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

Author Correction: Rhinovirus-induced epithelial RIG-I inflammasome suppresses antiviral immunity and promotes inflammation in asthma and COVID-19

Tue, 13/06/2023 - 12:00
Nat Commun. 2023 Jun 13;14(1):3493. doi: 10.1038/s41467-023-39275-x.NO ABSTRACTPMID:37311773 | DOI:10.1038/s41467-023-39275-x

Genomic adaptation of Burkholderia anthina to glyphosate uncovers a novel herbicide resistance mechanism

Tue, 13/06/2023 - 12:00
Environ Microbiol Rep. 2023 Jun 13. doi: 10.1111/1758-2229.13184. Online ahead of print.ABSTRACTGlyphosate (GS) specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase that converts phosphoenolpyruvate (PEP) and shikimate-3-phosphate to EPSP in the shikimate pathway of bacteria and other organisms. The inhibition of the EPSP synthase depletes the cell of the EPSP-derived aromatic amino acids as well as of folate and quinones. A variety of mechanisms (e.g., EPSP synthase modification) has been described that confer GS resistance to bacteria. Here, we show that the Burkholderia anthina strain DSM 16086 quickly evolves GS resistance by the acquisition of mutations in the ppsR gene. ppsR codes for the pyruvate/ortho-Pi dikinase PpsR that physically interacts and regulates the activity of the PEP synthetase PpsA. The mutational inactivation of ppsR causes an increase in the cellular PEP concentration, thereby abolishing the inhibition of the EPSP synthase by GS that competes with PEP for binding to the enzyme. Since the overexpression of the Escherichia coli ppsA gene in Bacillus subtilis and E. coli did not increase GS resistance in these organisms, the mutational inactivation of the ppsR gene resulting in PpsA overactivity is a GS resistance mechanism that is probably unique to B. anthina.PMID:37311711 | DOI:10.1111/1758-2229.13184

Graphical exploration of 600- and 60-MHz proton NMR spectral datasets from ground roast coffee extracts

Tue, 13/06/2023 - 12:00
Magn Reson Chem. 2023 Jun 13. doi: 10.1002/mrc.5373. Online ahead of print.ABSTRACTThis article uses a variety of graphical and mathematical approaches to analyse 600- and 60-MHz ('benchtop') proton NMR spectra acquired from lipophilic and hydrophilic extracts of roasted coffee beans. The collection of 40 authenticated samples comprised various coffee species, cultivars and hybrids. The spectral datasets were analysed by a combination of metabolomics approaches, cross-correlation and whole spectrum methods, assisted by visualisation and mathematical techniques not conventionally employed to treat NMR data. A large amount of information content was shared between the 600-MHz and benchtop datasets, including in its magnitude spectral form, suggesting the potential for a lower cost, lower tech route to conducting informative metabolomics studies.PMID:37311710 | DOI:10.1002/mrc.5373

Contribution of lipids to the organelle differential profile of in vitro-produced bovine embryos

Tue, 13/06/2023 - 12:00
Theriogenology. 2023 Jun 6;208:109-118. doi: 10.1016/j.theriogenology.2023.06.005. Online ahead of print.ABSTRACTEach living organism is unique because of the lipid identity of its organelles. The diverse distribution of these molecules also contributes to the role of each organelle in cellular activity. The lipid profiles of whole embryos are well documented in the literature. However, this approach can often lead to the loss of relevant information at the subcellular and consequently, metabolic levels, hindering a deeper understanding of key physiological processes during preimplantation development. Therefore, we aimed to characterize four organelles in vitro-produced bovine embryos: lipid droplets (LD), endoplasmic reticulum (ER), mitochondria (MIT), and nuclear membrane (NUC), and evaluate the contribution of the lipid species to each organelle evaluated. Expanded blastocysts were subjected to cell organelle isolation. Thereafter, lipid extraction from cell organelles and lipid analysis using the Multiple Reaction Monitoring (MRM) profiling method were performed. The LD and ER displayed a greater number of lipids (Phosphatidylcholine - PC, Ceramide - Cer, and Sphingomielin - SM) with high signal-to-noise intensities. This result is due to the high rate of biosynthesis, lipid distribution, and ability to store and recycle lipid species of these organelles. The NUC had a more distinct lipid profile than the other three organelles, with high relative intensities of PC, SM, and triacylglycerols (TG), which is consistent with its high nuclear activity. MIT had an intermediate profile that was close to that of LD and ER, which aligns with its autonomous metabolism for some classes of phospholipids (PL). Our study revealed the lipid composition of each organelle studied, and the roles of these lipids could be associated with the characteristic organellar activity. Our findings highlight the lipid species and classes that are relevant for the homeostasis and function of each associated organelle and provide tentative biomarkers for the determination of in vitro embryonic development and quality.PMID:37311262 | DOI:10.1016/j.theriogenology.2023.06.005

Toward Gene-Correlated Spatially Resolved Metabolomics with Fingerprint Coherent Raman Imaging

Tue, 13/06/2023 - 12:00
J Phys Chem B. 2023 Jun 13. doi: 10.1021/acs.jpcb.3c01446. Online ahead of print.ABSTRACTRaman spectroscopy has long been known to provide sufficient information to discriminate distinct cell phenotypes. Underlying this discriminating capability is that Raman spectra provide an overall readout of the metabolic profiles that change with transcriptomic activity. Robustly associating Raman spectral changes with the regulation of specific signaling pathways may be possible, but the spectral signals of interest may be weak and vary somewhat among individuals. Establishing a Raman-to-transcriptome mapping will thus require tightly controlled and easily manipulated biological systems and high-throughput spectral acquisition. We attempt to meet these requirements using broadband coherent anti-Stokes Raman scattering (BCARS) microscopy to spatio-spectrally map the C. elegans hermaphrodite gonad in vivo at subcellular resolution. The C. elegans hermaphrodite gonad is an ideal model system with a sequential, continuous process of highly regulated spatiotemporal cellular events. We demonstrate that the BCARS spatio-spectral signatures correlate with gene expression profiles in the gonad, evincing that BCARS has potential as a spatially resolved omics surrogate.PMID:37311254 | DOI:10.1021/acs.jpcb.3c01446

IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets

Tue, 13/06/2023 - 12:00
Anal Chem. 2023 Jun 13. doi: 10.1021/acs.analchem.3c00376. Online ahead of print.ABSTRACTPoor chemical annotation of high-resolution mass spectrometry data limits applications of untargeted metabolomics datasets. Our new software, the Integrated Data Science Laboratory for Metabolomics and Exposomics─Composite Spectra Analysis (IDSL.CSA) R package, generates composite mass spectra libraries from MS1-only data, enabling the chemical annotation of high-resolution mass spectrometry coupled with liquid chromatography peaks regardless of the availability of MS2 fragmentation spectra. We demonstrate comparable annotation rates for commonly detected endogenous metabolites in human blood samples using IDSL.CSA libraries versus MS/MS libraries in validation tests. IDSL.CSA can create and search composite spectra libraries from any untargeted metabolomics dataset generated using high-resolution mass spectrometry coupled to liquid or gas chromatography instruments. The cross-applicability of these libraries across independent studies may provide access to new biological insights that may be missed due to the lack of MS2 fragmentation data. The IDSL.CSA package is available in the R-CRAN repository at https://cran.r-project.org/package=IDSL.CSA. Detailed documentation and tutorials are provided at https://github.com/idslme/IDSL.CSA.PMID:37311059 | DOI:10.1021/acs.analchem.3c00376

xCT-mediated glutamate excretion in white adipocytes stimulates interferon-γ production by natural killer cells in obesity

Tue, 13/06/2023 - 12:00
Cell Rep. 2023 Jun 12;42(6):112636. doi: 10.1016/j.celrep.2023.112636. Online ahead of print.ABSTRACTObesity-mediated hypoxic stress underlies inflammation, including interferon (IFN)-γ production by natural killer (NK) cells in white adipose tissue. However, the effects of obesity on NK cell IFN-γ production remain obscure. Here, we show that hypoxia promotes xCT-mediated glutamate excretion and C-X-C motif chemokine ligand 12 (CXCL12) expression in white adipocytes, resulting in CXCR4+ NK cell recruitment. Interestingly, this spatial proximity between adipocytes and NK cells induces IFN-γ production in NK cells by stimulating metabotropic glutamate receptor 5 (mGluR5). IFN-γ then triggers inflammatory activation of macrophages and augments xCT and CXCL12 expression in adipocytes, forming a bidirectional pathway. Genetic or pharmacological inhibition of xCT, mGluR5, or IFN-γ receptor in adipocytes or NK cells alleviates obesity-related metabolic disorders in mice. Consistently, patients with obesity showed elevated levels of glutamate/mGluR5 and CXCL12/CXCR4 axes, suggesting that a bidirectional pathway between adipocytes and NK cells could be a viable therapeutic target in obesity-related metabolic disorders.PMID:37310859 | DOI:10.1016/j.celrep.2023.112636

Low-dose vanadium pentoxide perturbed lung metabolism associated with inflammation and fibrosis signaling in male animal and <em>in vitro</em> models

Tue, 13/06/2023 - 12:00
Am J Physiol Lung Cell Mol Physiol. 2023 Jun 13. doi: 10.1152/ajplung.00303.2022. Online ahead of print.ABSTRACTVanadium is available as a dietary supplement and also is known to be toxic if inhaled, yet little information is available concerning effects of vanadium on mammalian metabolism when at concentrations found in food and water. Vanadium pentoxide (V+5) is representative of the most common dietary and environmental exposures, and prior research shows low-dose V+5 exposure causes oxidative stress measured by glutathione oxidation and protein S-glutathionylation. We examined the metabolic impact of V+5 at relevant dietary and environmental doses (0.01, 0.1, 1 ppm for 24 h) in human lung fibroblasts (HLF) and male C57BL/6J mice (0.02, 0.2, 2 ppm in drinking water for 7 months). Untargeted metabolomics using liquid chromatography-high-resolution mass spectrometry (LC-HRMS) showed that V+5 induced significant metabolic perturbations in both HLF cells and mouse lungs. We noted 30% of the significantly altered pathways in HLF cells, including pyrimidines and aminosugars, fatty acids, mitochondrial and redox pathways, showed similar dose-dependent patterns in mouse lung tissues. Alterations in lipid metabolism included leukotrienes and prostaglandins involved in inflammatory signaling, which have been associated with the pathogenesis of idiopathic pulmonary fibrosis (IPF) and other disease processes. Elevated hydroxyproline levels and excessive collagen deposition were also present in lungs from V+5-treated mice. Taken together, these results show that oxidative stress from environmental V+5, ingested at low levels, could alter metabolism to contribute to common human lung diseases.PMID:37310758 | DOI:10.1152/ajplung.00303.2022

Integrating Genomics and Metabolomics for the Targeted Discovery of New Cyclopeptides with Antifungal Activity from a Marine-Derived Fungus <em>Beauveria felina</em>

Tue, 13/06/2023 - 12:00
J Agric Food Chem. 2023 Jun 13. doi: 10.1021/acs.jafc.3c02415. Online ahead of print.ABSTRACTSour rot, caused by Geotrichum citri-aurantii, is a major postharvest disease in citrus and results in significant economic losses. The genus Beauveria is recognized as a promising source of biocontrol agents for agricultural applications. Herein, we established a targeted strategy by integrating genomics and metabolomics to accelerate the discovery of new cyclopeptides from antagonistic metabolites produced by the marine-derived fungus Beauveria felina SYSU-MS7908. As a result, we isolated and characterized seven cyclopeptides, including six new molecules, isaridins I-N (1-6). Their chemical structures and conformational analysis were extensively elucidated using spectroscopic techniques (NMR, HRMS, and MS'MS data), modified Mosher's and Marfey's methods, and single-crystal X-ray diffraction. Notably, isaridin K (3) contains a peptide backbone with an N-methyl-2-aminobutyric acid residue rarely found in natural cyclopeptides. Bioassays showed that compound 2 could significantly inhibit the mycelial growth of G. citri-aurantii by destroying the cell membrane. These findings provide an effective strategy for searching for new fungal peptides for potential agrochemical fungicides and also pave the way for further exploration of applications in agriculture, food, and medicine.PMID:37310400 | DOI:10.1021/acs.jafc.3c02415

Classification of <em>Angelica</em> species found in various foods using an LC-QTOF/MS-based metabolomics approach

Tue, 13/06/2023 - 12:00
Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2023 Jun 13:1-10. doi: 10.1080/19440049.2023.2220827. Online ahead of print.ABSTRACTIn Korea, Angelica gigas is commonly known as Danggui. However, two other species on the market, Angelica acutiloba and Angelica sinensis, are also commonly called Danggui. Since the three Angelica species have different biologically active components, thus, different pharmacological activities, clear discrimination between them is needed to prevent their misuse. A. gigas is used not only as a cut or powdered product but also in processed foods, where it is mixed with other ingredients. To discriminate between the three Angelica species, reference samples were analysed as non-targeted using liquid chromatography-quadrupole time of flight/mass spectrometry (LC-QTOF/MS) and a metabolomics approach in which a discrimination model was established by partial least squares-discriminant analysis (PLS-DA). Then, the Angelica species in the processed foods were identified. First, 32 peaks were selected as marker compounds and a discrimination model was created using PLS-DA, and its validation was confirmed. Classification of the Angelica species was undertaken using the YPredPS value, and it was confirmed that all 21 foods examined contained the appropriate Angelica species indicated on the product packaging. Likewise, it was confirmed that all three Angelica species were accurately classified in the samples to which they were added.PMID:37310353 | DOI:10.1080/19440049.2023.2220827

Not always an innocent bystander: the impact of stabilised phosphopantetheine moieties when studying nonribosomal peptide biosynthesis

Tue, 13/06/2023 - 12:00
Chem Commun (Camb). 2023 Jun 13. doi: 10.1039/d3cc01578e. Online ahead of print.ABSTRACTNonribosomal peptide synthetases produce many important peptide natural products and are centred around carrier proteins (CPs) that deliver intermediates to various catalytic domains. We show that the replacement of CP substrate thioesters by stabilised ester analogues leads to active condensation domain complexes, whereas amide stabilisation generates non-functional complexes.PMID:37310188 | DOI:10.1039/d3cc01578e

Cerebral venous congestion alters brain metabolite profiles, impairing cognitive function

Tue, 13/06/2023 - 12:00
J Cereb Blood Flow Metab. 2023 Jun 13:271678X231182244. doi: 10.1177/0271678X231182244. Online ahead of print.ABSTRACTVascular cognitive impairment (VCI) represents the second most common cause of dementia after Alzheimer's disease, and pathological changes in cerebral vascular structure and function are pivotal causes of VCI. Cognitive impairment caused by arterial ischemia has been extensively studied the whole time; the influence of cerebral venous congestion on cognitive impairment draws doctors' attention in recent clinical practice, but the underlying neuropathophysiological alterations are not completely understood. This study elucidated the specific pathogenetic role of cerebral venous congestion in cognitive-behavioral deterioration and possible electrophysiological mechanisms. Using cerebral venous congestion rat models, we found these rats exhibited decreased long-term potentiation (LTP) in the hippocampal dentate gyrus and impaired spatial learning and memory. Based on untargeted metabolomics, N-acetyl-L-cysteine (NAC) deficiency was detected in cerebral venous congestion rats; supplementation with NAC appeared to ameliorate synaptic deficits, rescue impaired LTP, and mitigate cognitive impairment. In a cohort of cerebral venous congestion patients, NAC levels were decreased; NAC concentration was negatively correlated with subjective cognitive decline (SCD) score but positively correlated with mini-mental state examination (MMSE) score. These findings provide a new perspective on cognitive impairment and support further exploration of NAC as a therapeutic target for the prevention and treatment of VCI.PMID:37309740 | DOI:10.1177/0271678X231182244

Acyl-CoA dehydrogenase substrate promiscuity: Challenges and opportunities for development of substrate reduction therapy in disorders of valine and isoleucine metabolism

Tue, 13/06/2023 - 12:00
J Inherit Metab Dis. 2023 Jun 12. doi: 10.1002/jimd.12642. Online ahead of print.ABSTRACTToxicity of accumulating substrates is a significant problem in several disorders of valine and isoleucine degradation notably short-chain enoyl-CoA hydratase (ECHS1 or crotonase) deficiency, 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) deficiency, propionic acidemia (PA) and methylmalonic aciduria (MMA). Isobutyryl-CoA dehydrogenase (ACAD8) and short/branched-chain acyl-CoA dehydrogenase (SBCAD, ACADSB) function in the valine and isoleucine degradation pathways, respectively. Deficiencies of these acyl-CoA dehydrogenase (ACAD) enzymes are considered biochemical abnormalities with limited or no clinical consequences. We investigated whether substrate reduction therapy through inhibition of ACAD8 and SBCAD can limit the accumulation of toxic metabolic intermediates in disorders of valine and isoleucine metabolism. Using analysis of acylcarnitine isomers, we show that 2-methylenecyclopropaneacetic acid (MCPA) inhibited SBCAD, isovaleryl-CoA dehydrogenase, short-chain acyl-CoA dehydrogenase and medium-chain acyl-CoA dehydrogenase, but not ACAD8. MCPA treatment of wild-type and PA HEK-293 cells caused a pronounced decrease in C3-carnitine. Furthermore, deletion of ACADSB in HEK-293 cells led to an equally strong decrease in C3-carnitine when compared to wild-type cells. Deletion of ECHS1 in HEK-293 cells caused a defect in lipoylation of the E2 component of the pyruvate dehydrogenase complex, which was not rescued by ACAD8 deletion. MCPA was able to rescue lipoylation in ECHS1 KO cells, but only in cells with prior ACAD8 deletion. SBCAD was not the sole ACAD responsible for this compensation, which indicates substantial promiscuity of ACADs in HEK-293 cells for the isobutyryl-CoA substrate. Substrate promiscuity appeared less prominent for 2-methylbutyryl-CoA at least in HEK-293 cells. We suggest that pharmacological inhibition of SBCAD to treat PA should be investigated further. This article is protected by copyright. All rights reserved.PMID:37309295 | DOI:10.1002/jimd.12642

Variations in pleural microbiota and metabolic phenotype associated with malignant pleural effusion in human lung adenocarcinoma

Tue, 13/06/2023 - 12:00
Thorac Cancer. 2023 Jun 12. doi: 10.1111/1759-7714.14988. Online ahead of print.ABSTRACTBACKGROUND: Lung cancer is the most common cancer-related death worldwide. In 2022, the number of daily deaths of lung cancer was estimated to reach around 350 in the United States. Lung adenocarcinoma is the main subtype of lung cancer and patients with malignant pleural effusion (MPE) suffer from poor prognosis. Microbiota and its metabolites are associated with cancer progression. However, the effect of pleural microbiota on pleural metabolic profile of MPE in lung adenocarcinoma patients remains largely unknown.METHODS: Pleural effusion samples collected from lung adenocarcinoma patients with MPE (n = 14) and tuberculosis pleurisy patients with benign pleural effusion (BPE group, n = 10) were subjected to microbiome (16S rRNA gene sequencing) and metabolome (liquid chromatography tandem mass spectrometry [LC-MS/MS]) analyses. The datasets were analyzed individually and integrated for combined analysis using various bioinformatic approaches.RESULTS: The metabolic profile of MPE in lung adenocarcinoma patients were clearly distinguished from BPE with 121 differential metabolites across six significantly enriched pathways identified. Glycerophospholipids, fatty and carboxylic acids, and derivatives were the most common differential metabolites. Sequencing of microbial data revealed nine significantly enriched genera (i.e., Staphylococcus, Streptococcus, Lactobacillus) and 26 enriched ASVs (i.e., species Lactobacillus_delbrueckii) in MPE. Integrated analysis correlated MPE-associated microbes with metabolites, such as phosphatidylcholine and metabolites involved in the citrate cycle pathway.CONCLUSION: Our results provide substantial evidence of a novel interplay between the pleural microbiota and metabolome, which was drastically perturbed in MPE in lung adenocarcinoma patients. Microbe-associated metabolites can be used for further therapeutic explorations.PMID:37309281 | DOI:10.1111/1759-7714.14988

Lipidomics Profile Change of Skin Surface Lipids in Nummular Eczema

Mon, 12/06/2023 - 12:00
J Invest Dermatol. 2023 May;143(5):864-867.e9. doi: 10.1016/j.jid.2022.10.010. Epub 2022 Oct 29.NO ABSTRACTPMID:37306380 | DOI:10.1016/j.jid.2022.10.010

Pancreatic beta-cell specific BAG3 knockout results in chronic hyperinsulinemia inducing insulin resistance

Mon, 12/06/2023 - 12:00
Mol Metab. 2023 Jun 10:101752. doi: 10.1016/j.molmet.2023.101752. Online ahead of print.ABSTRACTBACKGROUND: Insulin, secreted from pancreatic islets of Langerhans, is of critical importance in regulating glucose homeostasis. Defective insulin secretion and/or the inability of tissues to respond to insulin results in insulin resistance and to several metabolic and organ alterations. We have previously demonstrated that BAG3 regulates insulin secretion. Herein we explored the consequences of beta-cells specific BAG3 deficiency in an animal model.METHODS: We generated a beta-cells specific BAG3 knockout mouse model. Glucose and insulin tolerance tests, proteomics, metabolomics, and immunohistochemical analysis were used to investigate the role of BAG3 in regulating insulin secretion and the effects of chronic exposure to excessive insulin release in vivo.RESULTS: Beta-cells specific BAG3 knockout results in primary hyperinsulinism due to excessive insulin exocytosis finally leading to insulin resistance. We demonstrate that resistance is mainly muscle-dependent while the liver remains insulin sensitive. The chronically altered metabolic condition leads in time to histopathological alterations in different organs. We observe elevated glycogen and lipid accumulation in the liver reminiscent of non-alcoholic fatty liver disease as well as mesangial matrix expansion and thickening of the glomerular basement membrane, resembling the histology of chronic kidney disease.CONCLUSION: Altogether, this study shows that BAG3 plays a role in insulin secretion and provides a model for the study of hyperinsulinemia and insulin resistance.PMID:37308077 | DOI:10.1016/j.molmet.2023.101752

Comprehensive metabolic profiling of diabetic retinopathy

Mon, 12/06/2023 - 12:00
Exp Eye Res. 2023 Jun 10:109538. doi: 10.1016/j.exer.2023.109538. Online ahead of print.ABSTRACTDiabetic retinopathy (DR) is an important complication of diabetes mellitus and a prevalent blind-causing ophthalmic disease. Despite years of efforts, rapid and accurate diagnosis of DR remains a challenging task. Metabolomics has been used as a diagnostic tool for disease progression and therapy monitoring. In this study, retinal tissues were collected from diabetic mice and age-matched non-diabetic mice. An unbiased metabolic profiling was performed to identify altered metabolites and metabolic pathways in DR. 311 differential metabolites were identified between diabetic retinas and non-diabetic retinas under the criteria of variable importance in projection (VIP) > 1 and P < 0.05. These differential metabolites were highly enriched in purine metabolism, amino acid metabolism, glycerophospholipid metabolism, and pantaothenate and CoA biosynthesis. We then evaluated the sensitivity and specificity of purine metabolites as the candidate biomarkers for DR through the area under the receiver-operating characteristic curves (AUC-ROCs). Compared with other purine metabolites, adenosine, guanine, and inosine had higher sensitivity, specificity, and accuracy for DR prediction. In conclusion, this study sheds new light on the metabolic mechanism of DR, which can facilitate clinical diagnosis, therapy, and prognosis of DR in the future.PMID:37308049 | DOI:10.1016/j.exer.2023.109538

Research into the anti-pulmonary fibrosis mechanism of Renshen Pingfei formula based on network pharmacology, metabolomics, and verification of AMPK/PPAR-γ pathway of active ingredients

Mon, 12/06/2023 - 12:00
J Ethnopharmacol. 2023 Jun 10:116773. doi: 10.1016/j.jep.2023.116773. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive disease with limited therapy. Renshen Pingfei Formula (RPFF), a classic Chinese medicine derivative formula, has been shown to exert therapeutic effects on IPF.AIM OF THE STUDY: The study aimed to explore the anti-pulmonary fibrosis mechanism of RPFF through network pharmacology, clinical plasma metabolomics, and in vitro experiment.METHODS: Network pharmacology was used to study the holistic pharmacological mechanism of RPFF in the treatment of IPF. The differential plasma metabolites for RPFF in the treatment of IPF were identified by untargeted metabolomics analysis. By integrated analysis of metabolomics and network pharmacology, the therapeutic target of RPFF for IPF and the corresponding herbal ingredients were identified. In addition, the effects of the main components of the formula, kaempferol and luteolin, which regulate the adenosine monophosphate (AMP)-activated protein kinase (AMPK)/peroxisome proliferator-activated receptor γ (PPAR-γ) pathway were observed in vitro according to the orthogonal design.RESULTS: A total of 92 potential targets for RPFF in the treatment of IPF were obtained. The Drug-Ingredients-Disease Target network showed that PTGS2, ESR1, SCN5A, PPAR-γ, and PRSS1 were associated with more herbal ingredients. The protein-protein interaction (PPI) network identified the key targets of RPFF in IPF treatment, including IL6, VEGFA, PTGS2, PPAR-γ, and STAT3. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis acquired the main enriched pathways, and PPAR-γ involved in multiple signaling pathways, including the AMPK signaling pathway. Untargeted clinical metabolomics analysis revealed plasma metabolite variations in patients with IPF versus controls and before versus after RPFF treatment for patients with IPF. Six differential metabolites were explored as differential plasma metabolites for RPFF in IPF treatment. Combined with network pharmacology, a therapeutic target PPAR-γ of RPFF in IPF treatment and the corresponding herbal components were identified. Based on the orthogonal experimental design, the experiments showed that kaempferol and luteolin can decrease the mRNA and protein expression of α-smooth muscle actin (α-SMA), and the combination of lower dose can inhibit α-SMA mRNA and protein expression by promoting the AMPK/PPAR-γ pathway in transforming growth factor beta 1 (TGF-β1)-treated MRC-5 cells.CONCLUSIONS: This study revealed that the therapeutic effects of RPFF are due to multiple ingredients and have multiple targets and pathways, and PPAR-γ is one of therapeutic targets for RPPF in IPF and involved in the AMPK signaling pathway. Two ingredients of RPFF, kaempferol and luteolin, can inhibit fibroblast proliferation and the myofibroblast differentiation of TGF-β1, and exert a synergistic effect through AMPK/PPAR-γ pathway activation.PMID:37308028 | DOI:10.1016/j.jep.2023.116773

Investigation of nephrotoxicity on mice exposed to polystyrene nanoplastics and the potential amelioration effects of DHA-enriched phosphatidylserine

Mon, 12/06/2023 - 12:00
Sci Total Environ. 2023 Jun 10:164808. doi: 10.1016/j.scitotenv.2023.164808. Online ahead of print.ABSTRACTNanoplastics (NPs) induce nephrotoxicity in mammals, but an understanding of the potential mechanism or amelioration strategies is lacking. Herein, we established the polystyrene nanoplastics (PS-NPs, 100 nm)-induced nephrotoxicity murine model, and investigated the potential molecular mechanism of docosahexaenoic acid-enriched phosphatidylserine (DHA-PS) alleviating effects. Based on the biochemical indices, H&E staining and kidney metabolomics, we found that PS-NPs did cause murine nephrotoxicity, mainly due to inflammation, oxidative stress, and lipid disturbance. DHA-PS administration alleviated these effects, mainly by decreasing renal levels of IL-6, IL-1β, TNF-α and MDA, increasing the level of IL-10, increasing the activities of SOD, GSH-Px, CAT, and alleviating lipid disturbance, mainly by modulating kidney glycerophospholipid metabolism, linoleic acid metabolism and the SIRT1-AMPK pathway. This is the first time that the amelioration effects of DHA-PS on PS-NPs-induced nephrotoxicity have been investigated from multiple perspectives, providing a potential mechanism of nephrotoxicity caused by PS-NPs.PMID:37308008 | DOI:10.1016/j.scitotenv.2023.164808

Mitochondrial folate metabolism-mediated α-linolenic acid exhaustion masks liver fibrosis resolution

Mon, 12/06/2023 - 12:00
J Biol Chem. 2023 Jun 10:104909. doi: 10.1016/j.jbc.2023.104909. Online ahead of print.ABSTRACTSustainable TGF-β1 signaling drives organ fibrogenesis. However, the cellular adaptation to maintain TGF-β1 signaling remains unclear. In this study, we revealed that dietary folate restriction promoted the resolution of liver fibrosis in mice with nonalcoholic steatohepatitis (NASH). In activated hepatic stellate cells (HSCs), folate shifted toward mitochondrial metabolism to sustain TGF-β1 signaling. Mechanistically, nontargeted metabolomics screening identified that α-linolenic acid (ALA) is exhausted by mitochondrial folate metabolism in activated HSCs. Knocking down serine hydroxymethyltransferase 2 (SHMT2) increases the bioconversion of ALA to docosahexaenoic acid (DHA) which inhibits TGF-β1 signaling. Finally, blocking mitochondrial folate metabolism promoted liver fibrosis resolution in NASH mice. In conclusion, mitochondrial folate metabolism/ALA exhaustion/TGF-βR1 reproduction is a feedforward signaling to sustain profibrotic TGF-β1 signaling and targeting mitochondrial folate metabolism is a promising strategy to enforce liver fibrosis resolution.PMID:37307917 | DOI:10.1016/j.jbc.2023.104909

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