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Rodrigues A, Massenet T, Dubois LM, Huet AC, Markey A, Wavreille J, Gengler N, Stefanuto PH, Focant JF. Development and validation of a classification model for boar taint detection in pork fat samples. Food Chem 2024; 443:138572. [PMID: 38295570 DOI: 10.1016/j.foodchem.2024.138572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024]
Abstract
This study aims to characterize a complete volatile organic compound profile of pork neck fat for boar taint prediction. The objectives are to identify specific compounds related to boar taint and to develop a classification model. In addition to the well-known androstenone, skatole and indole, 10 other features were found to be discriminant according to untargeted volatolomic analyses were conducted on 129 samples using HS-SPME-GC×GC-TOFMS. To select the odor-positive samples among the 129 analyzed, the selection was made by combining human nose evaluations with the skatole and androstenone concentrations determined using UHPLC-MS/MS. A comparison of the data of the two populations was performed and a statistical model analysis was built on 70 samples out of the total of 129 samples fully positive or fully negative through these two orthogonal methods for tainted prediction. Then, the model was applied to the 59 remaining samples. Finally, 7 samples were classified as tainted.
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Affiliation(s)
- Anaïs Rodrigues
- Organic and Biological Analytical Chemistry Group, MolSys Research Unit, University of Liège, 4000 Liège, Belgium.
| | - Thibault Massenet
- Organic and Biological Analytical Chemistry Group, MolSys Research Unit, University of Liège, 4000 Liège, Belgium.
| | - Lena M Dubois
- Organic and Biological Analytical Chemistry Group, MolSys Research Unit, University of Liège, 4000 Liège, Belgium.
| | | | - Alice Markey
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium.
| | - José Wavreille
- Animal Production Unit, Walloon Agricultural Research Centre, 5030 Gembloux, Belgium.
| | - Nicolas Gengler
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium.
| | - Pierre-Hugues Stefanuto
- Organic and Biological Analytical Chemistry Group, MolSys Research Unit, University of Liège, 4000 Liège, Belgium.
| | - Jean-François Focant
- Organic and Biological Analytical Chemistry Group, MolSys Research Unit, University of Liège, 4000 Liège, Belgium.
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2
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Nian J, Lan W, Wang Z, Zhang X, Yao H, Zhang F. Exploring the metabolic implications of blue light exposure during daytime in rats. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 278:116436. [PMID: 38723383 DOI: 10.1016/j.ecoenv.2024.116436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/11/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
Excessive exposure to light is a global issue. Artificial light pollution has been shown to disrupt the body's natural circadian rhythm. To investigate the impacts of light on metabolism, we studied Sprague-Dawley rats chronically exposed to red or blue light during daytime or nighttime. Rats in the experimental group were exposed to extended light for 4 hours during daytime or nighttime to simulate the effects of excessive light usage. Strikingly, we found systemic metabolic alterations only induced by blue light during daytime. Furthermore, we conducted metabolomic analyses of the cerebrospinal fluid, serum, heart, liver, spleen, adrenal, cerebellum, pituitary, prostate, spermatophore, hypothalamus and kidney from rats in the control and blue light exposure during daytime. Significant changes in metabolites have been observed in cerebrospinal fluid, serum, hypothalamus and kidney of rats exposed to blue light during daytime. Metabolic alterations observed in rats encompassing pyruvate metabolism, glutathione metabolism homocysteine degradation, phosphatidylethanolamine biosynthesis, and phospholipid biosynthesis, exhibit analogous patterns to those inherent in specific physiological processes, notably neurodevelopment, cellular injury, oxidative stress, and autophagic pathways. Our study provides insights into tissue-specific metabolic changes in rats exposed to blue light during the daytime and may help explain potential mechanisms of photopathogenesis.
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Affiliation(s)
- Jingjing Nian
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, PR China
| | - Wenning Lan
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, PR China
| | - Ziran Wang
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, PR China
| | - Xiaojing Zhang
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, PR China
| | - Hong Yao
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, PR China
| | - Fangrong Zhang
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, PR China; Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, PR China.
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3
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Jalabert C, Gray SL, Soma KK. An Aggressive Interaction Rapidly Increases Brain Androgens in a Male Songbird during the Non-breeding Season. J Neurosci 2024; 44:e1095232024. [PMID: 38658166 PMCID: PMC11154856 DOI: 10.1523/jneurosci.1095-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024] Open
Abstract
Aggression is a crucial behavior that impacts access to limited resources in different environmental contexts. Androgens synthesized by the gonads promote aggression during the breeding season. However, aggression can be expressed during the non-breeding season, despite low androgen synthesis by the gonads. The brain can also synthesize steroids ("neurosteroids"), including androgens, which might promote aggression during the non-breeding season. Male song sparrows, Melospiza melodia, are territorial year-round and allow the study of seasonal changes in the steroid modulation of aggression. Here, we quantified steroids following a simulated territorial intrusion (STI) for 10 min in wild adult male song sparrows during the breeding and non-breeding seasons. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we examined 11 steroids: pregnenolone, progesterone, corticosterone, dehydroepiandrosterone, androstenedione, testosterone, 5α-dihydrotestosterone, 17β-estradiol, 17α-estradiol, estriol, and estrone. Steroids were measured in blood and 10 microdissected brain regions that regulate social behavior. In both seasons, STI increased corticosterone in the blood and brain. In the breeding season, STI had no rapid effects on androgens or estrogens. Intriguingly, in the non-breeding season, STI increased testosterone and androstenedione in several behaviorally relevant regions, but not in the blood, where androgens remained non-detectable. Also in the non-breeding season, STI increased progesterone in the blood and specific brain regions. Overall, rapid socially modulated changes in brain steroid levels are more prominent during the non-breeding season. Brain steroid levels vary with season and social context in a region-specific manner and suggest a role for neuroandrogens in aggression during the non-breeding season.
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Affiliation(s)
- Cecilia Jalabert
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Sofia L Gray
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department of Psychology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Kiran K Soma
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department of Psychology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Graduate Program in Neuroscience, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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4
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Molina MA, Leenders WPJ, Huynen MA, Melchers WJG, Andralojc KM. Temporal composition of the cervicovaginal microbiome associates with hrHPV infection outcomes in a longitudinal study. BMC Infect Dis 2024; 24:552. [PMID: 38831406 PMCID: PMC11145797 DOI: 10.1186/s12879-024-09455-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/30/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Persistent infections with high-risk human papillomavirus (hrHPV) can cause cervical squamous intraepithelial lesions (SIL) that may progress to cancer. The cervicovaginal microbiome (CVM) correlates with SIL, but the temporal composition of the CVM after hrHPV infections has not been fully clarified. METHODS To determine the association between the CVM composition and infection outcome, we applied high-resolution microbiome profiling using the circular probe-based RNA sequencing technology on a longitudinal cohort of cervical smears obtained from 141 hrHPV DNA-positive women with normal cytology at first visit, of whom 51 were diagnosed by cytology with SIL six months later. RESULTS Here we show that women with a microbial community characterized by low diversity and high Lactobacillus crispatus abundance at both visits exhibit low risk to SIL development, while women with a microbial community characterized by high diversity and Lactobacillus depletion at first visit have a higher risk of developing SIL. At the level of individual species, we observed that a high abundance for Gardnerella vaginalis and Atopobium vaginae at both visits associate with SIL outcomes. These species together with Dialister micraerophilus showed a moderate discriminatory power for hrHPV infection progression. CONCLUSIONS Our results suggest that the CVM can potentially be used as a biomarker for cervical disease and SIL development after hrHPV infection diagnosis with implications on cervical cancer prevention strategies and treatment of SIL.
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Affiliation(s)
- Mariano A Molina
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands.
| | - Karolina M Andralojc
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
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Arias-Gaguancela O, Herrell E, Chapman KD. Ex vivo lipidomics reveal monoacylglycerols as substrates for a fatty acid amide hydrolase in the legume Medicago truncatula. FEBS Lett 2024. [PMID: 38831473 DOI: 10.1002/1873-3468.14944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/05/2024]
Abstract
Fatty acid amide hydrolase (FAAH) is a conserved hydrolase in eukaryotes with promiscuous activity toward a range of acylamide substrates. The native substrate repertoire for FAAH has just begun to be explored in plant systems outside the model Arabidopsis thaliana. Here, we used ex vivo lipidomics to identify potential endogenous substrates for Medicago truncatula FAAH1 (MtFAAH1). We incubated recombinant MtFAAH1 with lipid mixtures extracted from M. truncatula and resolved their profiles via gas chromatography-mass spectrometry (GC-MS). Data revealed that besides N-acylethanolamines (NAEs), sn-1 or sn-2 isomers of monoacylglycerols (MAGs) were substrates for MtFAAH1. Combined with in vitro and computational approaches, our data support both amidase and esterase activities for MtFAAH1. MAG-mediated hydrolysis via MtFAAH1 may be linked to biological roles that are yet to be discovered.
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Affiliation(s)
- Omar Arias-Gaguancela
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Emily Herrell
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Kent D Chapman
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, USA
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Sadova N, Blank-Landeshammer B, Curic D, Iken M, Weghuber J. Sex-specific pharmacokinetic response to phytoestrogens in Drosophila melanogaster. Biomed Pharmacother 2024; 175:116612. [PMID: 38663102 DOI: 10.1016/j.biopha.2024.116612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 06/03/2024] Open
Abstract
Drosophila melanogaster, or the fruit fly, is widely used for modeling numerous human diseases, such as neurodegeneration, tumor development, cachexia, and intestinal dysfunction. It is a suitable model organism for research targeting the physiology and pathophysiology of the intestinal epithelial barrier and has also been used as a model organism for preliminary drug and bioactive nutrient screening. However, the application of D. melanogaster in research on drug bioavailability and pharmacokinetic properties has not yet been well explored. In this study, we applied D. melanogaster to investigate the absorption and excretion of the orally administered phytoestrogens daidzein, glycitein, genistein, and their glycosides. Therefore, we established a quick, noninvasive method to quantify compound retention in D. melanogaster, suitable for the investigation of a broad variety of potentially bioactive substances. We showed that fruit fly sex plays a key role in the metabolization, transportation, and excretion of phytoestrogenic isoflavones. In particular, female fruit flies retained significantly more isoflavones than male fruit flies, which was reflected in the greater metabolic impact of isoflavones on females. Male fruit flies excreted more isoflavones than females did, which was linked to the upregulation of the xenobiotic transporter gene Mdr50. We also demonstrated that micellized isoflavones were more bioavailable than powdered isoflavones, independent of sex, age or the addition of dietary fibers.
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Affiliation(s)
- Nadiia Sadova
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels 4600, Austria
| | - Bernhard Blank-Landeshammer
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels 4600, Austria; FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, Tulln 3430, Austria
| | - David Curic
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels 4600, Austria
| | - Marcus Iken
- PM International AG, Schengen, Luxembourg 5445, Luxembourg
| | - Julian Weghuber
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels 4600, Austria; FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, Tulln 3430, Austria.
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7
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Sanmartín G, Sánchez-Adriá IE, Prieto JA, Estruch F, Randez-Gil F. Bioprospecting of sourdough microbial species from artisan bakeries in the city of Valencia. Food Microbiol 2024; 120:104474. [PMID: 38431320 DOI: 10.1016/j.fm.2024.104474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 03/05/2024]
Abstract
This work describes the characterization of an artisanal sourdough set of bakeries located in the city of Valencia. Culture-dependent and -independent analyses detected Fructilactobacillus sanfranciscensis, Saccharomyces cerevisiae and Kazachstania humilis as dominant species. Nevertheless, specific technological parameters, including backslopping temperature, dough yield, or the addition of salt affected microbial counting, LAB/Yeast ratio, and gassing performance, favouring the appearance of several species of Lactobacillus sp., Limosilactobacillus pontis or Torulaspora delbrueckii as additional players. Sourdough leavening activity was affected positively by yeast counts and negatively by the presence of salt. In addition, the predominance of a particular yeast species appeared to impact the dynamics of CO2 release. Seven important flavour-active compounds (ethyl acetate, 1-hexanol, 2-penthylfuran, 3-ethyl-2-methyl-1,3-hexadiene, 2-octen-1-ol, nonanal and 1-nonanol) were detected in all samples and together with 3-methyl butanol and hexyl acetate represented more than the 53% of volatile abundancy in nine of the ten sourdoughs analysed. Even so, the specific microbial composition of each sample influenced the volatile profile. For example, the occurrence of K. humilis or S. cerevisiae as dominant yeast influenced the composition of major alcohol species, while F. sanfranciscensis and L. pontis positively correlated with aldehydes and octanoic acid content. In addition, relevant correlations could be also found among different technological parameters and between these, volatile compounds and microbial species. Overall, our study emphasises on how differences in technological parameters generate biodiversity in a relatively small set of artisan sourdoughs providing opportunities for excellence and quality baking products.
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Affiliation(s)
- Gemma Sanmartín
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de Los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980, Paterna, Valencia, Spain
| | - Isabel E Sánchez-Adriá
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de Los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980, Paterna, Valencia, Spain
| | - Jose A Prieto
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de Los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980, Paterna, Valencia, Spain
| | - Francisco Estruch
- Department of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, 46100, Burjassot, Spain
| | - Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de Los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980, Paterna, Valencia, Spain.
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Tieghi H, Pereira LDA, Viana GS, Katchborian-Neto A, Santana DB, Mincato RL, Dias DF, Chagas-Paula DA, Soares MG, de Araújo WG, Bueno PCP. Effects of geographical origin and post-harvesting processing on the bioactive compounds and sensory quality of Brazilian specialty coffee beans. Food Res Int 2024; 186:114346. [PMID: 38729720 DOI: 10.1016/j.foodres.2024.114346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/02/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Specialty coffee beans are those produced, processed, and characterized following the highest quality standards, toward delivering a superior final product. Environmental, climatic, genetic, and processing factors greatly influence the green beans' chemical profile, which reflects on the quality and pricing. The present study focuses on the assessment of eight major health-beneficial bioactive compounds in green coffee beans aiming to underscore the influence of the geographical origin and post-harvesting processing on the quality of the final beverage. For that, we examined the non-volatile chemical profile of specialty Coffea arabica beans from Minas Gerais state, Brazil. It included samples from Cerrado (Savannah), and Matas de Minas and Sul de Minas (Atlantic Forest) regions, produced by two post-harvesting processing practices. Trigonelline, theobromine, theophylline, chlorogenic acid derivatives, caffeine, caffeic acid, ferulic acid, and p-coumaric acid were quantified in the green beans by high-performance liquid chromatography with diode array detection. Additionally, all samples were roasted and subjected to sensory analysis for coffee grading. Principal component analysis suggested that Cerrado samples tended to set apart from the other geographical locations. Those samples also exhibited higher levels of trigonelline as confirmed by two-way ANOVA analysis. Samples subjected to de-pulping processing showed improved chemical composition and sensory score. Those pulped coffees displayed 5.8% more chlorogenic acid derivatives, with an enhancement of 1.5% in the sensory score compared to unprocessed counterparts. Multivariate logistic regression analysis pointed out altitude, ferulic acid, p-coumaric acid, sweetness, and acidity as predictors distinguishing specialty coffee beans obtained by the two post-harvest processing. These findings demonstrate the influence of regional growth conditions and post-harvest treatments on the chemical and sensory quality of coffee. In summary, the present study underscores the value of integrating target metabolite analysis with statistical tools to augment the characterization of specialty coffee beans, offering novel insights for quality assessment with a focus on their bioactive compounds.
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Affiliation(s)
- Heloísa Tieghi
- Institute of Chemistry, Federal University of Alfenas. R. Gabriel Monteiro da Silva 700, 37130-001 Alfenas, MG, Brazil.
| | - Luana de Almeida Pereira
- Institute of Chemistry, Federal University of Alfenas. R. Gabriel Monteiro da Silva 700, 37130-001 Alfenas, MG, Brazil.
| | - Gabriel Silva Viana
- Institute of Chemistry, Federal University of Alfenas. R. Gabriel Monteiro da Silva 700, 37130-001 Alfenas, MG, Brazil.
| | - Albert Katchborian-Neto
- Institute of Chemistry, Federal University of Alfenas. R. Gabriel Monteiro da Silva 700, 37130-001 Alfenas, MG, Brazil.
| | - Derielsen Brandão Santana
- Institute of Natural Sciences, Federal University of Alfenas. R. Gabriel Monteiro da Silva 700, 37130-001 Alfenas, MG, Brazil.
| | - Ronaldo Luiz Mincato
- Institute of Natural Sciences, Federal University of Alfenas. R. Gabriel Monteiro da Silva 700, 37130-001 Alfenas, MG, Brazil.
| | - Danielle Ferreira Dias
- Institute of Chemistry, Federal University of Alfenas. R. Gabriel Monteiro da Silva 700, 37130-001 Alfenas, MG, Brazil.
| | | | - Marisi Gomes Soares
- Institute of Chemistry, Federal University of Alfenas. R. Gabriel Monteiro da Silva 700, 37130-001 Alfenas, MG, Brazil.
| | - Willem Guilherme de Araújo
- Technical Assistance and Rural Extension Company of Minas Gerais State, EMATER-MG, Belo Horizonte/MG, Brazil.
| | - Paula Carolina Pires Bueno
- Institute of Chemistry, Federal University of Alfenas. R. Gabriel Monteiro da Silva 700, 37130-001 Alfenas, MG, Brazil; Leibniz Institute of Vegetable and Ornamental Crops, IGZ. Theodor-Echermeyer-Weg 1, 14979 Großbeeren, Germany.
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9
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Leuti A, Fava M, Forte G, Pellegrini N, Oddi S, Scipioni L, Gomez EA, Dalli J, Maccarrone M. The endocannabinoid anandamide activates pro-resolving pathways in human primary macrophages by engaging both CB 2 and GPR18 receptors. FASEB J 2024; 38:e23675. [PMID: 38801406 DOI: 10.1096/fj.202301325r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
Resolution of inflammation is the cellular and molecular process that protects from widespread and uncontrolled inflammation and restores tissue function in the aftermath of acute immune events. This process is orchestrated by specialized pro-resolving mediators (SPM), a class of bioactive lipids able to reduce immune activation and promote removal of tissue debris and apoptotic cells by macrophages. Although SPMs are the lipid class that has been best studied for its role in facilitating the resolution of self-limited inflammation, a number of other lipid signals, including endocannabinoids, also exert protective immunomodulatory effects on immune cells, including macrophages. These observations suggest that endocannabinoids may also display pro-resolving actions. Interestingly, the endocannabinoid anandamide (AEA) is not only known to bind canonical type 1 and type 2 cannabinoid receptors (CB1 and CB2) but also to engage SPM-binding receptors such as GPR18. This suggests that AEA may also contribute to the governing of resolution processes. In order to interrogate this hypothesis, we investigated the ability of AEA to induce pro-resolving responses by classically-activated primary human monocyte-derived macrophages (MoDM). We found that AEA, at nanomolar concentration, enhances efferocytosis in MoDMs in a CB2- and GPR18-dependent manner. Using lipid mediator profiling, we also observed that AEA modulates SPM profiles in these cells, including levels of resolvin (Rv)D1, RvD6, maresin (MaR)2, and RvE1 in a CB2-dependent manner. AEA treatment also modulated the gene expression of SPM enzymes involved in both the formation and further metabolism of SPM such as 5-lipoxygenase and 15-Prostaglandin dehydrogenase. Our findings show, for the first time, a direct effect of AEA on the regulation of pro-resolving pathways in human macrophages. They also provide new insights into the complex interactions between different lipid pathways in activation of pro-resolving responses contributing to the reestablishment of homeostasis in the aftermath of acute inflammation.
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Affiliation(s)
- Alessandro Leuti
- Department of Medicine, Campus Bio-Medico University of Rome, Rome, Italy
- European Center for Brain Research/Institute for Research and Health Care (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Marina Fava
- European Center for Brain Research/Institute for Research and Health Care (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Giulia Forte
- Department of Medicine, Campus Bio-Medico University of Rome, Rome, Italy
| | - Niccolò Pellegrini
- Department of Medicine, Campus Bio-Medico University of Rome, Rome, Italy
| | - Sergio Oddi
- European Center for Brain Research/Institute for Research and Health Care (IRCCS) Santa Lucia Foundation, Rome, Italy
- Department of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Lucia Scipioni
- European Center for Brain Research/Institute for Research and Health Care (IRCCS) Santa Lucia Foundation, Rome, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Esteban A Gomez
- Centre for Inflammation and Therapeutic Innovation, Queen Mary University of London, London, UK
| | - Jesmond Dalli
- Centre for Inflammation and Therapeutic Innovation, Queen Mary University of London, London, UK
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Mauro Maccarrone
- European Center for Brain Research/Institute for Research and Health Care (IRCCS) Santa Lucia Foundation, Rome, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
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10
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Ye Q, Jo J, Wang CY, Oh H, Zhan J, Choy TJ, Kim KI, D'Alessandro A, Reshetnyak YK, Jung SY, Chen Z, Marrelli SP, Lee HK. Astrocytic Slc4a4 regulates blood-brain barrier integrity in healthy and stroke brains via a CCL2-CCR2 pathway and NO dysregulation. Cell Rep 2024; 43:114193. [PMID: 38709635 DOI: 10.1016/j.celrep.2024.114193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/11/2024] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Astrocytes play vital roles in blood-brain barrier (BBB) maintenance, yet how they support BBB integrity under normal or pathological conditions remains poorly defined. Recent evidence suggests that ion homeostasis is a cellular mechanism important for BBB integrity. In the current study, we investigated the function of an astrocyte-specific pH regulator, Slc4a4, in BBB maintenance and repair. We show that astrocytic Slc4a4 is required for normal astrocyte morphological complexity and BBB function. Multi-omics analyses identified increased astrocytic secretion of CCL2 coupled with dysregulated arginine-NO metabolism after Slc4a4 deletion. Using a model of ischemic stroke, we found that loss of Slc4a4 exacerbates BBB disruption, which was rescued by pharmacological or genetic inhibition of the CCL2-CCR2 pathway in vivo. Together, our study identifies the astrocytic Slc4a4-CCL2 and endothelial CCR2 axis as a mechanism controlling BBB integrity and repair, while providing insights for a therapeutic approach against BBB-related CNS disorders.
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Affiliation(s)
- Qi Ye
- Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Juyeon Jo
- Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Chih-Yen Wang
- Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 70101, Taiwan
| | - Heavin Oh
- Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Jiangshan Zhan
- Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Tiffany J Choy
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Cancer and Cell Biology Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyoung In Kim
- Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 77030, USA
| | - Yana K Reshetnyak
- Physics Department, University of Rhode Island, Kingston, RI 02881, USA
| | - Sung Yun Jung
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Sean P Marrelli
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hyun Kyoung Lee
- Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Cancer and Cell Biology Program, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
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11
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Huang T, Zhu Y, Shutta KH, Balasubramanian R, Zeleznik OA, Rexrode KM, Clish CB, Sun Q, Hu FB, Kubzansky LD, Hankinson SE. A Plasma Metabolite Score Related to Psychological Distress and Diabetes Risk: A Nested Case-control Study in US Women. J Clin Endocrinol Metab 2024; 109:e1434-e1441. [PMID: 38092374 DOI: 10.1210/clinem/dgad731] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Indexed: 05/18/2024]
Abstract
CONTEXT Psychological distress has been linked to diabetes risk. Few population-based, epidemiologic studies have investigated the potential molecular mechanisms (eg, metabolic dysregulation) underlying this association. OBJECTIVE To evaluate the association between a metabolomic signature for psychological distress and diabetes risk. METHODS We conducted a nested case-control study of plasma metabolomics and diabetes risk in the Nurses' Health Study, including 728 women (mean age: 55.2 years) with incident diabetes and 728 matched controls. Blood samples were collected between 1989 and 1990 and incident diabetes was diagnosed between 1992 and 2008. Based on our prior work, we calculated a weighted plasma metabolite-based distress score (MDS) comprised of 19 metabolites. We used conditional logistic regression accounting for matching factors and other diabetes risk factors to estimate odds ratios (OR) and 95% confidence intervals (CI) for diabetes risk according to MDS. RESULTS After adjusting for sociodemographic factors, family history of diabetes, and health behaviors, the OR (95% CI) for diabetes risk across quintiles of the MDS was 1.00 (reference) for Q1, 1.16 (0.77, 1.73) for Q2, 1.30 (0.88, 1.91) for Q3, 1.99 (1.36, 2.92) for Q4, and 2.47 (1.66, 3.67) for Q5. Each SD increase in MDS was associated with 36% higher diabetes risk (95% CI: 1.21, 1.54; P-trend <.0001). This association was moderately attenuated after additional adjustment for body mass index (comparable OR: 1.17; 95% CI: 1.02, 1.35; P-trend = .02). The MDS explained 17.6% of the association between self-reported psychological distress (defined as presence of depression or anxiety symptoms) and diabetes risk (P = .04). CONCLUSION MDS was significantly associated with diabetes risk in women. These results suggest that differences in multiple lipid and amino acid metabolites may underlie the observed association between psychological distress and diabetes risk.
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Affiliation(s)
- Tianyi Huang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Yiwen Zhu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Katherine H Shutta
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Raji Balasubramanian
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Oana A Zeleznik
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kathryn M Rexrode
- Division of Women's Health, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Boston, MA 02142, USA
| | - Qi Sun
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Frank B Hu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Laura D Kubzansky
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Susan E Hankinson
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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12
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He T, Xiong L, Lin K, Yi J, Duan C, Zhang J. Functional metabolomics reveals arsenic-induced inhibition of linoleic acid metabolism in mice kidney in drinking water. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123949. [PMID: 38636836 DOI: 10.1016/j.envpol.2024.123949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/27/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024]
Abstract
Arsenic (As) is a heavy metal known for its detrimental effects on the kidneys, but the precise mechanisms underlying its toxicity remain unclear. In this study, we employed an integrated approach combining traditional toxicology methods with functional metabolomics to explore the nephrotoxicity induced by As in mice. Our findings demonstrated that after 28 days of exposure to sodium arsenite, blood urea nitrogen, serum creatinine levels were significantly increased, and pathological examination of the kidneys revealed dilation of renal tubules and glomerular injury. Additionally, uric acid, total cholesterol, and low-density lipoprotein cholesterol levels were significant increased while triglyceride level was decreased, resulting in renal insufficiency and lipid disorders. Subsequently, the kidney metabolomics analysis revealed that As exposure disrupted 24 differential metabolites, including 14 up-regulated and 10 down-regulated differential metabolites. Ten metabolic pathways including linoleic acid and glycerophospholipid metabolism were significantly enriched. Then, 80 metabolic targets and 168 predicted targets were identified using metabolite network pharmacology analysis. Of particular importance, potential toxicity targets, such as glycine amidinotransferase, mitochondrial (GATM), and nitric oxide synthase, and endothelial (NOS3), were prioritized through the "metabolite-target-pathway" network. Receiver operating characteristics curve and molecular docking analyses suggested that 1-palmitoyl-2-myristoyl-sn-glycero-3-PC, linoleic acid, and L-hydroxyarginine might be functional metabolites associated with GATM and NOS3. Moreover, targeted verification result showed that the level of linoleic acid in As group was 0.4951 μg/mL, which was significantly decreased compared with the control group. And in vivo and in vitro protein expression experiments confirmed that As exposure inhibited the expression of GATM and NOS3. In conclusion, these results suggest that As-induced renal injury may be associated with the inhibition of linoleic acid metabolism through the down-regulation of GATM and NOS3, resulting in decreased levels of linoleic acid, 1-palmitoyl-2-myristoyl-sn-glycero-3-PC, and L-hydroxyarginine metabolites.
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Affiliation(s)
- Tianmu He
- School of Basic Medicine, Zunyi Medical University, Zunyi, 563000, China; School of Basic Medicine, Guizhou Medical University, Guiyang, 550025, China.
| | - Lijuan Xiong
- School of Pharmacy and Key Laboratory of Basic Pharmacology Ministry Education and Joint International Research Laboratory of Ethnomedicine Ministry of Education, Zunyi Medical University, Zunyi, 563000, China
| | - Kexin Lin
- School of Basic Medicine, Zunyi Medical University, Zunyi, 563000, China
| | - Jing Yi
- School of Basic Medicine, Zunyi Medical University, Zunyi, 563000, China
| | - Cancan Duan
- School of Pharmacy and Key Laboratory of Basic Pharmacology Ministry Education and Joint International Research Laboratory of Ethnomedicine Ministry of Education, Zunyi Medical University, Zunyi, 563000, China.
| | - Jianyong Zhang
- School of Pharmacy and Key Laboratory of Basic Pharmacology Ministry Education and Joint International Research Laboratory of Ethnomedicine Ministry of Education, Zunyi Medical University, Zunyi, 563000, China.
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13
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Uddin J, Yasmin S, Kamal GM, Asmari M, Saqib M, Chen H. Changes in Metabolite Profiles of Chinese Soy Sauce at Different Time Durations of Fermentation Studied by 1H-NMR-Based Metabolomics. Metabolites 2024; 14:285. [PMID: 38786762 PMCID: PMC11123076 DOI: 10.3390/metabo14050285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Fermentation parameters, especially the duration, are important in imparting a peculiar taste and flavor to soy sauce. The main purpose of this research was to monitor metabolic changes occurring during the various time intervals of the fermentation process. NMR-based metabolomics was used to monitor the compositional changes in soy sauce during fermentation. The 1H-NMR spectra of the soy sauce samples taken from the fermentation tanks at 0 to 8 months were analyzed using 1H-NMR spectroscopy, and the obtained spectra were analyzed by multivariate statistical analysis. The Principal Component Analysis (PCA) and Partial Least Square Discriminate analysis (PLSDA) revealed the separation of samples fermented for various time durations under identical conditions. Key metabolites shown by corresponding loading plots exhibited variations in amino acids (lysine, threonine, isoleucine, etc.), acetate, glucose, fructose, sucrose, ethanol, glycerol, and others. The levels of ethanol in soy sauce increased with longer fermentation durations, which can be influenced by both natural fermentation and the intentional addition of ethanol as a preservative. The study shows that the variation in metabolite can be very efficiently monitored using 1H-NMR-based metabolomics, thus suggestion to optimize the time duration to get the soy sauce product with the desired taste and flavor.
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Affiliation(s)
- Jalal Uddin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha 61441, Saudi Arabia
| | - Samra Yasmin
- Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
| | - Ghulam Mustafa Kamal
- Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
- Innovation Academy of Precision Measurement Science & Technology, University of Chinese Academy of Sciences Beijing, Wuhan 430071, China
| | - Mufarreh Asmari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha 61441, Saudi Arabia
| | - Muhammad Saqib
- Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
| | - Heyu Chen
- College of Mechanical and Electronic Engineering, Northwest A&F University, Xianyang 712100, China
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14
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Wang Y, Shen Y, Li Q, Xu H, Gao A, Li K, Rong Y, Gao S, Liang H, Zhang X. Exploring the causal association between genetically determined circulating metabolome and hemorrhagic stroke. Front Nutr 2024; 11:1376889. [PMID: 38812939 PMCID: PMC11133746 DOI: 10.3389/fnut.2024.1376889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024] Open
Abstract
Background Hemorrhagic stroke (HS), a leading cause of death and disability worldwide, has not been clarified in terms of the underlying biomolecular mechanisms of its development. Circulating metabolites have been closely associated with HS in recent years. Therefore, we explored the causal association between circulating metabolomes and HS using Mendelian randomization (MR) analysis and identified the molecular mechanisms of effects. Methods We assessed the causal relationship between circulating serum metabolites (CSMs) and HS using a bidirectional two-sample MR method supplemented with five ways: weighted median, MR Egger, simple mode, weighted mode, and MR-PRESSO. The Cochran Q-test, MR-Egger intercept test, and MR-PRESSO served for the sensitivity analyses. The Steiger test and reverse MR were used to estimate reverse causality. Metabolic pathway analyses were performed using MetaboAnalyst 5.0, and genetic effects were assessed by linkage disequilibrium score regression. Significant metabolites were further synthesized using meta-analysis, and we used multivariate MR to correct for common confounders. Results We finally recognized four metabolites, biliverdin (OR 0.62, 95% CI 0.40-0.96, PMVMR = 0.030), linoleate (18. 2n6) (OR 0.20, 95% CI 0.08-0.54, PMVMR = 0.001),1-eicosadienoylglycerophosphocholine* (OR 2.21, 95% CI 1.02-4.76, PMVMR = 0.044),7-alpha-hydroxy-3 -oxo-4-cholestenoate (7-Hoca) (OR 0.27, 95% CI 0.09-0.77, PMVMR = 0.015) with significant causal relation to HS. Conclusion We demonstrated significant causal associations between circulating serum metabolites and hemorrhagic stroke. Monitoring, diagnosis, and treatment of hemorrhagic stroke by serum metabolites might be a valuable approach.
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Affiliation(s)
- Yaolou Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yingjie Shen
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Qi Li
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Hangjia Xu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Aili Gao
- School of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Kuo Li
- School of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yiwei Rong
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Shang Gao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongsheng Liang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- NHC Key Laboratory of Cell Transplantation, Harbin, Heilongjiang, China
| | - Xiangtong Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- NHC Key Laboratory of Cell Transplantation, Harbin, Heilongjiang, China
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15
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Londoño-Osorio S, Leon-Carreño L, Cala MP, Sierra-Zapata L. The gut metabolome in a cohort of pregnant and lactating women from Antioquia-Colombia. Front Mol Biosci 2024; 11:1250413. [PMID: 38803424 PMCID: PMC11128665 DOI: 10.3389/fmolb.2024.1250413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/20/2024] [Indexed: 05/29/2024] Open
Abstract
Nutrition during the perinatal period is an essential component of health and one that can severely impact the correct development of a human being and its overall condition, in all the subsequent stages of life. The availability of several compounds, mainly macronutrients and micronutrients, plays a key role in the balanced nutrition of both mother and baby and is a process with direct relation to the gut microbiome. Thus, we hereby refer to the set of small molecules derived from gut microbiome metabolism as the gut metabolome. These continuous processes occurring in the gut of a gestating or lactating mother related to microbial communities and nutrients, can be revealed by metabolomics. In this study, we explore for the first time the gut metabolome of pregnant and lactating women, from our region of Antioquia-Colombia, applying untargeted metabolomics by LC-QTOF-MS, and molecular networking. Regarding the gut metabolome composition of the cohort, we found, key metabolites that can be used as biomarkers of microbiome function, overall metabolic health, dietary intake, pharmacology, and lifestyle. In our cohort, pregnant women evidenced a significantly higher abundance of prostaglandins, alkaloids, corticosteroids, organosilicons, and natural toxins, while in lactating women, lipids stand out. Our results suggest that unveiling the metabolic phenotype of the gut microbiome of an individual, by untargeted metabolomics, allows a broad visualization of the chemical space present in this important niche and enables the recognition of influential indicators of the host's health status and habits, especially of women during this significant perinatal period. This study constitutes the first evidence of the use of untargeted LC-QTOF-MS coupled with molecular networking analysis, of the gut microbiome in a Colombian cohort and establishes a methodology for finding relative abundances of key metabolites, with potential use in nutritional and physiological state assessments, for future personalized health and nutrition practices.
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Affiliation(s)
- Sara Londoño-Osorio
- CIBIOP Research Group, School of Applied Sciences and Engineering, Universidad EAFIT, Medellín, Colombia
| | - Lizeth Leon-Carreño
- MetCore–Metabolomics Core Facility, Vice-Presidency for Research, Universidad de Los Andes, Bogotá, Colombia
| | - Mónica P. Cala
- MetCore–Metabolomics Core Facility, Vice-Presidency for Research, Universidad de Los Andes, Bogotá, Colombia
| | - Laura Sierra-Zapata
- CIBIOP Research Group, School of Applied Sciences and Engineering, Universidad EAFIT, Medellín, Colombia
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16
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Knuth MM, Xue J, Elnagheeb M, Gharaibeh RZ, Schoenrock SA, McRitchie S, Brouwer C, Sumner SJ, Tarantino L, Valdar W, Rector RS, Simon JM, Ideraabdullah F. Early life exposure to vitamin D deficiency impairs molecular mechanisms that regulate liver cholesterol biosynthesis, energy metabolism, inflammation, and detoxification. Front Endocrinol (Lausanne) 2024; 15:1335855. [PMID: 38800476 PMCID: PMC11116800 DOI: 10.3389/fendo.2024.1335855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Emerging data suggests liver disease may be initiated during development when there is high genome plasticity and the molecular pathways supporting liver function are being developed. Methods Here, we leveraged our Collaborative Cross mouse model of developmental vitamin D deficiency (DVD) to investigate the role of DVD in dysregulating the molecular mechanisms underlying liver disease. We defined the effects on the adult liver transcriptome and metabolome and examined the role of epigenetic dysregulation. Given that the parental origin of the genome (POG) influences response to DVD, we used our established POG model [POG1-(CC011xCC001)F1 and POG2-(CC001xCC011)F1] to identify interindividual differences. Results We found that DVD altered the adult liver transcriptome, primarily downregulating genes controlling liver development, response to injury/infection (detoxification & inflammation), cholesterol biosynthesis, and energy production. In concordance with these transcriptional changes, we found that DVD decreased liver cell membrane-associated lipids (including cholesterol) and pentose phosphate pathway metabolites. Each POG also exhibited distinct responses. POG1 exhibited almost 2X more differentially expressed genes (DEGs) with effects indicative of increased energy utilization. This included upregulation of lipid and amino acid metabolism genes and increased intermediate lipid and amino acid metabolites, increased energy cofactors, and decreased energy substrates. POG2 exhibited broader downregulation of cholesterol biosynthesis genes with a metabolomics profile indicative of decreased energy utilization. Although DVD primarily caused loss of liver DNA methylation for both POGs, only one epimutation was shared, and POG2 had 6.5X more differentially methylated genes. Differential methylation was detected at DEGs regulating developmental processes such as amino acid transport (POG1) and cell growth & differentiation (e.g., Wnt & cadherin signaling, POG2). Conclusions These findings implicate a novel role for maternal vitamin D in programming essential offspring liver functions that are dysregulated in liver disease. Importantly, impairment of these processes was not rescued by vitamin D treatment at weaning, suggesting these effects require preventative measures. Substantial differences in POG response to DVD demonstrate that the parental genomic context of exposure determines offspring susceptibility.
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Affiliation(s)
- Megan M. Knuth
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jing Xue
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
| | - Marwa Elnagheeb
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Raad Z. Gharaibeh
- Department of Medicine, Division of Gastroenterology, University of Florida, Gainesville, FL, United States
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, United States
| | - Sarah A. Schoenrock
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Susan McRitchie
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
| | - Cory Brouwer
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
- University of North Carolina at Charlotte Bioinformatics Service Division, North Carolina Research Campus, Kannapolis, NC, United States
| | - Susan J. Sumner
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lisa Tarantino
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Psychiatry, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - William Valdar
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - R. Scott Rector
- Research Service, Harry S. Truman Memorial Veterans Medical Center, Columbia, MO, United States
- NextGen Precision Health, University of Missouri, Columbia, MO, United States
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, MO, United States
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, MO, United States
| | - Jeremy M. Simon
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Neuroscience Center Bioinformatics Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Folami Ideraabdullah
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Solosky AM, Claudio IM, Chappel JR, Kirkwood-Donelson KI, Janech MG, Bland AM, Gulland FMD, Neely BA, Baker ES. Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592757. [PMID: 38766156 PMCID: PMC11100735 DOI: 10.1101/2024.05.06.592757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Domoic acid is a neurotoxin secreted by the marine diatom genus, Pseudo-nitzschia, during toxic algal bloom events. California sea lions ( Zalophus californianus ) are exposed to domoic acid through ingestion of fish that feed on toxic diatoms, resulting in a domoic acid toxicosis (DAT), which can vary from mild to fatal. Sea lions with mild disease can be treated if toxicosis is detected early after exposure, therefore, rapid diagnosis of DAT is essential but also challenging. In this work, we performed multi-omics analyses, specifically proteomic and lipidomic, on blood samples from 31 California sea lions. Fourteen sea lions were diagnosed with DAT based on clinical signs and postmortem histological examination of brain tissue, and 17 had no evidence of DAT. Proteomic analyses revealed three apolipoproteins with statistically significant lower abundance in the DAT individuals compared to the non-DAT individuals. These proteins are known to transport lipids in the blood. Lipidomic analyses highlighted 29 lipid levels that were statistically different in the DAT versus non-DAT comparison, 28 of which were downregulated while only one was upregulated. Furthermore, of the 28 downregulated lipids, 15 were triglycerides, illustrating their connection with the perturbed apolipoproteins and showing their potential for use in rapid DAT diagnoses. SYNOPSIS Multi-omics evaluations reveal blood apolipoproteins and triglycerides are altered in domoic acid toxicosis in California sea lions.
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18
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Arora C, Matic M, Bisceglia L, Di Chiaro P, De Oliveira Rosa N, Carli F, Clubb L, Nemati Fard LA, Kargas G, Diaferia GR, Vukotic R, Licata L, Wu G, Natoli G, Gutkind JS, Raimondi F. The landscape of cancer-rewired GPCR signaling axes. CELL GENOMICS 2024; 4:100557. [PMID: 38723607 PMCID: PMC11099383 DOI: 10.1016/j.xgen.2024.100557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 02/17/2024] [Accepted: 04/10/2024] [Indexed: 05/15/2024]
Abstract
We explored the dysregulation of G-protein-coupled receptor (GPCR) ligand systems in cancer transcriptomics datasets to uncover new therapeutics opportunities in oncology. We derived an interaction network of receptors with ligands and their biosynthetic enzymes. Multiple GPCRs are differentially regulated together with their upstream partners across cancer subtypes and are associated to specific transcriptional programs and to patient survival patterns. The expression of both receptor-ligand (or enzymes) partners improved patient stratification, suggesting a synergistic role for the activation of GPCR networks in modulating cancer phenotypes. Remarkably, we identified many such axes across several cancer molecular subtypes, including many involving receptor-biosynthetic enzymes for neurotransmitters. We found that GPCRs from these actionable axes, including, e.g., muscarinic, adenosine, 5-hydroxytryptamine, and chemokine receptors, are the targets of multiple drugs displaying anti-growth effects in large-scale, cancer cell drug screens, which we further validated. We have made the results generated in this study freely available through a webapp (gpcrcanceraxes.bioinfolab.sns.it).
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Affiliation(s)
- Chakit Arora
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marin Matic
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Luisa Bisceglia
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Pierluigi Di Chiaro
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Natalia De Oliveira Rosa
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Francesco Carli
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Lauren Clubb
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lorenzo Amir Nemati Fard
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giorgos Kargas
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giuseppe R Diaferia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - Ranka Vukotic
- Azienda Ospedaliero-Universitaria Pisana, Via Roma, 67, 56126 Pisa, Italy
| | - Luana Licata
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Guanming Wu
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy
| | - J Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Francesco Raimondi
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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19
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Lahiri SK, Jin F, Zhou Y, Quick AP, Kramm CF, Wang MC, Wehrens XH. Altered myocardial lipid regulation in junctophilin-2-associated familial cardiomyopathies. Life Sci Alliance 2024; 7:e202302330. [PMID: 38438248 PMCID: PMC10912815 DOI: 10.26508/lsa.202302330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/06/2024] Open
Abstract
Myocardial lipid metabolism is critical to normal heart function, whereas altered lipid regulation has been linked to cardiac diseases including cardiomyopathies. Genetic variants in the JPH2 gene can cause hypertrophic cardiomyopathy (HCM) and, in some cases, dilated cardiomyopathy (DCM). In this study, we tested the hypothesis that JPH2 variants identified in patients with HCM and DCM, respectively, cause distinct alterations in myocardial lipid profiles. Echocardiography revealed clinically significant cardiac dysfunction in both knock-in mouse models of cardiomyopathy. Unbiased myocardial lipidomic analysis demonstrated significantly reduced levels of total unsaturated fatty acids, ceramides, and various phospholipids in both mice with HCM and DCM, suggesting a common metabolic alteration in both models. On the contrary, significantly increased di- and triglycerides, and decreased co-enzyme were only found in mice with HCM. Moreover, mice with DCM uniquely exhibited elevated levels of cholesterol ester. Further in-depth analysis revealed significantly altered metabolites from all the lipid classes with either similar or opposing trends in JPH2 mutant mice with HCM or DCM. Together, these studies revealed, for the first time, unique alterations in the cardiac lipid composition-including distinct increases in neutral lipids and decreases in polar membrane lipids-in mice with HCM and DCM were caused by distinct JPH2 variants. These studies may aid the development of novel biomarkers or therapeutics for these inherited disorders.
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Affiliation(s)
- Satadru K Lahiri
- https://ror.org/02pttbw34 Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Feng Jin
- https://ror.org/02pttbw34 Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yue Zhou
- https://ror.org/02pttbw34 Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Ann P Quick
- https://ror.org/02pttbw34 Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Carlos F Kramm
- https://ror.org/02pttbw34 Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Meng C Wang
- https://ror.org/02pttbw34 Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA
| | - Xander Ht Wehrens
- https://ror.org/02pttbw34 Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Center for Space Medicine, Baylor College of Medicine, Houston, TX, USA
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20
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Pang Z, Xu L, Viau C, Lu Y, Salavati R, Basu N, Xia J. MetaboAnalystR 4.0: a unified LC-MS workflow for global metabolomics. Nat Commun 2024; 15:3675. [PMID: 38693118 PMCID: PMC11063062 DOI: 10.1038/s41467-024-48009-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 04/18/2024] [Indexed: 05/03/2024] Open
Abstract
The wide applications of liquid chromatography - mass spectrometry (LC-MS) in untargeted metabolomics demand an easy-to-use, comprehensive computational workflow to support efficient and reproducible data analysis. However, current tools were primarily developed to perform specific tasks in LC-MS based metabolomics data analysis. Here we introduce MetaboAnalystR 4.0 as a streamlined pipeline covering raw spectra processing, compound identification, statistical analysis, and functional interpretation. The key features of MetaboAnalystR 4.0 includes an auto-optimized feature detection and quantification algorithm for LC-MS1 spectra processing, efficient MS2 spectra deconvolution and compound identification for data-dependent or data-independent acquisition, and more accurate functional interpretation through integrated spectral annotation. Comprehensive validation studies using LC-MS1 and MS2 spectra obtained from standards mixtures, dilution series and clinical metabolomics samples have shown its excellent performance across a wide range of common tasks such as peak picking, spectral deconvolution, and compound identification with good computing efficiency. Together with its existing statistical analysis utilities, MetaboAnalystR 4.0 represents a significant step toward a unified, end-to-end workflow for LC-MS based global metabolomics in the open-source R environment.
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Affiliation(s)
- Zhiqiang Pang
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Lei Xu
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Charles Viau
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Yao Lu
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Reza Salavati
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada.
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
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21
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Yazdanpanah M, Cameron J, Chappel C, Yuan L. Primary Hyperoxaluria Screening and Monitoring: Quantitative Measurement of Plasma Oxalate by Gas Chromatography-Mass Spectrometry With High Sensitivity. Ann Lab Med 2024; 44:235-244. [PMID: 37904578 PMCID: PMC10813830 DOI: 10.3343/alm.2023.0178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/17/2023] [Accepted: 09/14/2023] [Indexed: 11/01/2023] Open
Abstract
Background Plasma oxalate measurements can be used for the screening and therapeutic monitoring of primary hyperoxaluria. We developed a gas chromatography-mass spectrometry (GC-MS) assay for plasma oxalate measurements with high sensitivity and suitable testing volumes for pediatric populations. Methods Plasma oxalate was extracted, derivatized, and analyzed by GC-MS. We measured the ion at m/z 261.10 to quantify oxalate and the 13C2-oxalate ion (m/z: 263.15) as the internal standard. Method validation included determination of the linear range, limit of blank, limit of detection, lower limit of quantification, precision, recovery, carryover, interference, and dilution effect. The cut-off value between primary and non-primary hyperoxaluria in a pediatric population was analyzed. Results The detection limit was 0.78 μmol/L, and the linear range was up to 80.0 μmol/L. The between-day precision was 5.7% at 41.3 μmol/L and 13.1% at 1.6 μmol/L. The carryover was <0.2%. The recovery rate ranged from 90% to 110%. Interference analysis showed that Hb did not interfere with plasma oxalate quantification, whereas intralipids and bilirubin caused false elevation of oxalate concentrations. A cut-off of 13.9 μmol/L showed 63% specificity and 77% sensitivity, whereas a cut-off of 4.15 μmol/L showed 100% specificity and 20% sensitivity. The minimum required sample volume was 250 μL. The detected oxalate concentrations showed interference from instrument conditioning, sample preparation procedures, medications, and various clinical conditions. Conclusions GC-MS is a sensitive assay for quantifying plasma oxalate and is suitable for pediatric patients. Plasma oxalate concentrations should be interpreted in a clinical context.
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Affiliation(s)
- Mehrdad Yazdanpanah
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jessie Cameron
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Chandra Chappel
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Libin Yuan
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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22
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Sun J, Xia Y. Pretreating and normalizing metabolomics data for statistical analysis. Genes Dis 2024; 11:100979. [PMID: 38299197 PMCID: PMC10827599 DOI: 10.1016/j.gendis.2023.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 04/09/2023] [Indexed: 02/02/2024] Open
Abstract
Metabolomics as a research field and a set of techniques is to study the entire small molecules in biological samples. Metabolomics is emerging as a powerful tool generally for precision medicine. Particularly, integration of microbiome and metabolome has revealed the mechanism and functionality of microbiome in human health and disease. However, metabolomics data are very complicated. Preprocessing/pretreating and normalizing procedures on metabolomics data are usually required before statistical analysis. In this review article, we comprehensively review various methods that are used to preprocess and pretreat metabolomics data, including MS-based data and NMR -based data preprocessing, dealing with zero and/or missing values and detecting outliers, data normalization, data centering and scaling, data transformation. We discuss the advantages and limitations of each method. The choice for a suitable preprocessing method is determined by the biological hypothesis, the characteristics of the data set, and the selected statistical data analysis method. We then provide the perspective of their applications in the microbiome and metabolome research.
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Affiliation(s)
- Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, Department of Microbiology/Immunology, UIC Cancer Center, University of Illinois Chicago, Jesse Brown VA Medical Center Chicago (537), Chicago, IL 60612, USA
| | - Yinglin Xia
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA
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23
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Pradeep M, Saxena M, Mondal D, Franklin G. Do nanoparticles delivered to roots affect plant secondary metabolism? A comprehensive analysis in float seedling cultures of Hypericum perforatum L. CHEMOSPHERE 2024; 356:141789. [PMID: 38554871 DOI: 10.1016/j.chemosphere.2024.141789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
Since nanoparticles (NPs) released into the environment from household or industrial wastes and applied directly on plants as agrochemicals can accumulate in the rhizosphere, it is imperative to understand how these NPs affect plant secondary metabolism upon their contact with the roots of intact plants. Here, the effects of Pd, Au, ZnO and Fe2O3 NPs on secondary metabolism were comprehensively investigated in Hypericum perforatum L float seedlings by analyzing 41 major secondary metabolites using ultra-performance liquid chromatography coupled with photodiode array, fluorescence detector and high-resolution mass spectrometry (UPLC-PDA-FLR-HRMS). The results showed that exposure of H. perforatum roots to Pd, Au, ZnO and Fe2O3 NPs rapidly led to fluctuations in the levels of secondary metabolites. Although these fluctuations did not correlate with NP type, concentration and duration of treatment, a total of 22 compounds were significantly altered by the NPs tested. In particular, 1 ppm Au increased the content of quercetin 3-(2″-acetylgalactoside), cadensin G and leutoskyrin by 5.02-, 2.12- and 2.58-fold, respectively after 24 h; 25 ppm Pd NPs led to a 2.1-fold increase in miquelianin content after 6 h; 50 ppm Fe2O3 NPs increased the level of furohyperforin by 3.09-fold and decreased the content of miquelianin 5.22-fold after 24 h and 50 ppm ZnO led to a 2.13-fold increase in hypericin after 48 h. These results emphasise the need to understand the intricate interplay between NPs and plant secondary metabolism in order to enable safer and efficient applications of NPs in agriculture.
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Affiliation(s)
- Matam Pradeep
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzesynska 34, 60-479, Poznan, Poland
| | - Megha Saxena
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzesynska 34, 60-479, Poznan, Poland
| | - Dibyendu Mondal
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzesynska 34, 60-479, Poznan, Poland
| | - Gregory Franklin
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzesynska 34, 60-479, Poznan, Poland.
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24
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Sakarin S, Rungsipipat A, Roytrakul S, Jaresitthikunchai J, Phaonakrop N, Charoenlappanit S, Thaisakun S, Surachetpong S. Phosphoproteomics analysis of serum from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease. PeerJ 2024; 12:e17186. [PMID: 38708342 PMCID: PMC11067895 DOI: 10.7717/peerj.17186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/11/2024] [Indexed: 05/07/2024] Open
Abstract
Pulmonary hypertension (PH), a common complication in dogs affected by degenerative mitral valve disease (DMVD), is a progressive disorder characterized by increased pulmonary arterial pressure (PAP) and pulmonary vascular remodeling. Phosphorylation of proteins, impacting vascular function and cell proliferation, might play a role in the development and progression of PH. Unlike gene or protein studies, phosphoproteomic focuses on active proteins that function as end-target proteins within signaling cascades. Studying phosphorylated proteins can reveal active contributors to PH development. Early diagnosis of PH is crucial for effective management and improved clinical outcomes. This study aimed to identify potential serum biomarkers for diagnosing PH in dogs affected with DMVD using a phosphoproteomic approach. Serum samples were collected from healthy control dogs (n = 28), dogs with DMVD (n = 24), and dogs with DMVD and PH (n = 29). Phosphoproteins were enriched from the serum samples and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Data analysis was performed to identify uniquely expressed phosphoproteins in each group and differentially expressed phosphoproteins among groups. Phosphoproteomic analysis revealed nine uniquely expressed phosphoproteins in the serum of dogs in the DMVD+PH group and 15 differentially upregulated phosphoproteins in the DMVD+PH group compared to the DMVD group. The phosphoproteins previously implicated in PH and associated with pulmonary arterial remodeling, including small nuclear ribonucleoprotein G (SNRPG), alpha-2-macroglobulin (A2M), zinc finger and BTB domain containing 42 (ZBTB42), hemopexin (HPX), serotransferrin (TRF) and complement C3 (C3), were focused on. Their unique expression and differential upregulation in the serum of DMVD dogs with PH suggest their potential as biomarkers for PH diagnosis. In conclusion, this phosphoproteomic study identified uniquely expressed and differentially upregulated phosphoproteins in the serum of DMVD dogs with PH. Further studies are warranted to validate the diagnostic utility of these phosphoproteins.
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Affiliation(s)
- Siriwan Sakarin
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand, Bangkok, Thailand
| | - Anudep Rungsipipat
- Center of Excellence for Companion Animal Cancer, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand, Bangkok, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand, Bangkok, Thailand
| | - Janthima Jaresitthikunchai
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand, Bangkok, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand, Bangkok, Thailand
| | - Sawanya Charoenlappanit
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand, Bangkok, Thailand
| | - Siriwan Thaisakun
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand, Bangkok, Thailand
| | - Sirilak Surachetpong
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand, Bangkok, Thailand
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25
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Griffiths JA, Yoo BB, Thuy-Boun P, Cantu VJ, Weldon KC, Challis C, Sweredoski MJ, Chan KY, Thron TM, Sharon G, Moradian A, Humphrey G, Zhu Q, Shaffer JP, Wolan DW, Dorrestein PC, Knight R, Gradinaru V, Mazmanian SK. Peripheral neuronal activation shapes the microbiome and alters gut physiology. Cell Rep 2024; 43:113953. [PMID: 38517896 PMCID: PMC11132177 DOI: 10.1016/j.celrep.2024.113953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/07/2023] [Accepted: 02/27/2024] [Indexed: 03/24/2024] Open
Abstract
The gastrointestinal (GI) tract is innervated by intrinsic neurons of the enteric nervous system (ENS) and extrinsic neurons of the central nervous system and peripheral ganglia. The GI tract also harbors a diverse microbiome, but interactions between the ENS and the microbiome remain poorly understood. Here, we activate choline acetyltransferase (ChAT)-expressing or tyrosine hydroxylase (TH)-expressing gut-associated neurons in mice to determine effects on intestinal microbial communities and their metabolites as well as on host physiology. The resulting multi-omics datasets support broad roles for discrete peripheral neuronal subtypes in shaping microbiome structure, including modulating bile acid profiles and fungal colonization. Physiologically, activation of either ChAT+ or TH+ neurons increases fecal output, while only ChAT+ activation results in increased colonic contractility and diarrhea-like fluid secretion. These findings suggest that specific subsets of peripherally activated neurons differentially regulate the gut microbiome and GI physiology in mice without involvement of signals from the brain.
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Affiliation(s)
- Jessica A Griffiths
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Bryan B Yoo
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Peter Thuy-Boun
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Victor J Cantu
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, San Diego, CA, USA
| | - Collin Challis
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael J Sweredoski
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ken Y Chan
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Taren M Thron
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gil Sharon
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Annie Moradian
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Dennis W Wolan
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, San Diego, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Shu Chien-Gene Lay Department of Engineering, University of California, San Diego, San Diego, CA, USA; Halıcıoğlu Data Science Institute, University of California, San Diego, San Diego, CA, USA
| | - Viviana Gradinaru
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sarkis K Mazmanian
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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26
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Calzadilla N, Jayawardena D, Qazi A, Sharma A, Mongan K, Comiskey S, Eathara A, Saksena S, Dudeja PK, Alrefai WA, Gill RK. Serotonin Transporter Deficiency Induces Metabolic Alterations in the Ileal Mucosa. Int J Mol Sci 2024; 25:4459. [PMID: 38674044 PMCID: PMC11049861 DOI: 10.3390/ijms25084459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Serotonin transporter (SERT) deficiency has been implicated in metabolic syndrome, intestinal inflammation, and microbial dysbiosis. Interestingly, changes in microbiome metabolic capacity and several alterations in host gene expression, including lipid metabolism, were previously observed in SERT-/- mice ileal mucosa. However, the precise host or microbial metabolites altered by SERT deficiency that may contribute to the pleiotropic phenotype of SERT KO mice are not yet understood. This study investigated the hypothesis that SERT deficiency impacts lipid and microbial metabolite abundances in the ileal mucosa, where SERT is highly expressed. Ileal mucosal metabolomics was performed by Metabolon on wild-type (WT) and homozygous SERT knockout (KO) mice. Fluorescent-activated cell sorting (FACS) was utilized to measure immune cell populations in ileal lamina propria to assess immunomodulatory effects caused by SERT deficiency. SERT KO mice exhibited a unique ileal mucosal metabolomic signature, with the most differentially altered metabolites being lipids. Such changes included increased diacylglycerols and decreased monoacylglycerols in the ileal mucosa of SERT KO mice compared to WT mice. Further, the ileal mucosa of SERT KO mice exhibited several changes in microbial-related metabolites known to play roles in intestinal inflammation and insulin resistance. SERT KO mice also had a significant reduction in the abundance of ileal group 3 innate lymphoid cells (ILC3). In conclusion, SERT deficiency induces complex alterations in the ileal mucosal environment, indicating potential links between serotonergic signaling, gut microbiota, mucosal immunity, intestinal inflammation, and metabolic syndrome.
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Affiliation(s)
- Nathan Calzadilla
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL 60607, USA;
| | - Dulari Jayawardena
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.); (A.Q.); (A.S.); (K.M.); (S.C.); (A.E.); (S.S.); (P.K.D.); (W.A.A.)
| | - Aisha Qazi
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.); (A.Q.); (A.S.); (K.M.); (S.C.); (A.E.); (S.S.); (P.K.D.); (W.A.A.)
| | - Anchal Sharma
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.); (A.Q.); (A.S.); (K.M.); (S.C.); (A.E.); (S.S.); (P.K.D.); (W.A.A.)
| | - Kai Mongan
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.); (A.Q.); (A.S.); (K.M.); (S.C.); (A.E.); (S.S.); (P.K.D.); (W.A.A.)
| | - Shane Comiskey
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.); (A.Q.); (A.S.); (K.M.); (S.C.); (A.E.); (S.S.); (P.K.D.); (W.A.A.)
| | - Abhijith Eathara
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.); (A.Q.); (A.S.); (K.M.); (S.C.); (A.E.); (S.S.); (P.K.D.); (W.A.A.)
| | - Seema Saksena
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.); (A.Q.); (A.S.); (K.M.); (S.C.); (A.E.); (S.S.); (P.K.D.); (W.A.A.)
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Pradeep K. Dudeja
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.); (A.Q.); (A.S.); (K.M.); (S.C.); (A.E.); (S.S.); (P.K.D.); (W.A.A.)
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Waddah A. Alrefai
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.); (A.Q.); (A.S.); (K.M.); (S.C.); (A.E.); (S.S.); (P.K.D.); (W.A.A.)
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Ravinder K. Gill
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA; (D.J.); (A.Q.); (A.S.); (K.M.); (S.C.); (A.E.); (S.S.); (P.K.D.); (W.A.A.)
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
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27
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Berner J, Acharjee A. Cerebrospinal fluid metabolomes of treatment-resistant depression subtypes and ketamine response: a pilot study. DISCOVER MENTAL HEALTH 2024; 4:12. [PMID: 38630417 PMCID: PMC11024073 DOI: 10.1007/s44192-024-00066-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/07/2024] [Indexed: 04/20/2024]
Abstract
Depression is a disorder with variable presentation. Selecting treatments and dose-finding is, therefore, challenging and time-consuming. In addition, novel antidepressants such as ketamine have sparse optimization evidence. Insights obtained from metabolomics may improve the management of patients. The objective of this study was to determine whether compounds in the cerebrospinal fluid (CSF) metabolome correlate with scores on questionnaires and response to medication. We performed a retrospective pilot study to evaluate phenotypic and metabolomic variability in patients with treatment-resistant depression using multivariate data compression algorithms. Twenty-nine patients with treatment-resistant depression provided fasting CSF samples. Over 300 metabolites were analyzed in these samples with liquid chromatography-mass spectrometry. Chart review provided basic demographic information, clinical status with self-reported questionnaires, and response to medication. Of the 300 metabolites analyzed, 151 were present in all CSF samples and used in the analyses. Hypothesis-free multivariate analysis compressed the resultant data set into two dimensions using Principal Component (PC) analysis, accounting for ~ 32% of the variance. PC1 accounted for 16.9% of the variance and strongly correlated with age in one direction and 5-methyltetrahydrofolate, homocarnosine, and depression and anxiety scores in the opposite direction. PC2 accounted for 15.4% of the variance, with one end strongly correlated with autism scores, male gender, and cognitive fatigue scores, and the other end with bipolar diagnosis, lithium use, and ethylmalonate disturbance. This small pilot study suggests that complex treatment-resistant depression can be mapped onto a 2-dimensional pathophysiological domain. The results may have implications for treatment selection for depression subtypes.
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Affiliation(s)
- Jon Berner
- Woodinville Psychiatric Associates, 18500 156Th Ave NE #100, Woodinville, WA, 98072, USA.
| | - Animesh Acharjee
- Institute of Cancer and Genomics Sciences, University of Birmingham, Birmingham, UK
- Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- MRC Health Data Research UK (HDR UK), London, UK
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28
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Eichinger J, Reiche AM, Dohme-Meier F, Fuchsmann P. Optimization of volatile organic compounds sampling from dairy cow exhaled breath using polymer-based solid-phase extraction cartridges for gas chromatographic analysis. J Breath Res 2024; 18:036001. [PMID: 38547532 DOI: 10.1088/1752-7163/ad38d5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/28/2024] [Indexed: 04/17/2024]
Abstract
We explored appropriate technical setups for the detection of volatile organic compounds (VOCs) from exhaled cow breath by comparing six different polymer-based solid-phase extraction (SPE) cartridges currently on the market for gas chromatography/mass spectrometry (GC-MS) screening. Exhaled breath was sampled at a single timepoint from five lactating dairy cows using six different SPE cartridges (Bond Elut ENV (ENV); Chromabond HRX (HRX); Chromabond HRP (HRP); Chromabond HLB (HLB); Chromabond HR-XCW (XCW) and Chromabond HR-XAW (XAW)). The trapped VOCs were analyzed by dynamic headspace vacuum in-tube extraction GC-MS (DHS-V-ITEX-GC-MS). Depending on the SPE cartridge, we detected 1174-1312 VOCs per cartridge. Most VOCs were alkenes, alkanes, esters, ketones, alcohols, aldehydes, amines, nitriles, ethers, amides, carboxylic acids, alkynes, azoles, terpenes, pyridines, or sulfur-containing compounds. The six SPE cartridges differed in their specificity for the chemical compounds, with the XAW cartridge showing the best specificity for ketones. The greatest differences between the tested SPE cartridges appeared in the detection of specific VOCs. In total, 176 different VOCs were detected with a match factor >80%. The greatest number of specific VOCs was captured by XAW (149), followed by ENV (118), HLB (117), HRP (115), HRX (114), and XCW (114). We conclude that the tested SPE cartridges are suitable for VOC sampling from exhaled cow breath, but the SPE cartridge choice enormously affects the detected chemical groups and the number of detected VOCs. Therefore, an appropriate SPE adsorbent cartridge should be selected according to our proposed inclusion criteria. For targeted metabolomics approaches, the SPE cartridge choice depends on the VOCs or chemical compound groups of interest based on our provided VOC list. For untargeted approaches without information on the animals' metabolic condition, we suggest using multi-sorbent SPE cartridges or multiple cartridges per animal.
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Affiliation(s)
- Julia Eichinger
- Ruminant Nutrition and Emissions, Agroscope, Posieux, Switzerland
- University of Hohenheim, Institute of Animal Science, Stuttgart, Germany
| | | | | | - Pascal Fuchsmann
- Human Nutrition, Sensory Analysis and Flavour, Agroscope, Bern, Switzerland
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29
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Yheskel M, Hatch HAM, Pedrosa E, Terry BK, Siebels AA, Zheng XY, Blok LER, Fencková M, Sidoli S, Schenck A, Zheng D, Lachman HM, Secombe J. KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons. Nucleic Acids Res 2024:gkae261. [PMID: 38597673 DOI: 10.1093/nar/gkae261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/11/2024] Open
Abstract
Genes encoding the KDM5 family of transcriptional regulators are disrupted in individuals with intellectual disability (ID). To understand the link between KDM5 and ID, we characterized five Drosophila strains harboring missense alleles analogous to those observed in patients. These alleles disrupted neuroanatomical development, cognition and other behaviors, and displayed a transcriptional signature characterized by the downregulation of many ribosomal protein genes. A similar transcriptional profile was observed in KDM5C knockout iPSC-induced human glutamatergic neurons, suggesting an evolutionarily conserved role for KDM5 proteins in regulating this class of gene. In Drosophila, reducing KDM5 changed neuronal ribosome composition, lowered the translation efficiency of mRNAs required for mitochondrial function, and altered mitochondrial metabolism. These data highlight the cellular consequences of altered KDM5-regulated transcriptional programs that could contribute to cognitive and behavioral phenotypes. Moreover, they suggest that KDM5 may be part of a broader network of proteins that influence cognition by regulating protein synthesis.
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Affiliation(s)
- Matanel Yheskel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Bethany K Terry
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Aubrey A Siebels
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiang Yu Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laura E R Blok
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
| | - Michaela Fencková
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Ceske Budejovice 370 05, Czechia
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 Nijmegen, GA, The Netherlands
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Herbert M Lachman
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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30
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Ponzilacqua-Silva B, Dadelahi AS, Abushahba MFN, Moley CR, Skyberg JA. Vaccine Elicited Antibodies Restrict Glucose Availability to Control Brucella Infection. J Infect Dis 2024:jiae172. [PMID: 38586904 DOI: 10.1093/infdis/jiae172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 04/09/2024] Open
Abstract
The impact of vaccine-induced immune responses on host metabolite availability has not been well studied. Here we show prior vaccination alters the metabolic profile of mice challenged with Brucella melitensis. In particular, glucose levels were reduced in vaccinated mice in an antibody-dependent manner. We also found the glucose transporter gene, gluP, plays a lesser role in B. melitensis virulence in vaccinated wild-type mice relative to vaccinated mice unable to secrete antibodies. These data indicate vaccine-elicited antibodies protect the host in part by restricting glucose availability. Moreover, Brucella and other pathogens may need to employ different metabolic strategies in vaccinated hosts.
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Affiliation(s)
- Bárbara Ponzilacqua-Silva
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
- Laboratory for Infectious Disease Research, University of Missouri, Columbia, Missouri, USA
| | - Alexis S Dadelahi
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
- Laboratory for Infectious Disease Research, University of Missouri, Columbia, Missouri, USA
| | - Mostafa F N Abushahba
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
- Laboratory for Infectious Disease Research, University of Missouri, Columbia, Missouri, USA
- Department of Zoonoses, Faculty of Veterinary Medicine, Assiut University, Assiut, Egypt
| | - Charles R Moley
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
- Laboratory for Infectious Disease Research, University of Missouri, Columbia, Missouri, USA
| | - Jerod A Skyberg
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
- Laboratory for Infectious Disease Research, University of Missouri, Columbia, Missouri, USA
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31
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Pang Z, Lu Y, Zhou G, Hui F, Xu L, Viau C, Spigelman AF, MacDonald PE, Wishart DS, Li S, Xia J. MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation. Nucleic Acids Res 2024:gkae253. [PMID: 38587201 DOI: 10.1093/nar/gkae253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
We introduce MetaboAnalyst version 6.0 as a unified platform for processing, analyzing, and interpreting data from targeted as well as untargeted metabolomics studies using liquid chromatography - mass spectrometry (LC-MS). The two main objectives in developing version 6.0 are to support tandem MS (MS2) data processing and annotation, as well as to support the analysis of data from exposomics studies and related experiments. Key features of MetaboAnalyst 6.0 include: (i) a significantly enhanced Spectra Processing module with support for MS2 data and the asari algorithm; (ii) a MS2 Peak Annotation module based on comprehensive MS2 reference databases with fragment-level annotation; (iii) a new Statistical Analysis module dedicated for handling complex study design with multiple factors or phenotypic descriptors; (iv) a Causal Analysis module for estimating metabolite - phenotype causal relations based on two-sample Mendelian randomization, and (v) a Dose-Response Analysis module for benchmark dose calculations. In addition, we have also improved MetaboAnalyst's visualization functions, updated its compound database and metabolite sets, and significantly expanded its pathway analysis support to around 130 species. MetaboAnalyst 6.0 is freely available at https://www.metaboanalyst.ca.
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Affiliation(s)
- Zhiqiang Pang
- Institute of Parasitology, McGill University,Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Yao Lu
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Guangyan Zhou
- Institute of Parasitology, McGill University,Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Fiona Hui
- Institute of Parasitology, McGill University,Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Lei Xu
- Institute of Parasitology, McGill University,Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Charles Viau
- Institute of Parasitology, McGill University,Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Aliya F Spigelman
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Patrick E MacDonald
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - David S Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - Shuzhao Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- University of Connecticut School of Medicine, Farmington, CT, USA
| | - Jianguo Xia
- Institute of Parasitology, McGill University,Sainte-Anne-de-Bellevue, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
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32
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Bae G, Berezhnoy G, Flores A, Cannet C, Schäfer H, Dahlke MH, Michl P, Löffler MW, Königsrainer A, Trautwein C. Quantitative Metabolomics and Lipoprotein Analysis of PDAC Patients Suggests Serum Marker Categories for Pancreatic Function, Pancreatectomy, Cancer Metabolism, and Systemic Disturbances. J Proteome Res 2024; 23:1249-1262. [PMID: 38407039 PMCID: PMC11003419 DOI: 10.1021/acs.jproteome.3c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/29/2023] [Accepted: 02/03/2024] [Indexed: 02/27/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is difficult to diagnose in the early stages and lacks reliable biomarkers. The scope of this project was to establish quantitative nuclear magnetic resonance (NMR) spectroscopy to comprehensively study blood serum alterations in PDAC patients. Serum samples from 34 PDAC patients obtained before and after pancreatectomy as well as 83 age- and sex-matched control samples from healthy donors were analyzed with in vitro diagnostics research (IVDr) proton NMR spectroscopy at 600 MHz. Uni- and multivariate statistics were applied to identify significant biofluid alterations. We identified 29 significantly changed metabolites and 98 lipoproteins when comparing serum from healthy controls with those of PDAC patients. The most prominent features were assigned to (i) markers of pancreatic function (e.g., glucose and blood triglycerides), (ii) markers related to surgery (e.g., ketone bodies and blood cholesterols), (iii) PDAC-associated markers (e.g., amino acids and creatine), and (iv) markers for systemic disturbances in PDAC (e.g., gut metabolites DMG, TMAO, DMSO2, and liver lipoproteins). Quantitative serum NMR spectroscopy is suited as a diagnostic tool to investigate PDAC. Remarkably, 2-hydroxybutyrate (2-HB) as a previously suggested marker for insulin resistance was found in extraordinarily high levels only after pancreatectomy, suggesting this metabolite is the strongest marker for pancreatic loss of function.
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Affiliation(s)
- Gyuntae Bae
- Werner
Siemens Imaging Center, Department of Preclinical
Imaging and Radiopharmacy, University Hospital Tübingen, Tübingen 72076, Germany
- Cluster
of Excellence iFIT (EXC2180) ‘Image-Guided and Functionally
Instructed Tumor Therapies’, University
of Tübingen, Tübingen 72076, Germany
| | - Georgy Berezhnoy
- Werner
Siemens Imaging Center, Department of Preclinical
Imaging and Radiopharmacy, University Hospital Tübingen, Tübingen 72076, Germany
| | - Alejandra Flores
- Werner
Siemens Imaging Center, Department of Preclinical
Imaging and Radiopharmacy, University Hospital Tübingen, Tübingen 72076, Germany
| | - Claire Cannet
- Bruker
BioSpin GmbH & Co. KG, BioPharma and Applied Division, Ettlingen 76275, Germany
| | - Hartmut Schäfer
- Bruker
BioSpin GmbH & Co. KG, BioPharma and Applied Division, Ettlingen 76275, Germany
| | - Marc H. Dahlke
- Department
of General and Visceral Surgery, Robert-Bosch-Krankenhaus, Stuttgart 70376, Germany
| | - Patrick Michl
- Dept
of Internal Medicine IV, University Hospital
Heidelberg, Heidelberg 69120, Germany
| | - Markus W. Löffler
- Department
of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen 72076, Germany
- German Cancer
Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner
Site Tübingen, University of Tübingen, Tübingen 72076, Germany
- Cluster
of Excellence iFIT (EXC2180) ‘Image-Guided and Functionally
Instructed Tumor Therapies’, University
of Tübingen, Tübingen 72076, Germany
- Department
of Immunology, University of Tübingen, Tübingen 72076, Germany
- Department
of Clinical Pharmacology, University Hospital
Tübingen, Tübingen 72076, Germany
| | - Alfred Königsrainer
- Department
of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen 72076, Germany
- German Cancer
Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner
Site Tübingen, University of Tübingen, Tübingen 72076, Germany
- Cluster
of Excellence iFIT (EXC2180) ‘Image-Guided and Functionally
Instructed Tumor Therapies’, University
of Tübingen, Tübingen 72076, Germany
| | - Christoph Trautwein
- Werner
Siemens Imaging Center, Department of Preclinical
Imaging and Radiopharmacy, University Hospital Tübingen, Tübingen 72076, Germany
- Cluster
of Excellence iFIT (EXC2180) ‘Image-Guided and Functionally
Instructed Tumor Therapies’, University
of Tübingen, Tübingen 72076, Germany
- M3
Research Center for Malignome, Metabolome and Microbiome, Faculty of Medicine University Tübingen, Tübingen 72076, Germany
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Zwierzchowski G, Haxhiaj K, Wójcik R, Wishart DS, Ametaj BN. Identifying Predictive Biomarkers of Subclinical Mastitis in Dairy Cows through Urinary Metabotyping. Metabolites 2024; 14:205. [PMID: 38668333 PMCID: PMC11051925 DOI: 10.3390/metabo14040205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/22/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024] Open
Abstract
Mastitis is a significant infectious disease in dairy cows, resulting in milk yield loss and culling. Early detection of mastitis-prone cows is crucial for implementing effective preventive measures before disease onset. Current diagnosis of subclinical mastitis (SCM) relies on somatic cell count assessment post-calving, lacking predictive capabilities. This study aimed to identify metabolic changes in pre-SCM cows through targeted metabolomic analysis of urine samples collected 8 wks and 4 wks before calving, using mass spectrometry. A nested case-control design was employed, involving a total of 145 multiparous dairy cows, with disease occurrence monitored pre- and postpartum. Among them, 15 disease-free cows served as healthy controls (CON), while 10 cows exclusively had SCM, excluding those with additional diseases. Urinary metabolite profiling revealed multiple alterations in acylcarnitines, amino acids, and organic acids in pre-SCM cows. Metabotyping identified 27 metabolites that distinguished pre-SCM cows from healthy CON cows at both 8 and 4 wks before parturition. However, only four metabolites per week showed significant alterations (p < 0.005). Notably, a panel of four serum metabolites (asymmetric dimethylarginine, proline, leucine, and homovanillate) at 8 wks prepartum, and another panel (asymmetric dimethylarginine, methylmalonate, citrate, and spermidine) at 4 wks prepartum, demonstrated predictive ability as urinary biomarkers for SCM risk (AUC = 0.88; p = 0.02 and AUC = 0.88; p = 0.03, respectively). In conclusion, our findings indicate that metabolite testing can identify cows at risk of SCM as early as 8 and 4 wks before parturition. Validation of the two identified metabolite panels is warranted to implement these predictive biomarkers, facilitate early intervention strategies, and improve dairy cow management to mitigate the impact of SCM. Further research is needed to confirm the efficacy and applicability of these biomarkers in practical farm settings.
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Affiliation(s)
- Grzegorz Zwierzchowski
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (G.Z.); (K.H.)
- Faculty of Biology and Biotechnology, University of Warmia and Mazury, 1a Oczapowskiego Str., 10-719 Olsztyn, Poland
| | - Klevis Haxhiaj
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (G.Z.); (K.H.)
| | - Roman Wójcik
- Faculty of Veterinary Medicine, University of Warmia and Mazury, 1a Oczapowskiego Str., 10-719 Olsztyn, Poland;
| | - David S. Wishart
- Department of Biological and Computer Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Burim N. Ametaj
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (G.Z.); (K.H.)
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34
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Ben Gaied R, Sbissi I, Tarhouni M, Brígido C. Enhancing Pisum sativum growth and symbiosis under heat stress: the synergistic impact of co-inoculated bacterial consortia and ACC deaminase-lacking Rhizobium. Arch Microbiol 2024; 206:203. [PMID: 38573536 PMCID: PMC10995081 DOI: 10.1007/s00203-024-03943-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
The 1-aminocyclopropane-1-carboxylate (ACC) deaminase is a crucial bacterial trait, yet it is not widely distributed among rhizobia. Hence, employing a co-inoculation approach that combines selected plant growth-promoting bacteria with compatible rhizobial strains, especially those lacking ACC deaminase, presents a practical solution to alleviate the negative effects of diverse abiotic stresses on legume nodulation. Our objective was to explore the efficacy of three non-rhizobial endophytes, Phyllobacterium salinisoli (PH), Starkeya sp. (ST) and Pseudomonas turukhanskensis (PS), isolated from native legumes grown in Tunisian arid regions, in improving the growth of cool-season legume and fostering symbiosis with an ACC deaminase-lacking rhizobial strain under heat stress. Various combinations of these endophytes (ST + PS, ST + PH, PS + PH, and ST + PS + PH) were co-inoculated with Rhizobium leguminosarum 128C53 or its ΔacdS mutant derivative on Pisum sativum plants exposed to a two-week heat stress period.Our findings revealed that the absence of ACC deaminase activity negatively impacted both pea growth and symbiosis under heat stress. Nevertheless, these detrimental effects were successfully mitigated in plants co-inoculated with ΔacdS mutant strain and specific non-rhizobial endophytes consortia. Our results indicated that heat stress significantly altered the phenolic content of pea root exudates. Despite this, there was no impact on IAA production. Interestingly, these changes positively influenced biofilm formation in consortia containing the mutant strain, indicating synergistic bacteria-bacteria interactions. Additionally, no positive effects were observed when these endophytic consortia were combined with the wild-type strain. This study highlights the potential of non-rhizobial endophytes to improve symbiotic performance of rhizobial strains lacking genetic mechanisms to mitigate stress effects on their legume host, holding promising potential to enhance the growth and yield of targeted legumes by boosting symbiosis.
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Affiliation(s)
- Roukaya Ben Gaied
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
- MED - Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Ap. 94, Évora, 7006-554, Portugal
| | - Imed Sbissi
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
| | - Mohamed Tarhouni
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
| | - Clarisse Brígido
- MED-Mediterranean Institute for Agriculture, Environment and Development & CHANGE-Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Ap. 94, Évora, 7006-554, Portugal.
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35
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Harold KM, Matsuzaki S, Pranay A, Loveland BL, Batushansky A, Mendez Garcia MF, Eyster C, Stavrakis S, Chiao YA, Kinter M, Humphries KM. Loss of Cardiac PFKFB2 Drives Metabolic, Functional, and Electrophysiological Remodeling in the Heart. J Am Heart Assoc 2024; 13:e033676. [PMID: 38533937 DOI: 10.1161/jaha.123.033676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/20/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFK-2) is a critical glycolytic regulator responsible for upregulation of glycolysis in response to insulin and adrenergic signaling. PFKFB2, the cardiac isoform of PFK-2, is degraded in the heart in the absence of insulin signaling, contributing to diabetes-induced cardiac metabolic inflexibility. However, previous studies have not examined how the loss of PFKFB2 affects global cardiac metabolism and function. METHODS AND RESULTS To address this, we have generated a mouse model with a cardiomyocyte-specific knockout of PFKFB2 (cKO). Using 9-month-old cKO and control mice, we characterized the impacts of PFKFB2 on cardiac metabolism, function, and electrophysiology. cKO mice have a shortened life span of 9 months. Metabolically, cKO mice are characterized by increased glycolytic enzyme abundance and pyruvate dehydrogenase activity, as well as decreased mitochondrial abundance and beta oxidation, suggesting a shift toward glucose metabolism. This was supported by a decrease in the ratio of palmitoyl carnitine to pyruvate-dependent mitochondrial respiration in cKO relative to control animals. Metabolomic, proteomic, and Western blot data support the activation of ancillary glucose metabolism, including pentose phosphate and hexosamine biosynthesis pathways. Physiologically, cKO animals exhibited impaired systolic function and left ventricular dilation, represented by reduced fractional shortening and increased left ventricular internal diameter, respectively. This was accompanied by electrophysiological alterations including increased QT interval and other metrics of delayed ventricular conduction. CONCLUSIONS Loss of PFKFB2 results in metabolic remodeling marked by cardiac ancillary pathway activation. This could delineate an underpinning of pathologic changes to mechanical and electrical function in the heart.
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Affiliation(s)
- Kylene M Harold
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation Oklahoma City OK USA
- Department of Biochemistry and Molecular Physiology University of Oklahoma Health Sciences Center Oklahoma City OK USA
| | - Satoshi Matsuzaki
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation Oklahoma City OK USA
| | - Atul Pranay
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation Oklahoma City OK USA
| | - Brooke L Loveland
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation Oklahoma City OK USA
| | - Albert Batushansky
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation Oklahoma City OK USA
- Ilse Katz Institute for Nanoscale Science & Technology Ben-Gurion University of the Negev Beer Sheva Israel
| | - Maria F Mendez Garcia
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation Oklahoma City OK USA
| | - Craig Eyster
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation Oklahoma City OK USA
| | - Stavros Stavrakis
- Department of Medicine, Section of Cardiovascular Medicine University of Oklahoma Health Sciences Center Oklahoma City OK USA
| | - Ying Ann Chiao
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation Oklahoma City OK USA
- Department of Biochemistry and Molecular Physiology University of Oklahoma Health Sciences Center Oklahoma City OK USA
| | - Michael Kinter
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation Oklahoma City OK USA
| | - Kenneth M Humphries
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation Oklahoma City OK USA
- Department of Biochemistry and Molecular Physiology University of Oklahoma Health Sciences Center Oklahoma City OK USA
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Zepeda-Rivera M, Minot SS, Bouzek H, Wu H, Blanco-Míguez A, Manghi P, Jones DS, LaCourse KD, Wu Y, McMahon EF, Park SN, Lim YK, Kempchinsky AG, Willis AD, Cotton SL, Yost SC, Sicinska E, Kook JK, Dewhirst FE, Segata N, Bullman S, Johnston CD. A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche. Nature 2024; 628:424-432. [PMID: 38509359 PMCID: PMC11006615 DOI: 10.1038/s41586-024-07182-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 02/08/2024] [Indexed: 03/22/2024]
Abstract
Fusobacterium nucleatum (Fn), a bacterium present in the human oral cavity and rarely found in the lower gastrointestinal tract of healthy individuals1, is enriched in human colorectal cancer (CRC) tumours2-5. High intratumoural Fn loads are associated with recurrence, metastases and poorer patient prognosis5-8. Here, to delineate Fn genetic factors facilitating tumour colonization, we generated closed genomes for 135 Fn strains; 80 oral strains from individuals without cancer and 55 unique cancer strains cultured from tumours from 51 patients with CRC. Pangenomic analyses identified 483 CRC-enriched genetic factors. Tumour-isolated strains predominantly belong to Fn subspecies animalis (Fna). However, genomic analyses reveal that Fna, considered a single subspecies, is instead composed of two distinct clades (Fna C1 and Fna C2). Of these, only Fna C2 dominates the CRC tumour niche. Inter-Fna analyses identified 195 Fna C2-associated genetic factors consistent with increased metabolic potential and colonization of the gastrointestinal tract. In support of this, Fna C2-treated mice had an increased number of intestinal adenomas and altered metabolites. Microbiome analysis of human tumour tissue from 116 patients with CRC demonstrated Fna C2 enrichment. Comparison of 62 paired specimens showed that only Fna C2 is tumour enriched compared to normal adjacent tissue. This was further supported by metagenomic analysis of stool samples from 627 patients with CRC and 619 healthy individuals. Collectively, our results identify the Fna clade bifurcation, show that specifically Fna C2 drives the reported Fn enrichment in human CRC and reveal the genetic underpinnings of pathoadaptation of Fna C2 to the CRC niche.
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Affiliation(s)
- Martha Zepeda-Rivera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Samuel S Minot
- Data Core, Shared Resources, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Heather Bouzek
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hanrui Wu
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aitor Blanco-Míguez
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Paolo Manghi
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Dakota S Jones
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Ying Wu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elsa F McMahon
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun K Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | | | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | | | - Ewa Sicinska
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Floyd E Dewhirst
- Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Nicola Segata
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Susan Bullman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Christopher D Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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Muñoz Hoyos L, Anisha WP, Meng C, Kleigrewe K, Dawid C, Hückelhoven R, Stam R. Untargeted metabolomics reveals PTI-associated metabolites. PLANT, CELL & ENVIRONMENT 2024; 47:1224-1237. [PMID: 38164085 DOI: 10.1111/pce.14794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/09/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
Plants employ a multilayered immune system to combat pathogens. In one layer, recognition of Pathogen- or Microbe-Associated Molecular Patterns or elicitors, triggers a cascade that leads to defence against the pathogen and Pattern Triggered Immunity. Secondary or specialised metabolites (SMs) are expected to play a role, because they are potentially anti-fungal compounds. Tomato (Solanum lycopersicum) plants inoculated with Alternaria solani s.l. show symptoms of infection after inoculation. Plants inoculated with Alternaria alternata remain symptomless. We hypothesised that pattern-triggered induction of resistance related metabolites in tomato contributes to the resistance against A. alternata. We compared the metabolomic profile (metabolome) of tomato after treatments with A. alternata, A. solani and the fungal elicitor chitin, and identified SMs involved in early defence of tomato plants. We revealed differential metabolome fingerprints. The composition of A. alternata and chitin induced metabolomes show larger overlap with each other than with the A. solani induced metabolome. We identify 65 metabolites possibly associated with PTI in tomato plants, including NAD and trigonelline. We confirm that trigonelline inhibits fungal growth in vitro at physiological concentrations. Thus, a true pattern-triggered, chemical defence is mounted against A. alternata, which contains anti-fungal compounds that could be interesting for crop protection strategies.
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Affiliation(s)
- Lina Muñoz Hoyos
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Wan Petra Anisha
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chen Meng
- TUM School of Life Sciences, Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- TUM School of Life Sciences, Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Corinna Dawid
- TUM School of Life Sciences, Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Functional Phytometabolomics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Ralph Hückelhoven
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Remco Stam
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Department of Phytopathology and Crop protection, Institute of Phytopathology, Kiel University, Kiel, Germany
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Meier L, Bruginski E, Marafiga JR, Caus LB, Pasquetti MV, Calcagnotto ME, Campos FR. Hippocampal metabolic profile during epileptogenesis in the pilocarpine model of epilepsy. Biomed Chromatogr 2024; 38:e5820. [PMID: 38154955 DOI: 10.1002/bmc.5820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/30/2023]
Abstract
Temporal lobe epilepsy (TLE) is a common form of refractory epilepsy in adulthood. The metabolic profile of epileptogenesis is still poorly investigated. Elucidation of such a metabolic profile using animal models of epilepsy could help identify new metabolites and pathways involved in the mechanisms of epileptogenesis process. In this study, we evaluated the metabolic profile during the epileptogenesis periods. Using a pilocarpine model of epilepsy, we analyzed the global metabolic profile of hippocampal extracts by untargeted metabolomics based on ultra-performance liquid chromatography-high-resolution mass spectrometry, at three time points (3 h, 1 week, and 2 weeks) after status epilepticus (SE) induction. We demonstrated that epileptogenesis periods presented different hippocampal metabolic profiles, including alterations of metabolic pathways of amino acids and lipid metabolism. Six putative metabolites (tryptophan, N-acetylornithine, N-acetyl-L-aspartate, glutamine, adenosine, and cholesterol) showed significant different levels during epileptogenesis compared to their respective controls. These putative metabolites could be associated with the imbalance of neurotransmitters, mitochondrial dysfunction, and cell loss observed during both epileptogenesis and epilepsy. With these findings, we provided an overview of hippocampal metabolic profiles during different stages of epileptogenesis that could help investigate pathways and respective metabolites as predictive tools in epilepsy.
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Affiliation(s)
- Letícia Meier
- Biosciences and Mass Spectrometry Laboratory, Department of Pharmacy, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Graduate Program in Pharmaceutical Science, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Estevan Bruginski
- Biosciences and Mass Spectrometry Laboratory, Department of Pharmacy, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Graduate Program in Pharmaceutical Science, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Joseane Righes Marafiga
- Neurophysiology and Neurochemistry of Neuronal Excitability and Synaptic Plasticity Laboratory (NNNESP Lab.), Department of Biochemistry, ICBS, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Graduate Program in Biological Science: Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Letícia Barbieri Caus
- Neurophysiology and Neurochemistry of Neuronal Excitability and Synaptic Plasticity Laboratory (NNNESP Lab.), Department of Biochemistry, ICBS, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Mayara Vendramin Pasquetti
- Neurophysiology and Neurochemistry of Neuronal Excitability and Synaptic Plasticity Laboratory (NNNESP Lab.), Department of Biochemistry, ICBS, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Elisa Calcagnotto
- Neurophysiology and Neurochemistry of Neuronal Excitability and Synaptic Plasticity Laboratory (NNNESP Lab.), Department of Biochemistry, ICBS, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Graduate Program in Biological Science: Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Francinete Ramos Campos
- Biosciences and Mass Spectrometry Laboratory, Department of Pharmacy, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Graduate Program in Pharmaceutical Science, Universidade Federal do Paraná, Curitiba, PR, Brazil
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Marron MM, Yao S, Shah RV, Murthy VL, Newman AB. Metabolomic characterization of vigor to frailty among community-dwelling older Black and White men and women. GeroScience 2024; 46:2371-2389. [PMID: 37968423 PMCID: PMC10828147 DOI: 10.1007/s11357-023-01005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023] Open
Abstract
Older women and Black individuals are more likely to experience frailty. A metabolomic characterization of frailty may help inform more effective interventions aimed at improving health, reducing disparities, and preventing frailty with aging. We sought to identify metabolites and pathways associated with vigor to frailty and determine whether associations differed by sex and/or race among n = 2189 older Black and White men and women from the Health, Aging, and Body Composition (Health ABC) study. Fasting plasma metabolites were measured using liquid chromatography-mass spectrometry. Vigor to frailty was based on weight change, physical activity, gait speed, grip strength, and usual energy. We used linear regression of a single metabolite on vigor to frailty, adjusting for age, sex, race, study site, and multiple comparisons using a Bonferroni correction. Among 500 metabolites, 113 were associated with vigor to frailty (p < 0.0001). Associations between metabolites and vigor to frailty did not differ significantly by race and/or sex. Lower amino acids, glycerophospholipids, sphingolipids, and dehydroepiandrosterone sulfate and higher acylcarnitines, fatty acids, amino acid derivatives, organic acids, carbohydrates, citric acid cycle metabolites, and trimethylamine oxide were associated with frailer scores. Pathway analyses identified the citric acid cycle as containing more frailty-associated metabolites than expected by chance (p = 0.00005). Calories and protein intake did not differ by vigor to frailty. Frailer Health ABC participants may have lower utilization of energy pathways, potentially as a result of less demand and less efficient utilization of similar amounts of nutrients when compared to more vigorous participants.
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Affiliation(s)
- Megan M Marron
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Shanshan Yao
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ravi V Shah
- Vanderbilt Translational and Clinical Research Center, Cardiology Division, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Venkatesh L Murthy
- Division of Cardiovascular Medicine, Department of Medicine, and Frankel Cardiovascular Center, University of Michigan, Ann Arbor, MI, USA
| | - Anne B Newman
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Departments of Medicine and Clinical and Translational Science, University of Pittsburgh, Pittsburgh, PA, USA
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Sánchez-Adriá IE, Sanmartín G, Prieto JA, Estruch F, Randez-Gil F. Sourdough Yeast Strains Exhibit Thermal Tolerance, High Fermentative Performance, and a Distinctive Aromatic Profile in Beer Wort. Foods 2024; 13:1059. [PMID: 38611363 PMCID: PMC11011504 DOI: 10.3390/foods13071059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The increasing popularity of home brewing and the fast evolution of craft beer companies have fuelled the interest in novel yeasts as the main actors diversifying the beer portfolio. Here, we have characterized the thermal tolerance and brewing-related features of two sourdough (SD) isolates of Saccharomyces cerevisiae, SDy01 and SDy02, at different temperatures, 20 and 37 °C, comparing them with commercial brew strains, AaB and kNB. The SD strains exhibited tolerance to the main brewing-related stress conditions and increased growth rates and lower lag phases than the reference beer strains at both temperatures. Consistent with this, SDy01 and SDy02 displayed higher fermentative activity in terms of sugar rate depletion and the release of metabolic by-products. Moreover, SDy01 and SDy02 brewing at 20 °C increased their total amount of volatile compounds (VOCs), in particular, their esters and carboxyl compounds, as compared to the reference AaB strain. In contrast, fermentation at 37 °C resulted in a drastic reduction in the number of VOCs in wort fermented with SD yeast, especially in its level of esters. In conclusion, our results stress the high fermentative performance of SD strains in beer wort and their ability to provide a complex and specific aromatic profile at a wide range of temperatures.
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Affiliation(s)
- Isabel E. Sánchez-Adriá
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980 Paterna (Valencia), Spain (J.A.P.)
| | - Gemma Sanmartín
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980 Paterna (Valencia), Spain (J.A.P.)
| | - Jose A. Prieto
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980 Paterna (Valencia), Spain (J.A.P.)
| | - Francisco Estruch
- Department of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, 46100 Burjassot (Valencia), Spain;
| | - Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980 Paterna (Valencia), Spain (J.A.P.)
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41
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Bergum OET, Singleton AH, Røst LM, Bodein A, Scott-Boyer MP, Rye MB, Droit A, Bruheim P, Otterlei M. SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated. Front Microbiol 2024; 15:1373344. [PMID: 38596376 PMCID: PMC11002266 DOI: 10.3389/fmicb.2024.1373344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
The DNA damage inducible SOS response in bacteria serves to increase survival of the species at the cost of mutagenesis. The SOS response first initiates error-free repair followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response. Escherichia coli was grown in batch cultivation in bioreactors to ensure highly controlled conditions, and a low dose of the antibiotic ciprofloxacin was used to activate the SOS response while avoiding extensive cell death. Our results show that expression of genes involved in error-free and error-prone repair were both induced shortly after DNA damage, thus, challenging the established perception that the expression of error-prone repair genes is delayed. By combining transcriptomics and a sub-proteomics approach termed signalomics, we found that the temporal segregation of error-free and error-prone repair is primarily regulated after transcription, supporting the current literature. Furthermore, the heterology index (i.e., the binding affinity of LexA to the SOS box) was correlated to the maximum increase in gene expression and not to the time of induction of SOS genes. Finally, quantification of metabolites revealed increasing pyrimidine pools as a late feature of the SOS response. Our results elucidate how the SOS response is coordinated, showing a rapid transcriptional response and temporal regulation of mutagenesis on the protein and metabolite levels.
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Affiliation(s)
| | - Amanda Holstad Singleton
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Antoine Bodein
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Morten Beck Rye
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Arnaud Droit
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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Mitchell W, Goeminne LJE, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. eLife 2024; 12:RP90579. [PMID: 38517750 PMCID: PMC10959535 DOI: 10.7554/elife.90579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
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Affiliation(s)
- Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Ludger JE Goeminne
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Sirui Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Julie Y Chen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Kerry A Pierce
- Broad Institute of MIT and HarvardCambridgeUnited States
| | | | - Clary B Clish
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
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43
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Dos Reis JBA, Lorenzi AS, Pinho DB, Cortelo PC, do Vale HMM. The hidden treasures in endophytic fungi: a comprehensive review on the diversity of fungal bioactive metabolites, usual analytical methodologies, and applications. Arch Microbiol 2024; 206:185. [PMID: 38506928 DOI: 10.1007/s00203-024-03911-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
This review provides a comprehensive overview of the key aspects of the natural metabolite production by endophytic fungi, which has attracted significant attention due to its diverse biological activities and wide range of applications. Synthesized by various fungal species, these metabolites encompass compounds with therapeutic, agricultural, and commercial significance. We delved into strategies and advancements aimed at optimizing fungal metabolite production. Fungal cultivation, especially by Aspergillus, Penicillium, and Fusarium, plays a pivotal role in metabolite biosynthesis, and researchers have explored both submerged and solid-state cultivation processes to harness the full potential of fungal species. Nutrient optimization, pH, and temperature control are critical factors in ensuring high yields of the targeted bioactive metabolites especially for scaling up processes. Analytical methods that includes High-Performance Liquid Chromatography (HPLC), Liquid Chromatography-Mass Spectrometry (LC-MS), Gas Chromatography-Mass Spectrometry (GC-MS), Nuclear Magnetic Resonance (NMR), and Mass Spectrometry (MS), are indispensable for the identification and quantification of the compounds. Moreover, genetic engineering and metabolic pathway manipulation have emerged as powerful tools to enhance metabolite production and develop novel fungal strains with increased yields. Regulation and control mechanisms at the genetic, epigenetic, and metabolic levels are explored to fine-tune the biosynthesis of fungal metabolites. Ongoing research aims to overcome the complexity of the steps involved to ensure the efficient production and utilization of fungal metabolites.
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Affiliation(s)
| | - Adriana Sturion Lorenzi
- Department of Cellular Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
| | - Danilo Batista Pinho
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
| | | | - Helson Mario Martins do Vale
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
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Hernandez-Benitez R, Wang C, Shi L, Ouchi Y, Zhong C, Hishida T, Liao HK, Magill EA, Memczak S, Soligalla RD, Fresia C, Hatanaka F, Lamas V, Guillen I, Sahu S, Yamamoto M, Shao Y, Aguirre-Vazquez A, Nuñez Delicado E, Guillen P, Rodriguez Esteban C, Qu J, Reddy P, Horvath S, Liu GH, Magistretti P, Izpisua Belmonte JC. Intervention with metabolites emulating endogenous cell transitions accelerates muscle regeneration in young and aged mice. Cell Rep Med 2024; 5:101449. [PMID: 38508141 PMCID: PMC10983034 DOI: 10.1016/j.xcrm.2024.101449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/10/2023] [Accepted: 02/08/2024] [Indexed: 03/22/2024]
Abstract
Tissue regeneration following an injury requires dynamic cell-state transitions that allow for establishing the cell identities required for the restoration of tissue homeostasis and function. Here, we present a biochemical intervention that induces an intermediate cell state mirroring a transition identified during normal differentiation of myoblasts and other multipotent and pluripotent cells to mature cells. When applied in somatic differentiated cells, the intervention, composed of one-carbon metabolites, reduces some dedifferentiation markers without losing the lineage identity, thus inducing limited reprogramming into a more flexible cell state. Moreover, the intervention enabled accelerated repair after muscle injury in young and aged mice. Overall, our study uncovers a conserved biochemical transitional phase that enhances cellular plasticity in vivo and hints at potential and scalable biochemical interventions of use in regenerative medicine and rejuvenation interventions that may be more tractable than genetic ones.
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Affiliation(s)
- Reyna Hernandez-Benitez
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Altos Labs, Inc., San Diego, CA 92121, USA
| | - Chao Wang
- Altos Labs, Inc., San Diego, CA 92121, USA
| | - Lei Shi
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Yasuo Ouchi
- Altos Labs, Inc., San Diego, CA 92121, USA; Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
| | | | - Tomoaki Hishida
- Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, 25-1 Shichibancho, Wakayama 640-8156, Japan
| | - Hsin-Kai Liao
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Eric A Magill
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Rupa D Soligalla
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Chiara Fresia
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | | | | | | | | | | | | | - Estrella Nuñez Delicado
- Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos, Nº 135 12, 30107 Guadalupe, Spain
| | | | | | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | - Guang-Hui Liu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pierre Magistretti
- King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Altos Labs, Inc., San Diego, CA 92121, USA.
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Phan MD, Schirra HJ, Nhu NTK, Peters KM, Sarkar S, Allsopp LP, Achard MES, Kappler U, Schembri MA. Combined functional genomic and metabolomic approaches identify new genes required for growth in human urine by multidrug-resistant Escherichia coli ST131. mBio 2024; 15:e0338823. [PMID: 38353545 PMCID: PMC10936160 DOI: 10.1128/mbio.03388-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 03/14/2024] Open
Abstract
Urinary tract infections (UTIs) are one of the most common bacterial infections in humans, with ~400 million cases across the globe each year. Uropathogenic Escherichia coli (UPEC) is the major cause of UTI and increasingly associated with antibiotic resistance. This scenario has been worsened by the emergence and spread of pandemic UPEC sequence type 131 (ST131), a multidrug-resistant clone associated with extraordinarily high rates of infection. Here, we employed transposon-directed insertion site sequencing in combination with metabolomic profiling to identify genes and biochemical pathways required for growth and survival of the UPEC ST131 reference strain EC958 in human urine (HU). We identified 24 genes required for growth in HU, which mapped to diverse pathways involving small peptide, amino acid and nucleotide metabolism, the stringent response pathway, and lipopolysaccharide biosynthesis. We also discovered a role for UPEC resistance to fluoride during growth in HU, most likely associated with fluoridation of drinking water. Complementary nuclear magnetic resonance (NMR)-based metabolomics identified changes in a range of HU metabolites following UPEC growth, the most pronounced being L-lactate, which was utilized as a carbon source via the L-lactate dehydrogenase LldD. Using a mouse UTI model with mixed competitive infection experiments, we demonstrated a role for nucleotide metabolism and the stringent response in UPEC colonization of the mouse bladder. Together, our application of two omics technologies combined with different infection-relevant settings has uncovered new factors required for UPEC growth in HU, thus enhancing our understanding of this pivotal step in the UPEC infection pathway. IMPORTANCE Uropathogenic Escherichia coli (UPEC) cause ~80% of all urinary tract infections (UTIs), with increasing rates of antibiotic resistance presenting an urgent threat to effective treatment. To cause infection, UPEC must grow efficiently in human urine (HU), necessitating a need to understand mechanisms that promote its adaptation and survival in this nutrient-limited environment. Here, we used a combination of functional genomic and metabolomic techniques and identified roles for the metabolism of small peptides, amino acids, nucleotides, and L-lactate, as well as the stringent response pathway, lipopolysaccharide biosynthesis, and fluoride resistance, for UPEC growth in HU. We further demonstrated that pathways involving nucleotide metabolism and the stringent response are required for UPEC colonization of the mouse bladder. The UPEC genes and metabolic pathways identified in this study represent targets for the development of innovative therapeutics to prevent UPEC growth during human UTI, an urgent need given the rapidly rising rates of global antibiotic resistance.
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Affiliation(s)
- Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Horst Joachim Schirra
- School of Environment and Science, Griffith University, Nathan, Queensland, Australia
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Kate M. Peters
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Sohinee Sarkar
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Luke P. Allsopp
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Maud E. S. Achard
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Ulrike Kappler
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark A. Schembri
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
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46
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Rosas-Román I, Guillén-Alonso H, Moreno-Pedraza A, Winkler R. Technical Note: mzML and imzML Libraries for Processing Mass Spectrometry Data with the High-Performance Programming Language Julia. Anal Chem 2024; 96:3999-4004. [PMID: 38427332 PMCID: PMC10938284 DOI: 10.1021/acs.analchem.3c05853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Julia combines the virtues of high-level and low-level programming languages: The code is human-readable, and the performance of the created binaries competes with machine-orientated compilers. Thus, Julia is popular in "Big Data" sciences. Reading mass spectrometry (MS) data with Julia was impossible until now due to missing libraries. Here, we present a Julia library for importing mass spectrometry (MS) data in HUPO standard mzML and imzML formats and demonstrate its function with direct and ambient ionization MS, liquid chromatography-MS, and MS imaging data on standard platforms (Windows, Linux, and Mac OS). The processing speed of Julia for reading imzML MS imaging files was up to 214 times faster than the comparable code in R. Julia can remove bottlenecks for computationally demanding tasks in large-scale MS-Omics and MS imaging data processing workflows and supports their agile development. In addition, time-critical and complex data evaluation tasks become possible, such as following the real-time monitoring of biological processes and pattern recognition in large MS imaging projects. Our mzML/imzML libraries and code examples are available under the terms of the MIT license from https://github.com/CINVESTAV-LABI/julia_mzML_imzML.
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Affiliation(s)
- Ignacio Rosas-Román
- Universidad
de Guanajuato, División de Ciencias e Ingenierías, Loma del Bosque 103, Lomas del Campestre, 37150 León, Guanajuato, Mexico
| | - Héctor Guillén-Alonso
- Center
for Research and Advanced Studies (CINVESTAV) Irapuato, UGA-Langebio, Km.
9.6 Libramiento Norte Carr. Irapuato-León, 36824 Irapuato, Guanajuato, Mexico
- Department
of Biochemical Engineering, National Technological
Institute, 38010 Celaya, Guanajuato, Mexico
| | - Abigail Moreno-Pedraza
- Leibniz
Institute for Vegetable and Ornamental Crops (IGZ) e.V., Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany
- Institute
of Biodiversity, Friedrich Schiller University
Jena, Dornburger-Str.
159, 07743, Jena, Germany
| | - Robert Winkler
- Center
for Research and Advanced Studies (CINVESTAV) Irapuato, UGA-Langebio, Km.
9.6 Libramiento Norte Carr. Irapuato-León, 36824 Irapuato, Guanajuato, Mexico
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47
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Bonora M, Morganti C, van Gastel N, Ito K, Calura E, Zanolla I, Ferroni L, Zhang Y, Jung Y, Sales G, Martini P, Nakamura T, Lasorsa FM, Finkel T, Lin CP, Zavan B, Pinton P, Georgakoudi I, Romualdi C, Scadden DT, Ito K. A mitochondrial NADPH-cholesterol axis regulates extracellular vesicle biogenesis to support hematopoietic stem cell fate. Cell Stem Cell 2024; 31:359-377.e10. [PMID: 38458178 PMCID: PMC10957094 DOI: 10.1016/j.stem.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 11/16/2023] [Accepted: 02/08/2024] [Indexed: 03/10/2024]
Abstract
Mitochondrial fatty acid oxidation (FAO) is essential for hematopoietic stem cell (HSC) self-renewal; however, the mechanism by which mitochondrial metabolism controls HSC fate remains unknown. Here, we show that within the hematopoietic lineage, HSCs have the largest mitochondrial NADPH pools, which are required for proper HSC cell fate and homeostasis. Bioinformatic analysis of the HSC transcriptome, biochemical assays, and genetic inactivation of FAO all indicate that FAO-generated NADPH fuels cholesterol synthesis in HSCs. Interference with FAO disturbs the segregation of mitochondrial NADPH toward corresponding daughter cells upon single HSC division. Importantly, we have found that the FAO-NADPH-cholesterol axis drives extracellular vesicle (EV) biogenesis and release in HSCs, while inhibition of EV signaling impairs HSC self-renewal. These data reveal the existence of a mitochondrial NADPH-cholesterol axis for EV biogenesis that is required for hematopoietic homeostasis and highlight the non-stochastic nature of HSC fate determination.
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Affiliation(s)
- Massimo Bonora
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Departments of Oncology and Medicine, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY 10461, USA
| | - Claudia Morganti
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Departments of Oncology and Medicine, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY 10461, USA
| | - Nick van Gastel
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA; de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Kyoko Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Departments of Oncology and Medicine, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY 10461, USA
| | - Enrica Calura
- Department of Biology, University of Padova, 35121 Padua, Italy
| | - Ilaria Zanolla
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Letizia Ferroni
- Maria Cecilia Hospital, GVM Care & Research, Cotignola, 48033 Ravenna, Italy
| | - Yang Zhang
- Department of Biomedical Engineering, Tufts University, 4 Colby St, Medford, MA 02155, USA
| | - Yookyung Jung
- Department of Biomedical Engineering, Tufts University, 4 Colby St, Medford, MA 02155, USA; Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gabriele Sales
- Department of Biology, University of Padova, 35121 Padua, Italy
| | - Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, 25121 Brescia, Italy
| | - Takahisa Nakamura
- Divisions of Endocrinology and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Department of Metabolic Bioregulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Francesco Massimo Lasorsa
- Department of Biosciences Biotechnologies and Environment University of Bari and Institute of Biomembranes Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70125 Bari, Italy
| | - Toren Finkel
- Aging Institute and Department of Medicine, University of Pittsburgh School of Medicine/University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA
| | - Charles P Lin
- Center for Systems Biology and Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Barbara Zavan
- Maria Cecilia Hospital, GVM Care & Research, Cotignola, 48033 Ravenna, Italy; Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy; Translational Medicine Department, University of Ferrara, 44121 Ferrara, Italy
| | - Paolo Pinton
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; Maria Cecilia Hospital, GVM Care & Research, Cotignola, 48033 Ravenna, Italy; Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Irene Georgakoudi
- Department of Biomedical Engineering, Tufts University, 4 Colby St, Medford, MA 02155, USA
| | - Chiara Romualdi
- Department of Biology, University of Padova, 35121 Padua, Italy
| | - David T Scadden
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Keisuke Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Departments of Oncology and Medicine, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY 10461, USA; Montefiore Einstein Comprehensive Cancer Center and Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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48
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Maushagen J, Addin NS, Schuppert C, Ward-Caviness CK, Nattenmüller J, Adamski J, Peters A, Bamberg F, Schlett CL, Wang-Sattler R, Rospleszcz S. Serum metabolite signatures of cardiac function and morphology in individuals from a population-based cohort. Biomark Res 2024; 12:31. [PMID: 38444025 PMCID: PMC10916302 DOI: 10.1186/s40364-024-00578-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/24/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Changes in serum metabolites in individuals with altered cardiac function and morphology may exhibit information about cardiovascular disease (CVD) pathway dysregulations and potential CVD risk factors. We aimed to explore associations of cardiac function and morphology, evaluated using magnetic resonance imaging (MRI) with a large panel of serum metabolites. METHODS Cross-sectional data from CVD-free individuals from the population-based KORA cohort were analyzed. Associations between 3T-MRI-derived left ventricular (LV) function and morphology parameters (e.g., volumes, filling rates, wall thickness) and markers of carotid plaque with metabolite profile clusters and single metabolites as outcomes were assessed by adjusted multinomial logistic regression and linear regression models. RESULTS In 360 individuals (mean age 56.3 years; 41.9% female), 146 serum metabolites clustered into three distinct profiles that reflected high-, intermediate- and low-CVD risk. Higher stroke volume (relative risk ratio (RRR): 0.53, 95%-CI [0.37; 0.76], p-value < 0.001) and early diastolic filling rate (RRR: 0.51, 95%-CI [0.37; 0.71], p-value < 0.001) were most strongly protectively associated against the high-risk profile compared to the low-risk profile after adjusting for traditional CVD risk factors. Moreover, imaging markers were associated with 10 metabolites in linear regression. Notably, negative associations of stroke volume and early diastolic filling rate with acylcarnitine C5, and positive association of function parameters with lysophosphatidylcholines, diacylphosphatidylcholines, and acylalkylphosphatidylcholines were observed. Furthermore, there was a negative association of LV wall thickness with alanine, creatinine, and symmetric dimethylarginine. We found no significant associations with carotid plaque. CONCLUSIONS Serum metabolite signatures are associated with cardiac function and morphology even in individuals without a clinical indication of CVD.
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Affiliation(s)
- Juliane Maushagen
- Institute of Epidemiology, Helmholtz Munich, Neuherberg, Germany
- Chair of Epidemiology, Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Medical Faculty, Ludwig- Maximilians-Universität (LMU), München, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Nuha Shugaa Addin
- Institute of Epidemiology, Helmholtz Munich, Neuherberg, Germany
- Chair of Epidemiology, Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Medical Faculty, Ludwig- Maximilians-Universität (LMU), München, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Christopher Schuppert
- Department of Diagnostic and Interventional Radiology, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Cavin K Ward-Caviness
- Center for Public Health and Environmental Assessment, U.S. EPA, Chapel Hill, NC, USA
| | - Johanna Nattenmüller
- Department of Diagnostic and Interventional Radiology, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Jerzy Adamski
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore, Singapore
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000, Ljubljana, Slovenia
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Munich, Neuherberg, Germany
- Chair of Epidemiology, Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Medical Faculty, Ludwig- Maximilians-Universität (LMU), München, Germany
- German Center for Diabetes Research, DZD, Neuherberg, Germany
- German Center for Cardiovascular Disease Research (DZHK), Munich Heart Alliance, Munich, Germany
| | - Fabian Bamberg
- Department of Diagnostic and Interventional Radiology, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Christopher L Schlett
- Department of Diagnostic and Interventional Radiology, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Rui Wang-Sattler
- German Center for Diabetes Research, DZD, Neuherberg, Germany
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Susanne Rospleszcz
- Institute of Epidemiology, Helmholtz Munich, Neuherberg, Germany.
- Chair of Epidemiology, Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Medical Faculty, Ludwig- Maximilians-Universität (LMU), München, Germany.
- Department of Diagnostic and Interventional Radiology, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany.
- German Center for Cardiovascular Disease Research (DZHK), Munich Heart Alliance, Munich, Germany.
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49
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DeBartolo D, Arnold FJ, Liu Y, Molotsky E, Tang HY, Merry DE. Differentially disrupted spinal cord and muscle energy metabolism in spinal and bulbar muscular atrophy. JCI Insight 2024; 9:e178048. [PMID: 38452174 PMCID: PMC11128210 DOI: 10.1172/jci.insight.178048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
Prior studies showed that polyglutamine-expanded androgen receptor (AR) is aberrantly acetylated and that deacetylation of the mutant AR by overexpression of nicotinamide adenine dinucleotide-dependent (NAD+-dependent) sirtuin 1 is protective in cell models of spinal and bulbar muscular atrophy (SBMA). Based on these observations and reduced NAD+ in muscles of SBMA mouse models, we tested the therapeutic potential of NAD+ restoration in vivo by treating postsymptomatic transgenic SBMA mice with the NAD+ precursor nicotinamide riboside (NR). NR supplementation failed to alter disease progression and had no effect on increasing NAD+ or ATP content in muscle, despite producing a modest increase of NAD+ in the spinal cords of SBMA mice. Metabolomic and proteomic profiles of SBMA quadriceps muscles indicated alterations in several important energy-related pathways that use NAD+, in addition to the NAD+ salvage pathway, which is critical for NAD+ regeneration for use in cellular energy production. We also observed decreased mRNA levels of nicotinamide riboside kinase 2 (Nmrk2), which encodes a key kinase responsible for NR phosphorylation, allowing its use by the NAD+ salvage pathway. Together, these data suggest a model in which NAD+ levels are significantly decreased in muscles of an SBMA mouse model and intransigent to NR supplementation because of decreased levels of Nmrk2.
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Affiliation(s)
- Danielle DeBartolo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Frederick J. Arnold
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Yuhong Liu
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Elana Molotsky
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Shared Resource, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Diane E. Merry
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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50
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Mastrangelo A, Scotti GM, Manteiga JG, Gisslén M, Price RW, Bestetti A, Turrini F, Caccia R, Gorelik L, Morelli MJ, Castagna A, Cinque P. Alterations in glutamate, arginine, and energy metabolism characterize cerebrospinal fluid and plasma metabolome of persons with HIV-associated dementia. AIDS 2024; 38:299-308. [PMID: 37905996 DOI: 10.1097/qad.0000000000003773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
OBJECTIVES HIV-associated dementia (HAD) is the most severe clinical expression of HIV-mediated neuropathology, and the processes underlying its development remain poorly understood. We aimed to exploit high-dimensional metabolic profiling to gain insights into the pathological mechanisms associated to HAD. DESIGN In this cross-sectional study, we utilized metabolomics to profile matched cerebrospinal fluid (CSF) and plasma samples of HAD individuals ( n = 20) compared with neurologically asymptomatic people with HIV (ASYM, n = 20) and healthy controls (NEG, n = 20). METHODS Identification of plasma and CSF metabolites was performed by liquid-chromatography or gas-chromatography following a validated experimental pipeline. The resulting metabolic profiles were analyzed by machine-learning algorithms, and altered pathways were identified by comparison with KEGG pathway database. RESULTS In CSF, HAD patients displayed an imbalance in glutamine/glutamate ratio, decreased levels of isocitrate and arginine, and increased oxidative stress when compared with ASYM or NEG. These changes were confirmed in matched plasma samples, which in addition revealed an accumulation of eicosanoids and unsaturated fatty acids in HAD individuals. Pathway analysis in both biological fluids suggested that alterations in several metabolic processes, including protein biosynthesis, glutamate and arginine metabolism, and energy metabolism, in association to a perturbed eicosanoid metabolism in plasma, may represent the metabolic signature associated to HAD. CONCLUSION These findings show that HAD may be associated with metabolic modifications in CSF and plasma. These preliminary data may be useful to identify novel metabolic biomarkers and therapeutic targets in HIV-associated neurological impairment.
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Affiliation(s)
- Andrea Mastrangelo
- Vita-Salute San Raffaele University
- Centre Hopitalier Universitaire Vaudoise (CHUV), Lausanne, Switzerland
| | | | | | - Magnus Gisslén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
- Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Richard W Price
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Arabella Bestetti
- Unit of Neurovirology, IRCCS San Raffaele Scientific Institute
- Unit of Infectious Diseases, IRCCS San Raffaele Scientific Institute
| | - Filippo Turrini
- Unit of Neurovirology, IRCCS San Raffaele Scientific Institute
| | - Roberta Caccia
- Unit of Neurovirology, IRCCS San Raffaele Scientific Institute
- Division of Genetics and Cell Biology, IRCCS San Raffaele University, Milan, Italy
| | | | - Marco J Morelli
- Center for Omics Sciences, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Antonella Castagna
- Vita-Salute San Raffaele University
- Unit of Infectious Diseases, IRCCS San Raffaele Scientific Institute
| | - Paola Cinque
- Unit of Neurovirology, IRCCS San Raffaele Scientific Institute
- Unit of Infectious Diseases, IRCCS San Raffaele Scientific Institute
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