum) and witloof (C. intybus var. foliosum) are crops with an important economic value, mainly cultivated for inulin production and as a leafy vegetable, respectively. Both crops are rich in nutritionally relevant specialized metabolites with beneficial effects for human health. However, their bitter taste, caused by the sesquiterpene lactones (SLs) produced in leaves and taproot, limits wider applications in the food industry. Changing the bitterness would thus create new opportunities with a great economic impact. Known genes encoding enzymes involved in the SL biosynthetic pathway are GERMACRENE A SYNTHASE (GAS), GERMACRENE A OXIDASE (GAO), COSTUNOLIDE SYNTHASE (COS) and KAUNIOLIDE SYNTHASE (KLS). In this study, we integrated genome and transcriptome mining to further unravel SL biosynthesis. We found that C. intybus SL biosynthesis is controlled by the phytohormone methyl jasmonate (MeJA). Gene family annotation and MeJA inducibility enabled the pinpointing of candidate genes related with the SL biosynthetic pathway. We specifically focused on members of subclade CYP71 of the cytochrome P450 family. We verified the biochemical activity of 14 C. intybus CYP71 enzymes transiently produced in Nicotiana benthamiana and identified several functional paralogs for each of the GAO, COS and KLS genes, pointing to redundancy in and robustness of the SL biosynthetic pathway. Gene functionality was further analyzed using CRISPR/Cas9 genome editing in C. intybus. Metabolite profiling of mutant C. intybus lines demonstrated a successful reduction in SL metabolite production. Together, this study increases our insights into the C. intybus SL biosynthetic pathway and paves the way for the engineering of C. intybus bitterness.PMID:37426959 | PMC:PMC10324620 | DOI:10.3389/fpls.2023.1200253

A multi-omics approach identifies <em>bHLH71-like</em> as a positive regulator of yellowing leaf pepper mutants exposed to high-intensity light

Mon, 10/07/2023 - 12:00
Hortic Res. 2023 May 12;10(7):uhad098. doi: 10.1093/hr/uhad098. eCollection 2023 Jun.ABSTRACTLight quality and intensity can have a significant impact on plant health and crop productivity. Chlorophylls and carotenoids are classes of plant pigments that are responsible for harvesting light energy and protecting plants from the damaging effects of intense light. Our understanding of the role played by plant pigments in light sensitivity has been aided by light-sensitive mutants that change colors upon exposure to light of variable intensity. In this study, we conducted transcriptomic, metabolomic, and hormone analyses on a novel yellowing mutant of pepper (yl1) to shed light on the molecular mechanism that regulates the transition from green to yellow leaves in this mutant upon exposure to high-intensity light. Our results revealed greater accumulation of the carotenoid precursor phytoene and the carotenoids phytofluene, antheraxanthin, and zeaxanthin in yl1 compared with wild-type plants under high light intensity. A transcriptomic analysis confirmed that enzymes involved in zeaxanthin and antheraxanthin biosynthesis were upregulated in yl1 upon exposure to high-intensity light. We also identified a single basic helix-loop-helix (bHLH) transcription factor, bHLH71-like, that was differentially expressed and positively correlated with light intensity in yl1. Silencing of bHLH71-like in pepper plants suppressed the yellowing phenotype and led to reduced accumulation of zeaxanthin and antheraxanthin. We propose that the yellow phenotype of yl1 induced by high light intensity could be caused by an increase in yellow carotenoid pigments, concurrent with a decrease in chlorophyll accumulation. Our results also suggest that bHLH71-like functions as a positive regulator of carotenoid biosynthesis in pepper.PMID:37426880 | PMC:PMC10323627 | DOI:10.1093/hr/uhad098

Comprehensive investigation on flavonoids metabolites of Longjing tea in different cultivars, geographical origins, and storage time

Mon, 10/07/2023 - 12:00
Heliyon. 2023 Jun 14;9(6):e17305. doi: 10.1016/j.heliyon.2023.e17305. eCollection 2023 Jun.ABSTRACTIn this study, four kinds of Longjing tea, the famous flat green tea and the protected geographical indication product in China, were used to explore the quality difference of the same green tea due to the cultivar, geographic origin, and storage time under the premise of consistent picking conditions and processing technology using the widely targeted metabolomics. Results showed that 483 flavonoid metabolites with 10 subgroups of flavonoids were screened and 118 differential flavonoid metabolites were identified. The number and subgroups of differential flavonoid metabolites produced by different cultivars of Longjing tea were the largest, followed by storage time, and third by the geographic origin. Glycosidification and methylation or methoxylation were the main structural modifications of differential flavonoid metabolites. This study has enriched the understanding of the effects of the cultivar, the geographic origin, and the storage time on the flavonoid metabolic profiles of Longjing tea, and provided worthy information for the traceability of green tea.PMID:37426805 | PMC:PMC10329133 | DOI:10.1016/j.heliyon.2023.e17305

Pharmacological effects and mechanisms of YiYiFuZi powder in chronic heart disease revealed by metabolomics and network pharmacology

Mon, 10/07/2023 - 12:00
Front Mol Biosci. 2023 Jun 23;10:1203208. doi: 10.3389/fmolb.2023.1203208. eCollection 2023.ABSTRACTIntroduction: YiYiFuZi powder (YYFZ) is a classical formula in Chinese medicine, which is commonly used clinically for the treatment of Chronic Heart Disease (CHD), but it's pharmacological effects and mechanism of action are currently unclear. Methods: An adriamycin-induced CHD model rat was established to evaluate the pharmacological effects of YYFZ on CHD by the results of inflammatory factor level, histopathology and echocardiography. Metabolomic studies were performed on rat plasma using UPLC-Q-TOF/MS to screen biomarkers and enrich metabolic pathways; network pharmacology analysis was also performed to obtain the potential targets and pathways of YYFZ for the treatment of CHD. Results: The results showed that YYFZ significantly reduced the levels of TNF-α and BNP in the serum of rats, alleviated the disorder of cardiomyocyte arrangement and inflammatory cell infiltration, and improved the cardiac function of rats with CHD. The metabolomic analysis identified a total of 19 metabolites, related to amino acid metabolism, fatty acid metabolism, and other metabolic pathways. Network pharmacology showed that YYFZ acts through PI3K/Akt signaling pathway, MAPK signaling pathway and Ras signaling pathway. Discussion: YYFZ treatment of CHD modulates blood metabolic pattern and several protein phosphorylation cascades but importance specific changes for therapeutic effect require further studies.PMID:37426419 | PMC:PMC10327484 | DOI:10.3389/fmolb.2023.1203208

RespectM revealed metabolic heterogeneity powers deep learning for reshaping the DBTL cycle

Mon, 10/07/2023 - 12:00
iScience. 2023 Jun 8;26(7):107069. doi: 10.1016/j.isci.2023.107069. eCollection 2023 Jul 21.ABSTRACTSynthetic biology, relying on Design-Build-Test-Learn (DBTL) cycle, aims to solve medicine, manufacturing, and agriculture problems. However, the DBTL cycle's Learn (L) step lacks predictive power for the behavior of biological systems, resulting from the incompatibility between sparse testing data and chaotic metabolic networks. Herein, we develop a method, "RespectM," based on mass spectrometry imaging, which is able to detect metabolites at a rate of 500 cells per hour with high efficiency. In this study, 4,321 single cell level metabolomics data were acquired, representing metabolic heterogeneity. An optimizable deep neural network was applied to learn from metabolic heterogeneity and a "heterogeneity-powered learning (HPL)" based model was trained as well. By testing the HPL based model, we suggest minimal operations to achieve high triglyceride production for engineering. The HPL strategy could revolutionize rational design and reshape the DBTL cycle.PMID:37426353 | PMC:PMC10329182 | DOI:10.1016/j.isci.2023.107069

Compound-Specific 1D <sup>1</sup>H NMR Pulse Sequence Selection for Metabolomics Analyses

Mon, 10/07/2023 - 12:00
ACS Omega. 2023 Jun 21;8(26):23651-23663. doi: 10.1021/acsomega.3c01688. eCollection 2023 Jul 4.ABSTRACTNMR-based metabolomics approaches have been used in a wide range of applications, for example, with medical, plant, and marine samples. One-dimensional (1D) 1H NMR is routinely used to find out biomarkers in biofluids such as urine, blood plasma, and serum. To mimic biological conditions, most NMR studies have been carried out in an aqueous solution where the high intensity of the water peak is a major problem in obtaining a meaningful spectrum. Different methods have been used to suppress the water signal, including 1D Carr-Purcell-Meiboom-Gill (CPMG) presat, consisting of a T2 filter to suppress macromolecule signals and reduce the humped curve in the spectrum. 1D nuclear Overhauser enhancement spectroscopy (NOESY) is another method for water suppression that is used routinely in plant samples with fewer macromolecules than in biofluid samples. Other common 1D 1H NMR methods such as 1D 1H presat and 1D 1H ES have simple pulse sequences; their acquisition parameters can be set easily. The proton with presat has just one pulse and the presat block causes water suppression, while other 1D 1H NMR methods including those mentioned above have more pulses. However, it is not well known in metabolomics studies because it is used only occasionally and in a few types of samples by metabolomics experts. Another effective method is excitation sculpting to suppress water. Herein, we evaluate the effect of method selection on signal intensities of commonly detected metabolites. Different classes of samples including biofluid, plant, and marine samples were investigated, and recommendations on the advantages and limitations of each method are presented.PMID:37426221 | PMC:PMC10324067 | DOI:10.1021/acsomega.3c01688

Comprehensive analysis of the microbiome and metabolome in pus from pyogenic liver abscess patients with and without diabetes mellitus

Mon, 10/07/2023 - 12:00
Front Microbiol. 2023 Jun 23;14:1211835. doi: 10.3389/fmicb.2023.1211835. eCollection 2023.ABSTRACTINTRODUCTION: Pyogenic liver abscess (PLA) patients combined with diabetes mellitus (DM) tend to have more severe clinical manifestations than without DM. The mechanism responsible for this phenomenon is not entirely clear. The current study therefore aimed to comprehensively analyze the microbiome composition and metabolome in pus from PLA patients with and without DM, to determine the potential reasons for these differences.METHODS: Clinical data from 290 PLA patients were collected retrospectively. We analyzed the pus microbiota using 16S rDNA sequencing in 62 PLA patients. In addition, the pus metabolomes of 38 pus samples were characterized by untargeted metabolomics analysis. Correlation analyses of microbiota, metabolites and laboratory findings were performed to identify significant associations.RESULTS: PLA patients with DM had more severe clinical manifestations than PLA patients without DM. There were 17 discriminating genera between the two groups at the genus level, among which Klebsiella was the most discriminating taxa. The ABC transporters was the most significant differential metabolic pathway predicted by PICRUSt2. Untargeted metabolomics analysis showed that concentrations of various metabolites were significantly different between the two groups and seven metabolites were enriched in the ABC transporters pathway. Phosphoric acid, taurine, and orthophosphate in the ABC transporters pathway were negatively correlated with the relative abundance of Klebsiella and the blood glucose level.DISCUSSION: The results showed that the relative abundance of Klebsiella in the pus cavity of PLA patients with DM was higher than those without DM, accompanied by changes of various metabolites and metabolic pathways, which may be associated with more severe clinical manifestations.PMID:37426007 | PMC:PMC10328747 | DOI:10.3389/fmicb.2023.1211835

The metabolic role of vitamin D in children's neurodevelopment: a network study

Mon, 10/07/2023 - 12:00
bioRxiv. 2023 Jun 26:2023.06.23.546277. doi: 10.1101/2023.06.23.546277. Preprint.ABSTRACTAutism spectrum disorder (ASD) is a neurodevelopmental disorder with various proposed environmental risk factors and a rapidly increasing prevalence. Mounting evidence suggests a potential role of vitamin D deficiency in ASD pathogenesis, though causal mechanisms remain largely unknown. Here, we investigate the impact of vitamin D on child neurodevelopment through an integrative network approach that combines metabolomic profiles, clinical traits, and neurodevelopmental data from a pediatric cohort. Our results show that vitamin D deficiency is associated with changes in the metabolic networks of tryptophan, linoleic, and fatty acid metabolism. These changes correlate with distinct ASD-related outcomes, including delayed communication skills and respiratory dysfunctions. Additionally, our analysis suggests the kynurenine and serotonin sub-pathways might mediate the effect of vitamin D on early childhood communication development. Altogether, our findings provide metabolome-wide insights into the potential of vitamin D as a therapeutic option for ASD and other communication disorders.PMID:37425858 | PMC:PMC10327084 | DOI:10.1101/2023.06.23.546277

Combined cerebrospinal fluid metabolomic and cytokine profiling in tuberculosis meningitis reveals robust and prolonged changes in immunometabolic networks

Mon, 10/07/2023 - 12:00
medRxiv. 2023 Jun 29:2023.06.26.23291676. doi: 10.1101/2023.06.26.23291676. Preprint.ABSTRACTMuch of the high mortality in tuberculosis meningitis (TBM) is attributable to excessive inflammation, making it imperative to identify targets for host-directed therapies that reduce pathologic inflammation and mortality. In this study, we investigate how cytokines and metabolites in the cerebral spinal fluid (CSF) associate with TBM at diagnosis and during TBM treatment. At diagnosis, TBM patients demonstrate significant increases versus controls of cytokines and chemokines that promote inflammation and cell migration including IL-17A, IL-2, TNFα, IFNγ, and IL-1β. Inflammatory immune signaling was strongly correlated with immunomodulatory metabolites including kynurenine, lactic acid, carnitine, tryptophan, and itaconate. Inflammatory immunometabolic networks were only partially reversed with two months of effective TBM treatment and remained significantly different versus control CSF. Together, these data highlight a critical role for host metabolism in regulating the inflammatory response to TBM and indicate the timeline for restoration of immune homeostasis in the CSF is prolonged.PMID:37425849 | PMC:PMC10327257 | DOI:10.1101/2023.06.26.23291676

Metabolome-wide Mendelian randomization characterizes heterogeneous and shared causal effects of metabolites on human health

Mon, 10/07/2023 - 12:00
medRxiv. 2023 Jun 29:2023.06.26.23291721. doi: 10.1101/2023.06.26.23291721. Preprint.ABSTRACTMetabolites are small molecules that are useful for estimating disease risk and elucidating disease biology. Nevertheless, their causal effects on human diseases have not been evaluated comprehensively. We performed two-sample Mendelian randomization to systematically infer the causal effects of 1,099 plasma metabolites measured in 6,136 Finnish men from the METSIM study on risk of 2,099 binary disease endpoints measured in 309,154 Finnish individuals from FinnGen. We identified evidence for 282 causal effects of 70 metabolites on 183 disease endpoints (FDR<1%). We found 25 metabolites with potential causal effects across multiple disease domains, including ascorbic acid 2-sulfate affecting 26 disease endpoints in 12 disease domains. Our study suggests that N-acetyl-2-aminooctanoate and glycocholenate sulfate affect risk of atrial fibrillation through two distinct metabolic pathways and that N-methylpipecolate may mediate the causal effect of N6, N6-dimethyllysine on anxious personality disorder. This study highlights the broad causal impact of plasma metabolites and widespread metabolic connections across diseases.PMID:37425837 | PMC:PMC10327254 | DOI:10.1101/2023.06.26.23291721

Pages