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1.
Cell ; 187(7): 1801-1818.e20, 2024 Mar 28.
Artículo en Inglés | MEDLINE | ID: mdl-38471500

RESUMEN

The repertoire of modifications to bile acids and related steroidal lipids by host and microbial metabolism remains incompletely characterized. To address this knowledge gap, we created a reusable resource of tandem mass spectrometry (MS/MS) spectra by filtering 1.2 billion publicly available MS/MS spectra for bile-acid-selective ion patterns. Thousands of modifications are distributed throughout animal and human bodies as well as microbial cultures. We employed this MS/MS library to identify polyamine bile amidates, prevalent in carnivores. They are present in humans, and their levels alter with a diet change from a Mediterranean to a typical American diet. This work highlights the existence of many more bile acid modifications than previously recognized and the value of leveraging public large-scale untargeted metabolomics data to discover metabolites. The availability of a modification-centric bile acid MS/MS library will inform future studies investigating bile acid roles in health and disease.


Asunto(s)
Ácidos y Sales Biliares , Microbioma Gastrointestinal , Metabolómica , Espectrometría de Masas en Tándem , Animales , Humanos , Ácidos y Sales Biliares/química , Metabolómica/métodos , Poliaminas , Espectrometría de Masas en Tándem/métodos , Bases de Datos de Compuestos Químicos
2.
Nature ; 626(8000): 859-863, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38326609

RESUMEN

Bacteria in the gastrointestinal tract produce amino acid bile acid amidates that can affect host-mediated metabolic processes1-6; however, the bacterial gene(s) responsible for their production remain unknown. Herein, we report that bile salt hydrolase (BSH) possesses dual functions in bile acid metabolism. Specifically, we identified a previously unknown role for BSH as an amine N-acyltransferase that conjugates amines to bile acids, thus forming bacterial bile acid amidates (BBAAs). To characterize this amine N-acyltransferase BSH activity, we used pharmacological inhibition of BSH, heterologous expression of bsh and mutants in Escherichia coli and bsh knockout and complementation in Bacteroides fragilis to demonstrate that BSH generates BBAAs. We further show in a human infant cohort that BBAA production is positively correlated with the colonization of bsh-expressing bacteria. Lastly, we report that in cell culture models, BBAAs activate host ligand-activated transcription factors including the pregnane X receptor and the aryl hydrocarbon receptor. These findings enhance our understanding of how gut bacteria, through the promiscuous actions of BSH, have a significant role in regulating the bile acid metabolic network.


Asunto(s)
Aciltransferasas , Amidohidrolasas , Aminas , Ácidos y Sales Biliares , Biocatálisis , Microbioma Gastrointestinal , Humanos , Aciltransferasas/metabolismo , Amidohidrolasas/metabolismo , Aminas/química , Aminas/metabolismo , Bacteroides fragilis/enzimología , Bacteroides fragilis/genética , Bacteroides fragilis/metabolismo , Ácidos y Sales Biliares/química , Ácidos y Sales Biliares/metabolismo , Estudios de Cohortes , Escherichia coli/enzimología , Escherichia coli/genética , Escherichia coli/metabolismo , Microbioma Gastrointestinal/fisiología , Ligandos , Receptor X de Pregnano/metabolismo , Receptores de Hidrocarburo de Aril/metabolismo , Factores de Transcripción/metabolismo , Lactante , Técnicas de Cultivo de Célula
3.
PLoS Pathog ; 18(10): e1010926, 2022 10.
Artículo en Inglés | MEDLINE | ID: mdl-36306287

RESUMEN

The emergence of Plasmodium falciparum parasite resistance to dihydroartemisinin + piperaquine (PPQ) in Southeast Asia threatens plans to increase the global use of this first-line antimalarial combination. High-level PPQ resistance appears to be mediated primarily by novel mutations in the P. falciparum chloroquine resistance transporter (PfCRT), which enhance parasite survival at high PPQ concentrations in vitro and increase the risk of dihydroartemisinin + PPQ treatment failure in patients. Using isogenic Dd2 parasites expressing contemporary pfcrt alleles with differential in vitro PPQ susceptibilities, we herein characterize the molecular and physiological adaptations that define PPQ resistance in vitro. Using drug uptake and cellular heme fractionation assays we report that the F145I, M343L, and G353V PfCRT mutations differentially impact PPQ and chloroquine efflux. These mutations also modulate proteolytic degradation of host hemoglobin and the chemical inactivation of reactive heme species. Peptidomic analyses reveal significantly higher accumulation of putative hemoglobin-derived peptides in the PPQ-resistant mutant PfCRT isoforms compared to parental PPQ-sensitive Dd2. Joint transcriptomic and metabolomic profiling of late trophozoites from PPQ-resistant or -sensitive isogenic lines reveals differential expression of genes involved in protein translation and cellular metabolism. PPQ-resistant parasites also show increased susceptibility to an inhibitor of the P. falciparum M17 aminopeptidase that operates on short globin-derived peptides. These results reveal unique physiological changes caused by the gain of PPQ resistance and highlight the potential therapeutic value of targeting peptide metabolism in P. falciparum.


Asunto(s)
Antimaláricos , Artemisininas , Malaria Falciparum , Parásitos , Animales , Humanos , Plasmodium falciparum/genética , Plasmodium falciparum/metabolismo , Cloroquina/farmacología , Cloroquina/metabolismo , Parásitos/metabolismo , Proteínas Protozoarias/metabolismo , Resistencia a Medicamentos/genética , Malaria Falciparum/tratamiento farmacológico , Malaria Falciparum/genética , Malaria Falciparum/parasitología , Antimaláricos/metabolismo , Proteínas de Transporte de Membrana/genética , Proteínas de Transporte de Membrana/metabolismo , Artemisininas/farmacología , Mutación , Hemoglobinas/metabolismo , Hemo/metabolismo
4.
FASEB J ; 37(7): e23010, 2023 07.
Artículo en Inglés | MEDLINE | ID: mdl-37272852

RESUMEN

The aryl hydrocarbon receptor (AHR) mediates intestinal barrier homeostasis. Many AHR ligands are also CYP1A1/1B1 substrates, which can result in rapid clearance within the intestinal tract, limiting systemic exposure and subsequent AHR activation. This led us to the hypothesis that there are dietary substrates of CYP1A1/1B1 that functionally increase the half-life of potent AHR ligands. We examined the potential of urolithin A (UroA), a gut bacterial metabolite of ellagitannins, as a CYP1A1/1B1 substrate to enhance AHR activity in vivo. UroA is a competitive substrate for CYP1A1/1B1 in an in vitro competition assay. A broccoli-containing diet promotes the gastric formation of the potent hydrophobic AHR ligand and CYP1A1/1B1 substrate, 5,11-dihydroindolo[3,2-b]carbazole (ICZ). In mice, dietary exposure to UroA in a 10% broccoli diet led to a coordinated increase in duodenal, cardiac, and pulmonary AHR activity, but no increase in activity in the liver. Thus, CYP1A1 dietary competitive substrates can lead to enhanced systemic AHR ligand distribution from the gut, likely through the lymphatic system, increasing AHR activation in key barrier tissues. Finally, this report will lead to a reassessment of the dynamics of distribution of other hydrophobic chemicals present in the diet.


Asunto(s)
Citocromo P-450 CYP1A1 , Tracto Gastrointestinal , Pulmón , Receptores de Hidrocarburo de Aril , Animales , Ratones , Citocromo P-450 CYP1A1/genética , Citocromo P-450 CYP1A1/metabolismo , Ligandos , Hígado/metabolismo , Pulmón/metabolismo , Receptores de Hidrocarburo de Aril/metabolismo , Dieta , Tracto Gastrointestinal/metabolismo
5.
Int J Mol Sci ; 25(16)2024 Aug 06.
Artículo en Inglés | MEDLINE | ID: mdl-39201268

RESUMEN

2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a persistent organic pollutant and a potent aryl hydrocarbon receptor (AHR) ligand, causes delayed intestinal motility and affects the survival of enteric neurons. In this study, we investigated the specific signaling pathways and molecular targets involved in TCDD-induced enteric neurotoxicity. Immortalized fetal enteric neuronal (IM-FEN) cells treated with 10 nM TCDD exhibited cytotoxicity and caspase 3/7 activation, indicating apoptosis. Increased cleaved caspase-3 expression with TCDD treatment, as assessed by immunostaining in enteric neuronal cells isolated from WT mice but not in neural crest cell-specific Ahr deletion mutant mice (Wnt1Cre+/-/Ahrb(fl/fl)), emphasized the pivotal role of AHR in this process. Importantly, the apoptosis in IM-FEN cells treated with TCDD was mediated through a ceramide-dependent pathway, independent of endoplasmic reticulum stress, as evidenced by increased ceramide synthesis and the reversal of cytotoxic effects with myriocin, a potent inhibitor of ceramide biosynthesis. We identified Sptlc2 and Smpd2 as potential gene targets of AHR in ceramide regulation by a chromatin immunoprecipitation (ChIP) assay in IM-FEN cells. Additionally, TCDD downregulated phosphorylated Akt and phosphorylated Ser9-GSK-3ß levels, implicating the PI3 kinase/AKT pathway in TCDD-induced neurotoxicity. Overall, this study provides important insights into the mechanisms underlying TCDD-induced enteric neurotoxicity and identifies potential targets for the development of therapeutic interventions.


Asunto(s)
Apoptosis , Ceramidas , Estrés del Retículo Endoplásmico , Neuronas , Dibenzodioxinas Policloradas , Receptores de Hidrocarburo de Aril , Transducción de Señal , Receptores de Hidrocarburo de Aril/metabolismo , Receptores de Hidrocarburo de Aril/genética , Animales , Apoptosis/efectos de los fármacos , Estrés del Retículo Endoplásmico/efectos de los fármacos , Ratones , Transducción de Señal/efectos de los fármacos , Dibenzodioxinas Policloradas/toxicidad , Neuronas/metabolismo , Neuronas/efectos de los fármacos , Ceramidas/metabolismo , Sistema Nervioso Entérico/metabolismo , Sistema Nervioso Entérico/efectos de los fármacos
6.
Int J Mol Sci ; 23(15)2022 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-35897801

RESUMEN

Early life exposure to environmental pollutants may have long-term consequences and harmful impacts on health later in life. Here, we investigated the short- and long-term impact of early life 3,3',4,4',5-pentacholorobiphenyl (PCB 126) exposure (24 µg/kg body weight for five days) in mice on the host and gut microbiota using 16S rRNA gene sequencing, metagenomics, and 1H NMR- and mass spectrometry-based metabolomics. Induction of Cyp1a1, an aryl hydrocarbon receptor (AHR)-responsive gene, was observed at 6 days and 13 weeks after PCB 126 exposure consistent with the long half-life of PCB 126. Early life, Short-Term PCB 126 exposure resulted in metabolic abnormalities in adulthood including changes in liver amino acid and nucleotide metabolism as well as bile acid metabolism and increased hepatic lipogenesis. Interestingly, early life PCB 126 exposure had a greater impact on bacteria in adulthood at the community structure, metabolic, and functional levels. This study provides evidence for an association between early life environmental pollutant exposure and increased risk of metabolic disorders later in life and suggests the microbiome is a key target of environmental chemical exposure.


Asunto(s)
Contaminantes Ambientales , Microbioma Gastrointestinal , Microbiota , Bifenilos Policlorados , Animales , Contaminantes Ambientales/toxicidad , Microbioma Gastrointestinal/genética , Ratones , Bifenilos Policlorados/toxicidad , ARN Ribosómico 16S/genética , ARN Ribosómico 16S/metabolismo
7.
Drug Metab Dispos ; 47(2): 86-93, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30409838

RESUMEN

Intestinal bacteria play an important role in bile acid metabolism and in the regulation of multiple host metabolic pathways (e.g., lipid and glucose homeostasis) through modulation of intestinal farnesoid X receptor (FXR) activity. Here, we examined the effect of berberine (BBR), a natural plant alkaloid, on intestinal bacteria using in vitro and in vivo models. In vivo, the metabolomic response and changes in mouse intestinal bacterial communities treated with BBR (100 mg/kg) for 5 days were assessed using NMR- and mass spectrometry-based metabolomics coupled with multivariate data analysis. Short-term BBR exposure altered intestinal bacteria by reducing Clostridium cluster XIVa and IV and their bile salt hydrolase (BSH) activity, which resulted in the accumulation of taurocholic acid (TCA). The accumulation of TCA was associated with activation of intestinal FXR, which can mediate bile acid, lipid, and glucose metabolism. In vitro, isolated mouse cecal bacteria were incubated with three doses of BBR (0.1, 1, and 10 mg/ml) for 4 hours in an anaerobic chamber. NMR-based metabolomics combined with flow cytometry was used to evaluate the direct physiologic and metabolic effect of BBR on the bacteria. In vitro, BBR exposure not only altered bacterial physiology but also changed bacterial community composition and function, especially reducing BSH-expressing bacteria like Clostridium spp. These data suggest that BBR directly affects bacteria to alter bile acid metabolism and activate FXR signaling. These data provide new insights into the link between intestinal bacteria, nuclear receptor signaling, and xenobiotics.


Asunto(s)
Berberina/farmacología , Microbioma Gastrointestinal/efectos de los fármacos , Mucosa Intestinal/efectos de los fármacos , Receptores Citoplasmáticos y Nucleares/metabolismo , Amidohidrolasas/metabolismo , Animales , Proteínas Bacterianas/metabolismo , Ciego/efectos de los fármacos , Ciego/metabolismo , Ciego/microbiología , Clostridium/efectos de los fármacos , Clostridium/aislamiento & purificación , Clostridium/fisiología , Microbioma Gastrointestinal/fisiología , Mucosa Intestinal/metabolismo , Mucosa Intestinal/microbiología , Masculino , Metabolómica/métodos , Ratones , Ratones Endogámicos C57BL , Ácido Taurocólico/metabolismo
8.
Comput Stat Data Anal ; 105: 96-111, 2017 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-27667882

RESUMEN

Compared to other analytical platforms, comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC×GC-MS) has much increased separation power for analysis of complex samples and thus is increasingly used in metabolomics for biomarker discovery. However, accurate peak detection remains a bottleneck for wide applications of GC×GC-MS. Therefore, the normal-exponential-Bernoulli (NEB) model is generalized by gamma distribution and a new peak detection algorithm using the normal-gamma-Bernoulli (NGB) model is developed. Unlike the NEB model, the NGB model has no closed-form analytical solution, hampering its practical use in peak detection. To circumvent this difficulty, three numerical approaches, which are fast Fourier transform (FFT), the first-order and the second-order delta methods (D1 and D2), are introduced. The applications to simulated data and two real GC×GC-MS data sets show that the NGB-D1 method performs the best in terms of both computational expense and peak detection performance.

9.
J Proteome Res ; 14(9): 4050-8, 2015 Sep 04.
Artículo en Inglés | MEDLINE | ID: mdl-26216400

RESUMEN

The gut microbiota plays a critical role in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Increased fructose consumption and inadequate copper intake are two critical risk factors in the development of NAFLD. To gain insight into the role of gut microbiota, fecal metabolites, obtained from rats exposed to different dietary levels of copper with and without high fructose intake for 4 weeks, were analyzed by comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC × GC-TOF MS). In parallel, liver tissues were assessed by histology and triglyceride assay. Our data showed that high fructose feeding led to obvious hepatic steatosis in both marginal copper deficient rats and copper supplementation rats. Among the 38 metabolites detected with significant abundance alteration between groups, short chain fatty acids were markedly decreased with excessive fructose intake irrespective of copper levels. C15:0 and C17:0 long chain fatty acids, produced only by bacteria, were increased by either high copper level or high fructose intake. In addition, increased fecal urea and malic acid paralleled the increased hepatic fat accumulation. Collectively, GC × GC-TOF MS analysis of rat fecal samples revealed distinct fecal metabolome profiles associated with the dietary high fructose and copper level, with some metabolites possibly serving as potential noninvasive biomarkers of fructose induced-NAFLD.


Asunto(s)
Cobre/farmacología , Heces/química , Fructosa/metabolismo , Metaboloma/efectos de los fármacos , Animales , Cobre/administración & dosificación , Dieta , Fructosa/administración & dosificación , Cromatografía de Gases y Espectrometría de Masas , Masculino , Metabolómica , Enfermedad del Hígado Graso no Alcohólico/inducido químicamente , Enfermedad del Hígado Graso no Alcohólico/metabolismo , Ratas , Ratas Sprague-Dawley
10.
BMC Genomics ; 16: 279, 2015 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-25888140

RESUMEN

BACKGROUND: Despite the recent identification of several prognostic gene signatures, the lack of common genes among experimental cohorts has posed a considerable challenge in uncovering the molecular basis underlying hepatocellular carcinoma (HCC) recurrence for application in clinical purposes. To overcome the limitations of individual gene-based analysis, we applied a pathway-based approach for analysis of HCC recurrence. RESULTS: By implementing a permutation-based semi-supervised principal component analysis algorithm using the optimal principal component, we selected sixty-four pathways associated with hepatitis B virus (HBV)-positive HCC recurrence (p < 0.01), from our microarray dataset composed of 142 HBV-positive HCCs. In relation to the public HBV- and public hepatitis C virus (HCV)-positive HCC datasets, we detected 46 (71.9%) and 18 (28.1%) common recurrence-associated pathways, respectively. However, overlap of recurrence-associated genes between datasets was rare, further supporting the utility of the pathway-based approach for recurrence analysis between different HCC datasets. Non-supervised clustering of the 64 recurrence-associated pathways facilitated the classification of HCC patients into high- and low-risk subgroups, based on risk of recurrence (p < 0.0001). The pathways identified were additionally successfully applied to discriminate subgroups depending on recurrence risk within the public HCC datasets. Through multivariate analysis, these recurrence-associated pathways were identified as an independent prognostic factor (p < 0.0001) along with tumor number, tumor size and Edmondson's grade. Moreover, the pathway-based approach had a clinical advantage in terms of discriminating the high-risk subgroup (N = 12) among patients (N = 26) with small HCC (<3 cm). CONCLUSIONS: Using pathway-based analysis, we successfully identified the pathways involved in recurrence of HBV-positive HCC that may be effectively used as prognostic markers.


Asunto(s)
Carcinoma Hepatocelular/diagnóstico , Hepatitis B/diagnóstico , Neoplasias Hepáticas/diagnóstico , Adulto , Algoritmos , Carcinoma Hepatocelular/complicaciones , Carcinoma Hepatocelular/epidemiología , Análisis por Conglomerados , Bases de Datos Factuales , Supervivencia sin Enfermedad , Femenino , Hepacivirus/aislamiento & purificación , Hepatitis B/complicaciones , Hepatitis B/virología , Virus de la Hepatitis B/aislamiento & purificación , Humanos , Neoplasias Hepáticas/complicaciones , Neoplasias Hepáticas/epidemiología , Masculino , Persona de Mediana Edad , Recurrencia Local de Neoplasia , Análisis de Componente Principal , Pronóstico , Riesgo
11.
J Proteome Res ; 13(2): 547-554, 2014 Feb 07.
Artículo en Inglés | MEDLINE | ID: mdl-24328084

RESUMEN

Arsenic is a widely distributed environmental component that is associated with a variety of cancer and non-cancer adverse health effects. Additional lifestyle factors, such as diet, contribute to the manifestation of disease. Recently, arsenic was found to increase inflammation and liver injury in a dietary model of fatty liver disease. The purpose of the present study was to investigate potential mechanisms of this diet-environment interaction via a high-throughput metabolomics approach. GC×GC-TOF MS was used to identify metabolites that were significantly increased or decreased in the livers of mice fed a Western diet (a diet high in fat and cholesterol) and co-exposed to arsenic-contaminated drinking water. The results showed that there are distinct hepatic metabolomic profiles associated with eating a high fat diet, drinking arsenic-contaminated water, and the combination of the two. Among the metabolites that were decreased when arsenic exposure was combined with a high fat diet were short-chain and medium-chain fatty acid metabolites and the anti-inflammatory amino acid, glycine. These results are consistent with the observed increase in inflammation and cell death in the livers of these mice and point to potentially novel mechanisms by which these metabolic pathways could be altered by arsenic in the context of diet-induced fatty liver disease.


Asunto(s)
Arsénico/toxicidad , Dieta Alta en Grasa , Modelos Animales de Enfermedad , Hígado Graso/metabolismo , Metabolómica , Animales , Cromatografía de Gases , Hígado Graso/inducido químicamente , Masculino , Espectrometría de Masas , Ratones , Ratones Endogámicos C57BL
12.
Bioinformatics ; 29(14): 1786-92, 2013 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-23665844

RESUMEN

MOTIVATION: Due to the high complexity of metabolome, the comprehensive 2D gas chromatography time-of-flight mass spectrometry (GC×GC-TOF MS) is considered as a powerful analytical platform for metabolomics study. However, the applications of GC×GC-TOF MS in metabolomics are not popular owing to the lack of bioinformatics system for data analysis. RESULTS: We developed a computational platform entitled metabolomics profiling pipeline (MetPP) for analysis of metabolomics data acquired on a GC×GC-TOF MS system. MetPP can process peak filtering and merging, retention index matching, peak list alignment, normalization, statistical significance tests and pattern recognition, using the peak lists deconvoluted from the instrument data as its input. The performance of MetPP software was tested with two sets of experimental data acquired in a spike-in experiment and a biomarker discovery experiment, respectively. MetPP not only correctly aligned the spiked-in metabolite standards from the experimental data, but also correctly recognized their concentration difference between sample groups. For analysis of the biomarker discovery data, 15 metabolites were recognized with significant concentration difference between the sample groups and these results agree with the literature results of histological analysis, demonstrating the effectiveness of applying MetPP software for disease biomarker discovery. AVAILABILITY: The source code of MetPP is available at http://metaopen.sourceforge.net CONTACT: xiang.zhang@louisville.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Cromatografía de Gases y Espectrometría de Masas/métodos , Metabolómica/métodos , Programas Informáticos , Animales , Metaboloma , Ratones
13.
Analyst ; 139(10): 2507-14, 2014 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-24665464

RESUMEN

We report a compound identification method (SimMR), which simultaneously evaluates the mass spectrum similarity and the retention index distance using an empirical mixture score function, for the analysis of GC-MS data. The performance of the developed SimMR method was compared to that of two existing compound identification strategies. One is the mass spectrum matching method without incorporation of retention index information (SM). The other is the method that sequentially evaluates the mass spectrum similarity and retention index distance (SeqMR). For comparison purposes, we used the NIST/EPA/NIH Mass Spectral Library 2005. Our study demonstrates that SimMR performs the best among the three compound identification methods, by improving the overall identification accuracy up to 1.53% and 4.81% compared to SeqMR and SM, respectively.


Asunto(s)
Cromatografía de Gases y Espectrometría de Masas/métodos , Análisis de Fourier , Modelos Teóricos , Reproducibilidad de los Resultados , Espectrometría de Masa por Ionización de Electrospray
14.
Chemometr Intell Lab Syst ; 138: 193-202, 2014 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-25414536

RESUMEN

The goal of metabolic association networks is to identify topology of a metabolic network for a better understanding of molecular mechanisms. An accurate metabolic association network enables investigation of the functional behavior of metabolites in a cell or tissue. Gaussian Graphical model (GGM)-based methods have been widely used in genomics to infer biological networks. However, the performance of various GGM-based methods for the construction of metabolic association networks remains unknown in metabolomics. The performance of principle component regression (PCR), independent component regression (ICR), shrinkage covariance estimate (SCE), partial least squares regression (PLSR), and extrinsic similarity (ES) methods in constructing metabolic association networks was compared by estimating partial correlation coefficient matrices when the number of variables is larger than the sample size. To do this, the sample size and the network density (complexity) were considered as variables for network construction. Simulation studies show that PCR and ICR are more stable to the sample size and the network density than SCE and PLSR in terms of F1 scores. These methods were further applied to analysis of experimental metabolomics data acquired from metabolite extract of mouse liver. For the simulated data, the proposed methods PCR and ICR outperform other methods when the network density is large, while PLSR and SCE perform better when the network density is small. As for experimental metabolomics data, PCR and ICR discover more significant edges and perform better than PLSR and SCE when the discovered edges are evaluated using KEGG pathway. These results suggest that the metabolic network is more complex than the genomic network and therefore, PCR and ICR have the advantage over PLSR and SCE in constructing the metabolic association networks.

15.
J Leukoc Biol ; 116(1): 6-17, 2024 Jun 28.
Artículo en Inglés | MEDLINE | ID: mdl-38289835

RESUMEN

The mechanisms driving metabolic reprogramming during B cell activation are unclear, particularly roles for enzymatic pathways involved in lipid remodeling. We found that murine B cell activation with lipopolysaccharide (LPS) led to a 1.6-fold increase in total lipids that included higher levels of phosphatidylethanolamine (PE) and plasmenyl PE. Selenoprotein I (SELENOI) is an ethanolamine phospholipid transferase involved in the synthesis of both PE and plasmenyl PE, and SELENOI expression was also upregulated during activation. Selenoi knockout (KO) B cells exhibited decreased levels of plasmenyl PE, which plays an important antioxidant role. Lipid peroxidation was measured and found to increase ∼2-fold in KO vs. wild-type (WT) B cells. Cell death was not impacted by KO in LPS-treated B cells and proliferation was only slightly reduced, but differentiation into CD138 + Blimp-1+ plasma B cells was decreased ∼2-fold. This led to examination of B cell receptors important for differentiation that recognize the ligand B cell activating factor, and levels of TACI (transmembrane activator, calcium-modulator, and cytophilin ligand interactor) (CD267) were significantly decreased on KO B cells compared with WT control cells. Vaccination with ovalbumin/adjuvant led to decreased ovalbumin-specific immunoglobulin M (IgM) levels in sera of KO mice compared with WT mice. Real-time polymerase chain reaction analyses revealed a decreased switch from surface to secreted IgM in spleens of KO mice induced by vaccination or LP-BM5 retrovirus infection. Overall, these findings detail the lipidomic response of B cells to LPS activation and reveal the importance of upregulated SELENOI for promoting differentiation into IgM-secreting plasma B cells.


Asunto(s)
Linfocitos B , Diferenciación Celular , Inmunoglobulina M , Lipopolisacáridos , Activación de Linfocitos , Selenoproteínas , Animales , Lipopolisacáridos/farmacología , Inmunoglobulina M/sangre , Inmunoglobulina M/metabolismo , Ratones , Selenoproteínas/metabolismo , Selenoproteínas/genética , Linfocitos B/inmunología , Linfocitos B/metabolismo , Ratones Noqueados , Células Plasmáticas/metabolismo , Células Plasmáticas/inmunología , Lipidómica , Regulación hacia Arriba , Ratones Endogámicos C57BL
16.
Adv Sci (Weinh) ; : e2400794, 2024 Aug 29.
Artículo en Inglés | MEDLINE | ID: mdl-39207053

RESUMEN

Sphingolipids play vital roles in metabolism and regulation. Previously, the aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor, was reported to directly regulate ceramide synthesis genes by binding to their promoters. Herein, sphingosine kinase 2 (SPHK2), responsible for producing sphingosine-1-phosphate (S1P), was found to interact with AHR through LXXLL motifs, influencing AHR nuclear localization. Through mutagenesis and co-transfection studies, AHR activation and subsequent nuclear translocation was hindered by SPHK2 LXXLL mutants or SPHK2 lacking a nuclear localization signal (NLS). Similarly, an NLS-deficient AHR mutant impaired SPHK2 nuclear translocation. Silencing SPHK2 reduced AHR expression and its target gene CYP1A1, while SPHK2 overexpression enhanced AHR activity. SPHK2 was found enriched on the CYP1A1 promoter, underscoring its role in AHR target gene activation. Additionally, S1P rapidly increased AHR expression at both the mRNA and protein levels and promoted AHR recruitment to the CYP1A1 promoter. Using mouse models, AHR deficiency compromised SPHK2 nuclear translocation, illustrating a critical interaction where SPHK2 facilitates AHR nuclear localization and supports a positive feedback loop between AHR and sphingolipid enzyme activity in the nucleus. These findings highlight a novel function of SPHK2 in regulating AHR activity and gene expression.

17.
Environ Health Perspect ; 132(8): 87005, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-39140734

RESUMEN

BACKGROUND: Exposure to persistent organic pollutants (POPs) and disruptions in the gastrointestinal microbiota have been positively correlated with a predisposition to factors such as obesity, metabolic syndrome, and type 2 diabetes; however, it is unclear how the microbiome contributes to this relationship. OBJECTIVE: This study aimed to explore the association between early life exposure to a potent aryl hydrocarbon receptor (AHR) agonist and persistent disruptions in the microbiota, leading to impaired metabolic homeostasis later in life. METHODS: This study used metagenomics, nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics, and biochemical assays to analyze the gut microbiome composition and function, as well as the physiological and metabolic effects of early life exposure to 2,3,7,8-tetrachlorodibenzofuran (TCDF) in conventional, germ-free (GF), and Ahr-null mice. The impact of TCDF on Akkermansia muciniphila (A. muciniphila) in vitro was assessed using optical density (OD 600), flow cytometry, transcriptomics, and MS-based metabolomics. RESULTS: TCDF-exposed mice exhibited lower abundances of A. muciniphila, lower levels of cecal short-chain fatty acids (SCFAs) and indole-3-lactic acid (ILA), as well as lower levels of the gut hormones glucagon-like peptide 1 (GLP-1) and peptide YY (PYY), findings suggestive of disruption in the gut microbiome community structure and function. Importantly, microbial and metabolic phenotypes associated with early life POP exposure were transferable to GF recipients in the absence of POP carry-over. In addition, AHR-independent interactions between POPs and the microbiota were observed, and they were significantly associated with growth, physiology, gene expression, and metabolic activity outcomes of A. muciniphila, supporting suppressed activity along the ILA pathway. CONCLUSIONS: These data obtained in a mouse model point to the complex effects of POPs on the host and microbiota, providing strong evidence that early life, short-term, and self-limiting POP exposure can adversely impact the microbiome, with effects persisting into later life with associated health implications. https://doi.org/10.1289/EHP13356.


Asunto(s)
Benzofuranos , Microbioma Gastrointestinal , Homeostasis , Ratones Endogámicos C57BL , Receptores de Hidrocarburo de Aril , Animales , Microbioma Gastrointestinal/efectos de los fármacos , Microbioma Gastrointestinal/fisiología , Receptores de Hidrocarburo de Aril/metabolismo , Ratones , Homeostasis/efectos de los fármacos , Contaminantes Orgánicos Persistentes , Masculino , Ligandos
18.
bioRxiv ; 2024 Feb 04.
Artículo en Inglés | MEDLINE | ID: mdl-38352460

RESUMEN

Inter-organellar communication is critical for cellular metabolic homeostasis. One of the most abundant inter-organellar interactions are those at the endoplasmic reticulum and mitochondria contact sites (ERMCS). However, a detailed understanding of the mechanisms governing ERMCS regulation and their roles in cellular metabolism are limited by a lack of tools that permit temporal induction and reversal. Through unbiased screening approaches, we identified fedratinib, an FDA-approved drug, that dramatically increases ERMCS abundance by inhibiting the epigenetic modifier BRD4. Fedratinib rapidly and reversibly modulates mitochondrial and ER morphology and alters metabolic homeostasis. Moreover, ERMCS modulation depends on mitochondria electron transport chain complex III function. Comparison of fedratinib activity to other reported inducers of ERMCS revealed common mechanisms of induction and function, providing clarity and union to a growing body of experimental observations. In total, our results uncovered a novel epigenetic signaling pathway and an endogenous metabolic regulator that connects ERMCS and cellular metabolism.

19.
Sci Transl Med ; 16(766): eadk8446, 2024 Sep 25.
Artículo en Inglés | MEDLINE | ID: mdl-39321267

RESUMEN

Activation of extracellular matrix-producing hepatic stellate cells (HSCs) is a key event in liver fibrogenesis. We showed that the expression of the heme-thiolate monooxygenase cytochrome P450 1B1 (CYP1B1) was elevated in human and mouse fibrotic livers and activated HSCs. Systemic or HSC-specific ablation and pharmacological inhibition of CYP1B1 attenuated HSC activation and protected male but not female mice from thioacetamide (TAA)-, carbon tetrachloride (CCl4)-, or bile duct ligation (BDL)-induced liver fibrosis. Metabolomic analysis revealed an increase in the disaccharide trehalose in CYP1B1-deficient HSCs resulting from intestinal suppression of the trehalose-metabolizing enzyme trehalase, whose gene we found to be a target of RARα. Trehalose or its hydrolysis-resistant derivative lactotrehalose exhibited potent antifibrotic activity in vitro and in vivo by functioning as an HSC-specific autophagy inhibitor, which may account for the antifibrotic effect of CYP1B1 inhibition. Our study thus reveals an endobiotic function of CYP1B1 in liver fibrosis in males, mediated by liver-intestine cross-talk and trehalose. At the translational level, pharmacological inhibition of CYP1B1 or the use of trehalose/lactotrehalose may represent therapeutic strategies for liver fibrosis.


Asunto(s)
Citocromo P-450 CYP1B1 , Células Estrelladas Hepáticas , Cirrosis Hepática , Trehalosa , Trehalosa/farmacología , Trehalosa/análogos & derivados , Trehalosa/metabolismo , Trehalosa/uso terapéutico , Animales , Células Estrelladas Hepáticas/metabolismo , Células Estrelladas Hepáticas/efectos de los fármacos , Células Estrelladas Hepáticas/patología , Cirrosis Hepática/patología , Cirrosis Hepática/metabolismo , Masculino , Humanos , Femenino , Citocromo P-450 CYP1B1/metabolismo , Ratones , Autofagia/efectos de los fármacos , Ratones Endogámicos C57BL
20.
Bioinformatics ; 28(8): 1158-63, 2012 Apr 15.
Artículo en Inglés | MEDLINE | ID: mdl-22333245

RESUMEN

MOTIVATION: The compound identification in gas chromatography-mass spectrometry (GC-MS) is achieved by matching the experimental mass spectrum to the mass spectra in a spectral library. It is known that the intensities with higher m/z value in the GC-MS mass spectrum are the most diagnostic. Therefore, to increase the relative significance of peak intensities of higher m/z value, the intensities and m/z values are usually transformed with a set of weight factors. A poor quality of weight factors can significantly decrease the accuracy of compound identification. With the significant enrichment of the mass spectral database and the broad application of GC-MS, it is important to re-visit the methods of discovering the optimal weight factors for high confident compound identification. RESULTS: We developed a novel approach to finding the optimal weight factors only through a reference library for high accuracy compound identification. The developed approach first calculates the ratio of skewness to kurtosis of the mass spectral similarity scores among spectra (compounds) in a reference library and then considers a weight factor with the maximum ratio as the optimal weight factor. We examined our approach by comparing the accuracy of compound identification using the mass spectral library maintained by the National Institute of Standards and Technology. The results demonstrate that the optimal weight factors for fragment ion peak intensity and m/z value found by the developed approach outperform the current weight factors for compound identification. AVAILABILITY: The results and R package are available at http://stage.louisville.edu/faculty/x0zhan17/software/ software-development.


Asunto(s)
Cromatografía de Gases y Espectrometría de Masas/métodos , Programas Informáticos , Estándares de Referencia
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