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Bueschl C, Riquelme G, Zabalegui N, Rey MA, Monge ME. Tidy-Direct-to-MS: An Open-Source Data-Processing Pipeline for Direct Mass Spectrometry-Based Metabolomics Experiments. J Proteome Res 2024; 23:3208-3216. [PMID: 38833568 DOI: 10.1021/acs.jproteome.3c00784] [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] [Indexed: 06/06/2024]
Abstract
Direct-to-Mass Spectrometry and ambient ionization techniques can be used for biochemical fingerprinting in a fast way. Data processing is typically accomplished with vendor-provided software tools. Here, a novel, open-source functionality, entitled Tidy-Direct-to-MS, was developed for data processing of direct-to-MS data sets. It allows for fast and user-friendly processing using different modules for optional sample position detection and separation, mass-to-charge ratio drift detection and correction, consensus spectra calculation, and bracketing across sample positions as well as feature abundance calculation. The tool also provides functionality for the automated comparison of different sets of parameters, thereby assisting the user in the complex task of finding an optimal combination to maximize the total number of detected features while also checking for the detection of user-provided reference features. In addition, Tidy-Direct-to-MS has the capability for data quality review and subsequent data analysis, thereby simplifying the workflow of untargeted ambient MS-based metabolomics studies. Tidy-Direct-to-MS is implemented in the Python programming language as part of the TidyMS library and can thus be easily extended. Capabilities of Tidy-Direct-to-MS are showcased in a data set acquired in a marine metabolomics study reported in MetaboLights (MTBLS1198) using a transmission mode Direct Analysis in Real Time-Mass Spectrometry (TM-DART-MS)-based method.
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Affiliation(s)
- Christoph Bueschl
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad de Buenos Aires, Argentina
| | - Gabriel Riquelme
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad de Buenos Aires, Argentina
| | - Nicolás Zabalegui
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad de Buenos Aires, Argentina
| | - Maximilian A Rey
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad de Buenos Aires, Argentina
- Departamento de Química Inorgánica Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad de Buenos Aires, Argentina
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2
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Guo Z, Chen Y, Wu Y, Zhan S, Wang L, Li L, Zhang H, Xu Z, Qiu S, Cao J, Guo J, Niu L, Zhong T. Changes in meat quality, metabolites and microorganisms of mutton during cold chain storage. Food Res Int 2024; 189:114551. [PMID: 38876590 DOI: 10.1016/j.foodres.2024.114551] [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: 02/27/2024] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 06/16/2024]
Abstract
During the cold chain storage process, changes in metabolites and microorganisms are highly likely to lead to changes in meat quality. To elucidate the changes in the composition of metabolites and microbiota during cold chain storage of mutton, this study utilized untargeted metabolome and 5R 16S rRNA sequencing analyses to investigate the changes in the longissimus dorsi under different cold chain temperatures (4 °C and -20 °C). With the extension of cold chain storage time, the meat color darkened and the content of C18:2n-6, C20:3n-6, and C23:0 were significantly increased in mutton. In this study, nine metabolites, including 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine, alanylphenylala-nine, indole-3-acrylic acid and the others, were significantly altered during cold chain storage. The abundance of the dominant microorganisms, including Brachymonas, Aeromonas, Corynebacterium and Steroidobacter, was significantly altered. Furthermore, a high correlation was observed between the different metabolites and microorganisms. These findings provide an in-depth understanding of the effects of different cold chain storage temperatures and times on the quality of mutton.
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Affiliation(s)
- Ziwei Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yibing Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuqin Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhenying Xu
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
| | - Shixiu Qiu
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
| | - Jiaxue Cao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
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3
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Martí-Andrés P, Finamor I, Torres-Cuevas I, Pérez S, Rius-Pérez S, Colino-Lage H, Guerrero-Gómez D, Morato E, Marina A, Michalska P, León R, Cheng Q, Jurányi EP, Borbényi-Galambos K, Millán I, Nagy P, Miranda-Vizuete A, Schmidt EE, Martínez-Ruiz A, Arnér ES, Sastre J. TRP14 is the rate-limiting enzyme for intracellular cystine reduction and regulates proteome cysteinylation. EMBO J 2024; 43:2789-2812. [PMID: 38811853 PMCID: PMC11217419 DOI: 10.1038/s44318-024-00117-1] [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: 04/17/2023] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
It has remained unknown how cells reduce cystine taken up from the extracellular space, which is a required step for further utilization of cysteine in key processes such as protein or glutathione synthesis. Here, we show that the thioredoxin-related protein of 14 kDa (TRP14, encoded by TXNDC17) is the rate-limiting enzyme for intracellular cystine reduction. When TRP14 is genetically knocked out, cysteine synthesis through the transsulfuration pathway becomes the major source of cysteine in human cells, and knockout of both pathways becomes lethal in C. elegans subjected to proteotoxic stress. TRP14 can also reduce cysteinyl moieties on proteins, rescuing their activities as here shown with cysteinylated peroxiredoxin 2. Txndc17 knockout mice were, surprisingly, protected in an acute pancreatitis model, concomitant with activation of Nrf2-driven antioxidant pathways and upregulation of transsulfuration. We conclude that TRP14 is the evolutionarily conserved enzyme principally responsible for intracellular cystine reduction in C. elegans, mice, and humans.
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Affiliation(s)
- Pablo Martí-Andrés
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Burjassot, Valencia, Spain
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77, Stockholm, Sweden
| | - Isabela Finamor
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Burjassot, Valencia, Spain
- Department of Physiology and Pharmacology, Federal University of Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - Isabel Torres-Cuevas
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Burjassot, Valencia, Spain
| | - Salvador Pérez
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Burjassot, Valencia, Spain
| | - Sergio Rius-Pérez
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Burjassot, Valencia, Spain
| | - Hildegard Colino-Lage
- Redox Homeostasis Group, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - David Guerrero-Gómez
- Redox Homeostasis Group, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Esperanza Morato
- Centro de Biología Molecular "Severo Ochoa" (CBMSO), CSIC-UAM, Madrid, Spain
| | - Anabel Marina
- Centro de Biología Molecular "Severo Ochoa" (CBMSO), CSIC-UAM, Madrid, Spain
- Unidad de Técnicas Bioanalíticas (BAT), Instituto de Investigación de Ciencias de la Alimentación (CIAL), CSIC-UAM, Madrid, Spain
| | - Patrycja Michalska
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
| | - Rafael León
- Institute of Medical Chemistry, CSIC, Madrid, Spain
| | - Qing Cheng
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77, Stockholm, Sweden
| | - Eszter Petra Jurányi
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, Budapest, Hungary
- Molecular Medicine Division, Semmelweis University Doctoral College, Budapest, Hungary
| | - Klaudia Borbényi-Galambos
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, Budapest, Hungary
- Kálmán Laki Doctoral School, University of Debrecen, Debrecen, Hungary
| | - Iván Millán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Paterna, Valencia, Spain
| | - Péter Nagy
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, Budapest, Hungary
- Department of Anatomy and Histology, HUN-REN-UVMB Laboratory of Redox Biology, University of Veterinary Medicine, Budapest, Hungary
- Chemistry Institute, University of Debrecen, Debrecen, Hungary
| | - Antonio Miranda-Vizuete
- Redox Homeostasis Group, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Edward E Schmidt
- Department of Anatomy and Histology, HUN-REN-UVMB Laboratory of Redox Biology, University of Veterinary Medicine, Budapest, Hungary
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Antonio Martínez-Ruiz
- Unidad de Investigación, Hospital Universitario Santa Cristina, Instituto de Investigación Sanitaria Princesa (IIS_IP), Madrid, Spain
| | - Elias Sj Arnér
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77, Stockholm, Sweden.
- Department of Selenoprotein Research and the National Tumor Biology Laboratory, National Insitute of Oncology, Budapest, Hungary.
| | - Juan Sastre
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Burjassot, Valencia, Spain.
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Tian B, Xu LL, Jiang LD, Lin X, Shen J, Shen H, Su KJ, Gong R, Qiu C, Luo Z, Yao JH, Wang ZQ, Xiao HM, Zhang LS, Deng HW. Identification of the serum metabolites associated with cow milk consumption in Chinese Peri-/Postmenopausal women. Int J Food Sci Nutr 2024:1-13. [PMID: 38918932 DOI: 10.1080/09637486.2024.2366223] [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: 12/22/2023] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Cow milk consumption (CMC) and downstream alterations of serum metabolites are commonly considered important factors regulating human health status. Foods may lead to metabolic changes directly or indirectly through remodelling gut microbiota (GM). We sought to identify the metabolic alterations in Chinese Peri-/Postmenopausal women with habitual CMC and explore if the GM mediates the CMC-metabolite associations. 346 Chinese Peri-/Postmenopausal women participants were recruited in this study. Fixed effects regression and partial least squares discriminant analysis (PLS-DA) were applied to reveal alterations of serum metabolic features in different CMC groups. Spearman correlation coefficient was computed to detect metabolome-metagenome association. 36 CMC-associated metabolites including palmitic acid (FA(16:0)), 7alpha-hydroxy-4-cholesterin-3-one (7alphaC4), citrulline were identified by both fixed effects regression (FDR < 0.05) and PLS-DA (VIP score > 2). Some significant metabolite-GM associations were observed, including FA(16:0) with gut species Bacteroides ovatus, Bacteroides sp.D2. These findings would further prompt our understanding of the effect of cow milk on human health.
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Affiliation(s)
- Bo Tian
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, China
| | - Lu-Lu Xu
- School of Physical Science and Engineering, College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Lin-Dong Jiang
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Xu Lin
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- Shunde Hospital of Southern Medical University (The First People's Hospital of Shunde), Foshan, China
| | - Jie Shen
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Kuan-Jui Su
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Rui Gong
- Shunde Hospital of Southern Medical University (The First People's Hospital of Shunde), Foshan, China
- Department of Cadre Ward Endocrinology, Gansu Provincial Hospital, Lanzhou, China
| | - Chuan Qiu
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Zhe Luo
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Jia-Heng Yao
- School of Physical Science and Engineering, College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Zhuo-Qi Wang
- School of Physical Science and Engineering, College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Hong-Mei Xiao
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, China
| | - Li-Shu Zhang
- School of Physical Science and Engineering, College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, School of Medicine, Tulane University, New Orleans, LA, USA
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5
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Alzahrani AR, Hosny N, Mohamed DI, Abo Nahas HH, Albogami A, Al-Hazani TMI, Ibrahim IAA, Falemban AH, Bamagous GA, Saied EM. Unveiling the multifaceted antiproliferative efficacy of Cichorium endivia root extract by dual modulation of apoptotic and inflammatory genes, inducing cell cycle arrest, and targeting COX-2. RSC Adv 2024; 14:19400-19427. [PMID: 38887636 PMCID: PMC11182420 DOI: 10.1039/d4ra02131b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Chicory (Cichorium endivia L. divaricatum) is a renowned medicinal plant traditionally used for various ailments, yet the pharmacological potential of its roots, particularly in terms of antitumor activity, remains elusive. In the present study, we explore, for the first time, the metabolomic profile of ethanolic extract from Cichorium endivia roots (CIR) and further unveil its antiproliferative potential. The untargeted phytochemical analysis UPLC/T-TOF-MS/MS identified 131 metabolites in the CIR extract, covering acids, amino acids, flavonoids, alkaloids, nucleotides, and carbohydrates. The antiproliferative activity of the CIR extract was tested in 14 cancer cell lines, revealing significant cytotoxicity (IC50: 2.85-29.15 μg mL-1) and a high selectivity index. Among the cells examined, the CIR extract recorded the most potent antiproliferative activity and selectivity toward HepG2 and Panc-1 cells, with an IC50 of 2.85 μg mL-1 and 3.86 μg mL-1, respectively, and SI > 10. Insights into the mode of action of the antiproliferative activity revealed that CIR extract induces cell arrest in the S phase while diminishing cell distribution in the G0/G1 and G2/M phases in HepG-2 and Panc-1 cells. Flow cytometric and RT-PCR analysis revealed that the CIR extract significantly triggers apoptosis and modulates the expression of pro-apoptotic and anti-apoptotic genes. Furthermore, the CIR extract exhibited a pronounced anti-inflammatory activity, as evidenced by down-regulating key cytokines in LPS-induced RAW 264.7 cells and selectively inhibiting the COX-2 enzyme. Finally, the CIR extract showed a robust total antioxidant capacity, together with potent free radicals and metal scavenging properties, highlighting its role in alleviating oxidative stress. Taken together, this study highlights the multifaceted therapeutic potential of CIR extract as a natural-based antitumor supplement.
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Affiliation(s)
- Abdullah R Alzahrani
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University Makkah Saudi Arabia
| | - Nora Hosny
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Suez Canal University Ismailia 41522 Egypt
- Center of Excellence in Molecular and Cellular Medicine, Faculty of Medicine, Suez Canal University Ismailia Egypt
| | - Doaa I Mohamed
- Department of Clinical Pharmacology and Therapeutics, Faculty of Medicine, Ain Shams University Cairo 11566 Egypt
| | | | - Abdulaziz Albogami
- Biology Department, Faculty of Science, Al-Baha University Al Aqiq Saudi Arabia
| | - Tahani Mohamed Ibrahim Al-Hazani
- Biology Department, College of Science and Humanities, Prince Sattam bin Abdulaziz University P. O. Box: 83 Al-Kharj 11940 Saudi Arabia
| | - Ibrahim Abdel Aziz Ibrahim
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University Makkah Saudi Arabia
| | - Alaa Hisham Falemban
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University Makkah Saudi Arabia
| | - Ghazi A Bamagous
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University Makkah Saudi Arabia
| | - Essa M Saied
- Chemistry Department, Faculty of Science, Suez Canal University 41522 Ismailia Egypt
- Institute for Chemistry, Humboldt Universität zu Berlin 12489 Berlin Germany
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Liu H, Bi L, Chen Q, He X, Yan H, Ni W, Wu W, He L, Liu H. Enrichment process, structural prediction, isolation, in vitro cytotoxic and anti-inflammatory effects of triterpenoid saponins in Camellia japonica L. leaves water extract through UPLC-Q-TOF based mass spectrometry similarity networking. Food Chem 2024; 441:138360. [PMID: 38219361 DOI: 10.1016/j.foodchem.2024.138360] [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: 09/21/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 01/16/2024]
Abstract
Camellia japonica L. is rich in bioactive compounds, but its health-enhancing potential is often overshadowed by its ornamental value. Notably, triterpenoid saponins are prominent due to their surfactant properties. MolNetEnhancer revealed 537 compounds in C. japonica leaves water extract, classified into 32 categories, including 38 triterpenoid saponins. To enrich triterpenoid saponins, the process of D101 resin chromatography was employed. Molecular networking analysis based on UPLC-Q-TOF and quantitative analysis based on HPLC revealed saponins concentrated in fractions 3 and 4 (68.3% transfer). MS2LDA and NAP predicted structures for 38 triterpenoid saponins, revealing nearly half of them are potential new compounds. Comprehensive chromatographic and spectroscopic methods were used for purification and structural illustration of triterpenoid saponins, yielding 13, including 7 new compounds. Statistical analysis and in vitro assays revealed the cytotoxic and anti-inflammatory activities of these triterpenoid saponins played a crucial role in the anticancer effects.
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Affiliation(s)
- Hui Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Characteristic Plant Extraction Laboratory, Kunming 650106, China
| | - Lisha Bi
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Characteristic Plant Extraction Laboratory, Kunming 650106, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Qirun Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Characteristic Plant Extraction Laboratory, Kunming 650106, China
| | - Xiaozhi He
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Characteristic Plant Extraction Laboratory, Kunming 650106, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Huan Yan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Characteristic Plant Extraction Laboratory, Kunming 650106, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Wei Ni
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Characteristic Plant Extraction Laboratory, Kunming 650106, China
| | - Wenjuan Wu
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Li He
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, China; Skin Health Research Center, Yunnan Characteristic Plant Extraction Laboratory, Kunming 650106, China.
| | - Haiyang Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Yunnan Characteristic Plant Extraction Laboratory, Kunming 650106, China.
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7
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Zhang Y, Spitzer BW, Zhang Y, Wallace DA, Yu B, Qi Q, Argos M, Avilés-Santa ML, Boerwinkle E, Daviglus ML, Kaplan R, Cai J, Redline S, Sofer T. Untargeted Metabolome Atlas for Sleep Phenotypes in the Hispanic Community Health Study/Study of Latinos. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.17.24307286. [PMID: 38798578 PMCID: PMC11118618 DOI: 10.1101/2024.05.17.24307286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Sleep is essential to maintaining health and wellbeing of individuals, influencing a variety of outcomes from mental health to cardiometabolic disease. This study aims to assess the relationships between various sleep phenotypes and blood metabolites. Utilizing data from the Hispanic Community Health Study/Study of Latinos, we performed association analyses between 40 sleep phenotypes, grouped in several domains (i.e., sleep disordered breathing (SDB), sleep duration, timing, insomnia symptoms, and heart rate during sleep), and 768 metabolites measured via untargeted metabolomics profiling. Network analysis was employed to visualize and interpret the associations between sleep phenotypes and metabolites. The patterns of statistically significant associations between sleep phenotypes and metabolites differed by superpathways, and highlighted subpathways of interest for future studies. For example, some xenobiotic metabolites were associated with sleep duration and heart rate phenotypes (e.g. 1H-indole-7-acetic acid, 4-allylphenol sulfate), while ketone bodies and fatty acid metabolism metabolites were associated with sleep timing measures (e.g. 3-hydroxybutyrate (BHBA), 3-hydroxyhexanoylcarnitine (1)). Heart rate phenotypes had the overall largest number of detected metabolite associations. Many of these associations were shared with both SDB and with sleep timing phenotypes, while SDB phenotypes shared relatively few metabolite associations with sleep duration measures. A number of metabolites were associated with multiple sleep phenotypes, from a few domains. The amino acids vanillylmandelate (VMA) and 1-carboxyethylisoleucine were associated with the greatest number of sleep phenotypes, from all domains other than insomnia. This atlas of sleep-metabolite associations will facilitate hypothesis generation and further study of the metabolic underpinnings of sleep health.
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Affiliation(s)
- Ying Zhang
- Division of Sleep Medicine and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Brian W Spitzer
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Yu Zhang
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Danielle A Wallace
- Division of Sleep Medicine and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Bing Yu
- Department of Epidemiology, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Maria Argos
- Department of Epidemiology and Biostatistics, School of Public Health, University of Illinois Chicago, Chicago, IL, USA
- Department of Environmental Health, School of Public Health, Boston University, Boston, MA, USA
| | - M Larissa Avilés-Santa
- Division of Clinical and Health Services Research, National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Eric Boerwinkle
- Department of Epidemiology, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jianwen Cai
- Collaborative Studies Coordinating Center, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Susan Redline
- Division of Sleep Medicine and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Tamar Sofer
- Division of Sleep Medicine and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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8
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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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9
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Silva E, Dantas R, Barbosa JC, Berlinck RGS, Fill T. Metabolomics approach to understand molecular mechanisms involved in fungal pathogen-citrus pathosystems. Mol Omics 2024; 20:154-168. [PMID: 38273771 DOI: 10.1039/d3mo00182b] [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: 01/27/2024]
Abstract
Citrus is a crucial crop with a significant economic impact globally. However, postharvest decay caused by fungal pathogens poses a considerable threat, leading to substantial financial losses. Penicillium digitatum, Penicillium italicum, Geotrichum citri-aurantii and Phyllosticta citricarpa are the main fungal pathogens, causing green mold, blue mold, sour rot and citrus black spot diseases, respectively. The use of chemical fungicides as a control strategy in citrus raises concerns about food and environmental safety. Therefore, understanding the molecular basis of host-pathogen interactions is essential to find safer alternatives. This review highlights the potential of the metabolomics approach in the search for bioactive compounds involved in the pathogen-citrus interaction, and how the integration of metabolomics and genomics contributes to the understanding of secondary metabolites associated with fungal virulence and the fungal infection mechanisms. Our goal is to provide a pipeline combining metabolomics and genomics that can effectively guide researchers to perform studies aiming to contribute to the understanding of the fundamental chemical and biochemical aspects of pathogen-host interactions, in order to effectively develop new alternatives for fungal diseases in citrus cultivation. We intend to inspire the scientific community to question unexplored biological systems, and to employ diverse analytical approaches and metabolomics techniques to address outstanding questions about the non-studied pathosystems from a chemical biology perspective.
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Affiliation(s)
- Evandro Silva
- State University of Campinas, Institute of Chemistry, CEP, 13083-970 Campinas, SP, Brazil.
- University of São Paulo, Institute of Chemistry, CEP 13566-590, São Carlos, SP, Brazil
| | - Rodolfo Dantas
- State University of Campinas, Institute of Chemistry, CEP, 13083-970 Campinas, SP, Brazil.
| | - Júlio César Barbosa
- State University of Campinas, Institute of Chemistry, CEP, 13083-970 Campinas, SP, Brazil.
| | - Roberto G S Berlinck
- University of São Paulo, Institute of Chemistry, CEP 13566-590, São Carlos, SP, Brazil
| | - Taicia Fill
- State University of Campinas, Institute of Chemistry, CEP, 13083-970 Campinas, SP, Brazil.
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10
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Davis CC, Choisy P. Medicinal plants meet modern biodiversity science. Curr Biol 2024; 34:R158-R173. [PMID: 38412829 DOI: 10.1016/j.cub.2023.12.038] [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: 02/29/2024]
Abstract
Plants have been an essential source of human medicine for millennia. In this review, we argue that a holistic, interdisciplinary approach to the study of medicinal plants that combines methods and insights from three key disciplines - evolutionary ecology, molecular biology/biochemistry, and ethnopharmacology - is poised to facilitate new breakthroughs in science, including pharmacological discoveries and rapid advancements in human health and well-being. Such interdisciplinary research leverages data and methods spanning space, time, and species associated with medicinal plant species evolution, ecology, genomics, and metabolomic trait diversity, all of which build heavily on traditional Indigenous knowledge. Such an interdisciplinary approach contrasts sharply with most well-funded and successful medicinal plant research during the last half-century, which, despite notable advancements, has greatly oversimplified the dynamic relationships between plants and humans, kept hidden the larger human narratives about these relationships, and overlooked potentially important research and discoveries into life-saving medicines. We suggest that medicinal plants and people should be viewed as partners whose relationship involves a complicated and poorly explored set of (socio-)ecological interactions including not only domestication but also commensalisms and mutualisms. In short, medicinal plant species are not just chemical factories for extraction and exploitation. Rather, they may be symbiotic partners that have shaped modern societies, improved human health, and extended human lifespans.
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Affiliation(s)
- Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA.
| | - Patrick Choisy
- LVMH Research, 185 Avenue de Verdun, 45804 Saint Jean de Braye CEDEX, France
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11
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Wang W, Zhen S, Ping Y, Wang L, Zhang Y. Metabolomic biomarkers in liquid biopsy: accurate cancer diagnosis and prognosis monitoring. Front Oncol 2024; 14:1331215. [PMID: 38384814 PMCID: PMC10879439 DOI: 10.3389/fonc.2024.1331215] [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: 10/31/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
Liquid biopsy, a novel detection method, has recently become an active research area in clinical cancer owing to its unique advantages. Studies on circulating free DNA, circulating tumor cells, and exosomes obtained by liquid biopsy have shown great advances and they have entered clinical practice as new cancer biomarkers. The metabolism of the body is dynamic as cancer originates and progresses. Metabolic abnormalities caused by cancer can be detected in the blood, sputum, urine, and other biological fluids via systemic or local circulation. A considerable number of recent studies have focused on the roles of metabolic molecules in cancer. The purpose of this review is to provide an overview of metabolic markers from various biological fluids in the latest clinical studies, which may contribute to cancer screening and diagnosis, differentiation of cancer typing, grading and staging, and prediction of therapeutic response and prognosis.
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Affiliation(s)
- Wenqian Wang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Key Laboratory for Tumor Immunology and Biotherapy of Henan Province, Zhengzhou, Henan, China
| | - Shanshan Zhen
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Key Laboratory for Tumor Immunology and Biotherapy of Henan Province, Zhengzhou, Henan, China
| | - Yu Ping
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Key Laboratory for Tumor Immunology and Biotherapy of Henan Province, Zhengzhou, Henan, China
| | - Liping Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Key Laboratory for Tumor Immunology and Biotherapy of Henan Province, Zhengzhou, Henan, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
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12
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Chang CW, Hsu JY, Lo YT, Liu YH, Mee-inta O, Lee HT, Kuo YM, Liao PC. Characterization of Hair Metabolome in 5xFAD Mice and Patients with Alzheimer's Disease Using Mass Spectrometry-Based Metabolomics. ACS Chem Neurosci 2024; 15:527-538. [PMID: 38269400 PMCID: PMC10853927 DOI: 10.1021/acschemneuro.3c00587] [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: 09/10/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/26/2024] Open
Abstract
Hair emerged as a biospecimen for long-term investigation of endogenous metabolic perturbations, reflecting the chemical composition circulating in the blood over the past months. Despite its potential, the use of human hair for metabolomics in Alzheimer's disease (AD) research remains limited. Here, we performed both untargeted and targeted metabolomic approaches to profile the key metabolic pathways in the hair of 5xFAD mice, a widely used AD mouse model. Furthermore, we applied the discovered metabolites to human subjects. Hair samples were collected from 6-month-old 5xFAD mice, a stage marked by widespread accumulation of amyloid plaques in the brain, followed by sample preparation and high-resolution mass spectrometry analysis. Forty-five discriminatory metabolites were discovered in the hair of 6-month-old 5xFAD mice compared to wild-type control mice. Enrichment analysis revealed three key metabolic pathways: arachidonic acid metabolism, sphingolipid metabolism, and alanine, aspartate, and glutamate metabolism. Among these pathways, six metabolites demonstrated significant differences in the hair of 2-month-old 5xFAD mice, a stage prior to the onset of amyloid plaque deposition. These findings suggest their potential involvement in the early stages of AD pathogenesis. When evaluating 45 discriminatory metabolites for distinguishing patients with AD from nondemented controls, a combination of l-valine and arachidonic acid significantly differentiated these two groups, achieving a 0.88 area under the curve. Taken together, these findings highlight the potential of hair metabolomics in identifying disease-specific metabolic alterations and developing biomarkers for improving disease detection and monitoring.
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Affiliation(s)
- Chih-Wei Chang
- Department
of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Jen-Yi Hsu
- Department
of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Yu-Tai Lo
- Department
of Geriatrics and Gerontology, National Cheng Kung University Hospital,
College of Medicine, National Cheng Kung
University, Tainan 704, Taiwan
- Department
of Public Health, College of Medicine, National
Cheng Kung University, Tainan 704, Taiwan
| | - Yu-Hsuan Liu
- Department
of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Onanong Mee-inta
- Institute
of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Hsueh-Te Lee
- Institute
of Anatomy and Cell Biology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yu-Min Kuo
- Institute
of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Department
of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Pao-Chi Liao
- Department
of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Department
of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
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13
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Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024; 31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [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: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly. METHODS In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification. RESULTS Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well. CONCLUSION The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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14
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Varghese B, Babu S, Jala A, Das P, Raju R, Borkar RM, Adela R. Integrative Placental Multi-Omics Analysis Reveals Perturbed Pathways and Potential Prognostic Biomarkers in Gestational Hypertension. Arch Med Res 2024; 55:102909. [PMID: 37984232 DOI: 10.1016/j.arcmed.2023.102909] [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: 06/16/2023] [Revised: 09/26/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Gestational hypertension (GH) is a severe complication that occurs after 20 weeks of pregnancy; however, its molecular mechanisms are not yet fully understood. OBJECTIVE Through this case-control discovery phase study, we aimed to find disease-specific candidate placental microRNAs (miRNAs) and metabolite markers for differentiating GH by integrating next-generation sequencing and metabolomics multi-omics analysis of placenta. Using small RNA sequencing and metabolomics of placental tissues of healthy pregnant (HP, n = 24) and GH subjects (n = 20), the transcriptome and metabolome were characterized in both groups. RESULTS The study identified a total of 44 downregulated placental miRNAs which includes three novel, three mature and 38 precursor miRNAs. Six miRNAs including three mature (hsa-miR-181a-5p, hsa-miR-498-5p, and hsa-miR-26b-5p) and three novel (NC_000016.10_1061, NC_000005.10_475, and NC_000001.11_53) were considered for final target prediction and functional annotation. Integrative analysis of differentially expressed miRNAs and metabolites yielded five pathways such as purine, glutathione, glycerophospholipid, inositol phosphate and β-alanine to be significantly perturbed in GH. We present fourteen genes (LPCAT1, LPCAT2, DGKH, PISD, GPAT2, PTEN, SACM1L, PGM2, AMPD3, AK7, AK3, CNDP1, IDH2, and ODC1) and eight metabolites (xanthosine, xanthine, spermine, glycine, CDP-Choline, glyceraldehyde 3-phosphate, β-alanine, and histidine) with potential to distinguish GH and HP. CONCLUSION The differential expression of miRNAs, their target genes, altered metabolites and metabolic pathways in GH patients were identified for the first time in our study. Further, the altered miRNAs and metabolites were integrated to build their inter-connectivity network. The findings obtained from our study may be used as a valuable source to further unravel the molecular pathways associated with GH and also for the evaluation of prognostic markers.
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Affiliation(s)
- Bincy Varghese
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Guwahati, Assam, India
| | - Sreeranjini Babu
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, India; Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Aishwarya Jala
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research, Guwahati, Assam, India
| | - Panchanan Das
- Department of Obstetrics and Gynecology, Gauhati Medical College, Guwahati, Assam, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, India
| | - Roshan M Borkar
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research, Guwahati, Assam, India
| | - Ramu Adela
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research, Guwahati, Assam, India.
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15
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Sharma A, Choudhary P, Chakdar H, Shukla P. Molecular insights and omics-based understanding of plant-microbe interactions under drought stress. World J Microbiol Biotechnol 2023; 40:42. [PMID: 38105277 DOI: 10.1007/s11274-023-03837-4] [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: 09/29/2023] [Accepted: 11/11/2023] [Indexed: 12/19/2023]
Abstract
The detrimental effects of adverse environmental conditions are always challenging and remain a major concern for plant development and production worldwide. Plants deal with such constraints by physiological, biochemical, and morphological adaptations as well as acquiring mutual support of beneficial microorganisms. As many stress-responsive traits of plants are influenced by microbial activities, plants have developed a sophisticated interaction with microbes to cope with adverse environmental conditions. The production of numerous bioactive metabolites by rhizospheric, endo-, or epiphytic microorganisms can directly or indirectly alter the root system architecture, foliage production, and defense responses. Although plant-microbe interactions have been shown to improve nutrient uptake and stress resilience in plants, the underlying mechanisms are not fully understood. "Multi-omics" application supported by genomics, transcriptomics, and metabolomics has been quite useful to investigate and understand the biochemical, physiological, and molecular aspects of plant-microbe interactions under drought stress conditions. The present review explores various microbe-mediated mechanisms for drought stress resilience in plants. In addition, plant adaptation to drought stress is discussed, and insights into the latest molecular techniques and approaches available to improve drought-stress resilience are provided.
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Affiliation(s)
- Aditya Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Prassan Choudhary
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India
| | - Hillol Chakdar
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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16
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Vieira de Sousa T, Guedes de Pinho P, Pinto J. Metabolomic Signatures of Treatment Response in Bladder Cancer. Int J Mol Sci 2023; 24:17543. [PMID: 38139377 PMCID: PMC10743932 DOI: 10.3390/ijms242417543] [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: 11/24/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Bladder cancer (BC) stands as one of the most prevalent urological malignancies, with over 500 thousand newly diagnosed cases annually. Treatment decisions in BC depend on factors like the risk of recurrence, the type of tumor, and the stage of the disease. While standard therapeutic approaches encompass transurethral resection of the bladder tumor, radical cystectomy, and chemo- or immunotherapy, these methods exhibit limited efficacy in mitigating the aggressive and recurrent nature of bladder tumors. To overcome this challenge, it is crucial to develop innovative methods for monitoring and predicting treatment responses among patients with BC. Metabolomics is gaining recognition as a promising approach for discovering biomarkers. It has the potential to reveal metabolic disruptions that precisely reflect how BC patients respond to particular treatments, providing a revolutionary method to improve accuracy in monitoring and predicting outcomes. In this article, we present a comprehensive review of studies employing metabolomics approaches to investigate the metabolic responses associated with different treatment modalities for BC. The review encompasses an exploration of various models, samples, and analytical techniques applied in this context. Special emphasis is placed on the reported changes in metabolite levels derived from these studies, highlighting their potential as biomarkers for personalized medicine in BC.
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Affiliation(s)
- Tiago Vieira de Sousa
- Associate Laboratory i4HB–Institute for Health and Bioeconomy, University of Porto, 4050-313 Porto, Portugal;
- UCIBIO–Applied Molecular Biosciences Unit, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Paula Guedes de Pinho
- Associate Laboratory i4HB–Institute for Health and Bioeconomy, University of Porto, 4050-313 Porto, Portugal;
- UCIBIO–Applied Molecular Biosciences Unit, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Joana Pinto
- Associate Laboratory i4HB–Institute for Health and Bioeconomy, University of Porto, 4050-313 Porto, Portugal;
- UCIBIO–Applied Molecular Biosciences Unit, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
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17
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Ndlovu IS, Tshilwane SI, Ngcamphalala PI, Vosloo A, Chaisi M, Mukaratirwa S. Metabolomics (Non-Targeted) of Induced Type 2 Diabetic Sprague Dawley Rats Comorbid with a Tissue-Dwelling Nematode Parasite. Int J Mol Sci 2023; 24:17211. [PMID: 38139040 PMCID: PMC10743009 DOI: 10.3390/ijms242417211] [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: 10/12/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Type 2 diabetes is a non-communicable metabolic syndrome that is characterized by the dysfunction of pancreatic β-cells and insulin resistance. Both animal and human studies have been conducted, demonstrating that helminth infections are associated with a decreased prevalence of type 2 diabetes mellitus (T2DM). However, there is a paucity of information on the impact that helminths have on the metabolome of the host and how the infection ameliorates T2DM or its progression. Therefore, this study aimed at using a non-targeted metabolomics approach to systematically identify differentiating metabolites from serum samples of T2DM-induced Sprague Dawley (SD) rats infected with a tissue-dwelling nematode, Trichinella zimbabwensis, and determine the metabolic pathways impacted during comorbidity. Forty-five male SD rats with a body weight between 160 g and 180 g were used, and these were randomly selected into control (non-diabetic and not infected with T. zimbabwensis) (n = 15) and T2DM rats infected with T. zimbabwensis (TzDM) (n = 30). The results showed metabolic separation between the two groups, where d-mannitol, d-fructose, and glucose were upregulated in the TzDM group, when compared to the control group. L-tyrosine, glycine, diglycerol, L-lysine, and L-hydroxyproline were downregulated in the TzDM group when compared to the control group. Metabolic pathways which were highly impacted in the TzDM group include biotin metabolism, carnitine synthesis, and lactose degradation. We conclude from our study that infecting T2DM rats with a tissue-dwelling nematode, T. zimbabwensis, causes a shift in the metabolome, causing changes in different metabolic pathways. Additionally, the infection showed the potential to regulate or improve diabetes complications by causing a decrease in the amino acid concentration that results in metabolic syndrome.
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Affiliation(s)
- Innocent Siyanda Ndlovu
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa; (I.S.N.); (P.I.N.); (A.V.)
| | - Selaelo Ivy Tshilwane
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa; (S.I.T.); (M.C.)
| | - Philile Ignecious Ngcamphalala
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa; (I.S.N.); (P.I.N.); (A.V.)
| | - Andre’ Vosloo
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa; (I.S.N.); (P.I.N.); (A.V.)
| | - Mamohale Chaisi
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa; (S.I.T.); (M.C.)
- Foundational Biodiversity Science, South African National Biodiversity Institute, Pretoria 0001, South Africa
| | - Samson Mukaratirwa
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa; (I.S.N.); (P.I.N.); (A.V.)
- One Health Center for Zoonoses and Tropical Veterinary Medicine, School of Veterinary Medicine, Ross University, Basseterre KN0101, Saint Kitts and Nevis
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18
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Jeppesen MJ, Powers R. Multiplatform untargeted metabolomics. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:628-653. [PMID: 37005774 PMCID: PMC10948111 DOI: 10.1002/mrc.5350 10.1002/mrc.5350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 06/23/2024]
Abstract
Metabolomics samples like human urine or serum contain upwards of a few thousand metabolites, but individual analytical techniques can only characterize a few hundred metabolites at best. The uncertainty in metabolite identification commonly encountered in untargeted metabolomics adds to this low coverage problem. A multiplatform (multiple analytical techniques) approach can improve upon the number of metabolites reliably detected and correctly assigned. This can be further improved by applying synergistic sample preparation along with the use of combinatorial or sequential non-destructive and destructive techniques. Similarly, peak detection and metabolite identification strategies that employ multiple probabilistic approaches have led to better annotation decisions. Applying these techniques also addresses the issues of reproducibility found in single platform methods. Nevertheless, the analysis of large data sets from disparate analytical techniques presents unique challenges. While the general data processing workflow is similar across multiple platforms, many software packages are only fully capable of processing data types from a single analytical instrument. Traditional statistical methods such as principal component analysis were not designed to handle multiple, distinct data sets. Instead, multivariate analysis requires multiblock or other model types for understanding the contribution from multiple instruments. This review summarizes the advantages, limitations, and recent achievements of a multiplatform approach to untargeted metabolomics.
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Affiliation(s)
- Micah J. Jeppesen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
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19
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Jeppesen MJ, Powers R. Multiplatform untargeted metabolomics. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:628-653. [PMID: 37005774 PMCID: PMC10948111 DOI: 10.1002/mrc.5350] [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: 01/16/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Metabolomics samples like human urine or serum contain upwards of a few thousand metabolites, but individual analytical techniques can only characterize a few hundred metabolites at best. The uncertainty in metabolite identification commonly encountered in untargeted metabolomics adds to this low coverage problem. A multiplatform (multiple analytical techniques) approach can improve upon the number of metabolites reliably detected and correctly assigned. This can be further improved by applying synergistic sample preparation along with the use of combinatorial or sequential non-destructive and destructive techniques. Similarly, peak detection and metabolite identification strategies that employ multiple probabilistic approaches have led to better annotation decisions. Applying these techniques also addresses the issues of reproducibility found in single platform methods. Nevertheless, the analysis of large data sets from disparate analytical techniques presents unique challenges. While the general data processing workflow is similar across multiple platforms, many software packages are only fully capable of processing data types from a single analytical instrument. Traditional statistical methods such as principal component analysis were not designed to handle multiple, distinct data sets. Instead, multivariate analysis requires multiblock or other model types for understanding the contribution from multiple instruments. This review summarizes the advantages, limitations, and recent achievements of a multiplatform approach to untargeted metabolomics.
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Affiliation(s)
- Micah J. Jeppesen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
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20
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Shastry A, Dunham-Snary K. Metabolomics and mitochondrial dysfunction in cardiometabolic disease. Life Sci 2023; 333:122137. [PMID: 37788764 DOI: 10.1016/j.lfs.2023.122137] [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: 08/01/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 10/05/2023]
Abstract
Circulating metabolites are indicators of systemic metabolic dysfunction and can be detected through contemporary techniques in metabolomics. These metabolites are involved in numerous mitochondrial metabolic processes including glycolysis, fatty acid β-oxidation, and amino acid catabolism, and changes in the abundance of these metabolites is implicated in the pathogenesis of cardiometabolic diseases (CMDs). Epigenetic regulation and direct metabolite-protein interactions modulate metabolism, both within cells and in the circulation. Dysfunction of multiple mitochondrial components stemming from mitochondrial DNA mutations are implicated in disease pathogenesis. This review will summarize the current state of knowledge regarding: i) the interactions between metabolites found within the mitochondrial environment during CMDs, ii) various metabolites' effects on cellular and systemic function, iii) how harnessing the power of metabolomic analyses represents the next frontier of precision medicine, and iv) how these concepts integrate to expand the clinical potential for translational cardiometabolic medicine.
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Affiliation(s)
- Abhishek Shastry
- Department of Medicine, Queen's University, Kingston, ON, Canada
| | - Kimberly Dunham-Snary
- Department of Medicine, Queen's University, Kingston, ON, Canada; Department of Biomedical & Molecular Sciences, Queen's University, Kingston, ON, Canada.
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21
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Choueiry F, Xu R, Meyrath K, Zhu J. Database-assisted, globally optimized targeted secondary electrospray ionization high resolution mass spectrometry (dGOT-SESI-HRMS) and spectral stitching enhanced volatilomics analysis of bacterial metabolites. Analyst 2023; 148:5673-5683. [PMID: 37819163 PMCID: PMC10841745 DOI: 10.1039/d3an01487h] [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] [Indexed: 10/13/2023]
Abstract
Secondary electrospray ionization high-resolution mass spectrometry (SESI-HRMS) is an innovative analytical technique for the rapid and non-invasive analysis of volatile organic compounds (VOCs). However, compound annotation and ion suppression in the SESI source has hindered feature detection, stability and reproducibility of SESI-HRMS in untargeted volatilomics. To address this, we have developed and optimized a novel pseudo-targeted approach, database-assisted globally optimized targeted (dGOT)-SESI-HRMS using the microbial-VOC (mVOC) database, and spectral stitching methods to enhance metabolite detection in headspace of anaerobic bacterial cultures. Headspace volatiles from representative bacteria strains were assessed using full scan with data dependent acquisition (DDA), conventional globally optimized targeted (GOT) method, and spectral stitching supported dGOT experiments based on a MS peaks list derived from mVOC. Our results indicate that spectral stitching supported dGOT-SESI-HRMS can proportionally fragment peaks with respect to different analysis windows, with a total of 109 VOCs fragmented from 306 targeted compounds. Of the collected spectra, 88 features were confirmed as culture derived volatiles with respect to media blanks. Annotation was also achieved with a total of 25 unique volatiles referenced to standard databases allowing for biological interpretation. Principal component analysis (PCA) summarizing the headspace volatile demonstrated improved separation of clusters when data was acquired using the dGOT method. Collectively, our dGOT-SESI-HRMS method afforded robust capability of capturing unique VOC profiles from different bacterial strains and culture conditions when compared to conventional GOT and DDA modes, suggesting the newly developed approach can serve as a more reliable analytical method for the sensitive monitoring of gut microbial metabolism.
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Affiliation(s)
- Fouad Choueiry
- Department of Human Sciences, The Ohio State University, USA.
- James Comprehensive Cancer Center, The Ohio State University, 400 W 12th Ave, Columbus, OH 43210, USA
| | - Rui Xu
- Department of Human Sciences, The Ohio State University, USA.
| | - Kelly Meyrath
- Department of Human Sciences, The Ohio State University, USA.
| | - Jiangjiang Zhu
- Department of Human Sciences, The Ohio State University, USA.
- James Comprehensive Cancer Center, The Ohio State University, 400 W 12th Ave, Columbus, OH 43210, USA
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22
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Fuica-Carrasco C, Toro-Núñez Ó, Lira-Noriega A, Pérez AJ, Hernández V. Metabolome expression in Eucryphia cordifolia populations: Role of seasonality and ecological niche centrality hypothesis. JOURNAL OF PLANT RESEARCH 2023; 136:827-839. [PMID: 37486392 DOI: 10.1007/s10265-023-01483-3] [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: 02/14/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
The ecological niche centrality hypothesis states that population abundance is determined by the position in the ecological niche, expecting higher abundances towards the center of the niche and lower at the periphery. However, the variations in the conditions that favor the persistence of populations between the center and the periphery of the niche can be a surrogate of stress factors that are reflected in the production of metabolites in plants. In this study we tested if metabolomic similarity and diversity in populations of the tree species Eucryphia cordifolia Cav. vary according to their position with respect to the structure of the ecological niche. We hypothesize that populations growing near the centroid should exhibit lower metabolites diversity than plants growing at the periphery of the niche. The ecological niche of the species was modeled using correlative approaches and bioclimatic variables to define central and peripheral localities from which we chose four populations to obtain their metabolomic information using UHPLC-DAD-QTOF-MS. We observed that populations farther away from the centroid tend to have higher metabolome diversity, thus supporting our expectation of the niche centrality hypothesis. Nonetheless, the Shannon index showed a marked variation in metabolome diversity at the seasonal level, with summer and autumn being the periods with higher metabolite diversity compared to winter and spring. We conclude that both the environmental variation throughout the year in combination with the structure of the ecological niche are relevant to understand the variation in expression of metabolites in plants.
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Affiliation(s)
- Camila Fuica-Carrasco
- Laboratorio de Química de Productos Naturales, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, CP 40300000, Chile.
| | - Óscar Toro-Núñez
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, CP 40300000, Chile
| | - Andrés Lira-Noriega
- CONAHCyT Research Fellow, Red de Estudios Moleculares Avanzados, Instituto de Ecología, Mexico City, A.C, México
| | - Andy J Pérez
- Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Casilla 160-C, Concepción, CP 40300000, Chile
| | - Víctor Hernández
- Laboratorio de Química de Productos Naturales, Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, CP 40300000, Chile
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23
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Randall LV, Kim DH, Abdelrazig SMA, Bollard NJ, Hemingway-Arnold H, Hyde RM, Thompson JS, Green MJ. Predicting lameness in dairy cattle using untargeted liquid chromatography-mass spectrometry-based metabolomics and machine learning. J Dairy Sci 2023; 106:7033-7042. [PMID: 37500436 PMCID: PMC10570404 DOI: 10.3168/jds.2022-23118] [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: 12/06/2022] [Accepted: 03/20/2023] [Indexed: 07/29/2023]
Abstract
Lameness in dairy cattle is a highly prevalent condition that impacts on the health and welfare of dairy cows. Prompt detection and implementation of effective treatment is important for managing lameness. However, major limitations are associated with visual assessment of lameness, which is the most commonly used method to detect lameness. The aims of this study were to investigate the use of metabolomics and machine learning to develop novel methods to detect lameness. Untargeted metabolomics using liquid chromatography-mass spectrometry (LC-MS) alongside machine learning models and a stability selection method were utilized to evaluate the predictive accuracy of differences in the metabolomics profile of first-lactation dairy cows before (during the transition period) and at the time of lameness (based on visual assessment using the 0-3 scale of the Agriculture and Horticulture Development Board). Urine samples were collected from 2 cohorts of dairy heifers and stored at -86°C before analysis using LC-MS. Cohort 1 (n = 90) cows were recruited as current first-lactation cows with weekly mobility scores recorded over a 4-mo timeframe, from which newly lame and nonlame cows were identified. Cohort 2 (n = 30) cows were recruited within 3 wk before calving, and lameness events (based on mobility score) were recorded through lactation until a minimum of 70 d in milk (DIM). All cows were matched paired by DIM ± 14 d. The median DIM at lameness identification was 187.5 and 28.5 for cohort 1 and 2, respectively. The best performing machine learning models predicted lameness at the time of lameness with an accuracy of between 81 and 82%. Using stability selection, the prediction accuracy at the time of lameness was 80 to 81%. For samples collected before and after calving, the best performing machine learning model predicted lameness with an accuracy of 71 and 75%, respectively. The findings from this study demonstrate that untargeted LC-MS profiling combined with machine learning methods can be used to predict lameness as early as before calving and before observable changes in gait in first-lactation dairy cows. The methods also provide accuracies for detecting lameness at the time of observable changes in gait of up to 82%. The findings demonstrate that these methods could provide substantial advancements in the early prediction and prevention of lameness risk. Further external validation work is required to confirm these findings are generalizable; however, this study provides the basis from which future work can be conducted.
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Affiliation(s)
- Laura V Randall
- University of Nottingham, School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, United Kingdom.
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, Advanced Materials & Healthcare Technologies Division, School of Pharmacy, University of Nottingham, School of Pharmacy, Nottingham, NG7 2RD, United Kingdom
| | - Salah M A Abdelrazig
- Centre for Analytical Bioscience, Advanced Materials & Healthcare Technologies Division, School of Pharmacy, University of Nottingham, School of Pharmacy, Nottingham, NG7 2RD, United Kingdom
| | - Nicola J Bollard
- University of Nottingham, School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, United Kingdom
| | - Heather Hemingway-Arnold
- University of Nottingham, School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, United Kingdom
| | - Robert M Hyde
- University of Nottingham, School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, United Kingdom
| | - Jake S Thompson
- University of Nottingham, School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, United Kingdom
| | - Martin J Green
- University of Nottingham, School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, United Kingdom
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24
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Gill B, Schwecht I, Rahman N, Dhawan T, Verschoor C, Nazli A, Kaushic C. Metabolic signature for a dysbiotic microbiome in the female genital tract: A systematic review and meta-analysis. Am J Reprod Immunol 2023; 90:e13781. [PMID: 37766408 DOI: 10.1111/aji.13781] [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: 04/14/2023] [Revised: 07/06/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The vaginal microbiome (VMB) is a critical determinant of reproductive health, where a microbial shift towards a dysbiotic environment has implications for susceptibility to, and clinical presentation of sexually transmitted infections (STIs). Metabolomic profiling of the vaginal microenvironment has led to the identification of metabolic responses to clinical conditions of dysbiosis. However, no studies have examined metabolic markers that are common across conditions and can serve as a signature for vaginal dysbiosis. METHOD OF STUDY We have conducted a comprehensive systematic review and meta-analysis to identify consistently deregulated metabolites along with their impact on host and microbial metabolism during dysbiosis. We employed two complementary approaches including a vote counting analysis for all eligible studies identified in the systematic review, in addition to a meta-analysis for a subset of studies with sufficient available data. Significantly deregulated metabolites were then selected for pathway enrichment analysis. RESULTS Our results revealed a total of 502 altered metabolites reported across 10 dysbiotic conditions from 16 studies. Following a rigorous, collective analysis, six metabolites which were consistently downregulated and could be generalized to all dysbiotic conditions were identified. In addition, five downregulated and one upregulated metabolite was identified from a bacterial vaginosis (BV) focused sub-analysis. These metabolites have the potential to serve as a metabolic signature for vaginal dysbiosis. Their role in eight altered metabolic pathways indicates a disruption of amino acid, carbohydrate, and energy metabolism during dysbiosis. CONCLUSION Based on this analysis, we propose a schematic model outlining the common metabolic perturbations associated with vaginal dysbiosis, which can be potential targets for therapeutics and prophylaxis.
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Affiliation(s)
- Biban Gill
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Ingrid Schwecht
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Nuzhat Rahman
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Tushar Dhawan
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Chris Verschoor
- Health Sciences North Research Institute, Northern Ontario School of Medicine, Sudbury, ON, Canada
| | - Aisha Nazli
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Charu Kaushic
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Center, Michael G. DeGroote Center for Learning and Discovery, McMaster University, Hamilton, ON, Canada
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25
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de Jesus JR, de Araujo Andrade T, de Figueiredo EC. Biomarkers in psychiatric disorders. Adv Clin Chem 2023; 116:183-208. [PMID: 37852719 DOI: 10.1016/bs.acc.2023.05.005] [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] [Indexed: 10/20/2023]
Abstract
Psychiatric disorders represent a significant socioeconomic and healthcare burden worldwide. Of these, schizophrenia, bipolar disorder, major depressive disorder and anxiety are among the most prevalent. Unfortunately, diagnosis remains problematic and largely complicated by the lack of disease specific biomarkers. Accordingly, much research has focused on elucidating these conditions to more fully understand underlying pathophysiology and potentially identify biomarkers, especially those of early stage disease. In this chapter, we review current status of this endeavor as well as the potential development of novel biomarkers for clinical applications and future research study.
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Affiliation(s)
| | | | - Eduardo Costa de Figueiredo
- Faculty of Pharmaceutical Sciences, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, Alfenas, Minas Gerais, Brazil
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26
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Di Giovanni N, Meuwis MA, Louis E, Focant JF. Correlations for untargeted GC × GC-HRTOF-MS metabolomics of colorectal cancer. Metabolomics 2023; 19:85. [PMID: 37740774 DOI: 10.1007/s11306-023-02047-1] [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: 04/15/2022] [Accepted: 08/28/2023] [Indexed: 09/25/2023]
Abstract
INTRODUCTION Modern comprehensive instrumentations provide an unprecedented coverage of complex matrices in the form of high-dimensional, information rich data sets. OBJECTIVES In addition to the usual biomarker research that focuses on the detection of the studied condition, we aimed to define a proper strategy to conduct a correlation analysis on an untargeted colorectal cancer case study with a data set of 102 variables corresponding to metabolites obtained from serum samples analyzed with comprehensive two-dimensional gas chromatography coupled to high-resolution time-of-flight mass spectrometry (GC × GC-HRTOF-MS). Indeed, the strength of association existing between the metabolites contains potentially valuable information about the molecular mechanisms involved and the underlying metabolic network associated to a global perturbation, at no additional analytical effort. METHODS Following Anscombe's quartet, we took particular attention to four main aspects. First, the presence of non-linear relationships through the comparison of parametric and non-parametric correlation coefficients: Pearson's r, Spearman's rho, Kendall's tau and Goodman-Kruskal's gamma. Second, the visual control of the detected associations through scatterplots and their associated regressions and angles. Third, the effect and handling of atypical samples and values. Fourth, the role of the precision of the data on the attribution of the ranks through the presence of ties. RESULTS Kendall's tau was found the method of choice for the data set at hand. Its application highlighted 17 correlations significantly altered in the active state of colorectal cancer (CRC) in comparison to matched healthy controls (HC), from which 10 were specific to this state in comparison to the remission one (R-CRC) investigated on distinct patients. 15 metabolites involved in the correlations of interest, on the 25 unique ones obtained, were annotated (Metabolomics Standards Initiative level 2). CONCLUSIONS The metabolites highlighted could be used to better understand the pathology. The systematic investigation of the methodological aspects that we expose allows to implement correlation analysis to various fields and many specific cases.
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Affiliation(s)
- Nicolas Di Giovanni
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août,B6c, B-4000, Liège, Sart Tilman, Belgium
| | - Marie-Alice Meuwis
- GIGA Institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de L'Hôpital 13, B34-35, B-4000, Liège, Belgium
| | - Edouard Louis
- GIGA Institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de L'Hôpital 13, B34-35, B-4000, Liège, Belgium
| | - Jean-François Focant
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août,B6c, B-4000, Liège, Sart Tilman, Belgium.
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27
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Zhang S, Qiu X, Zhang Y, Huang C, Lin D. Metabolomic Analysis of Trehalose Alleviating Oxidative Stress in Myoblasts. Int J Mol Sci 2023; 24:13346. [PMID: 37686153 PMCID: PMC10488301 DOI: 10.3390/ijms241713346] [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: 08/01/2023] [Revised: 08/10/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Trehalose, a naturally occurring non-toxic disaccharide, has attracted considerable attention for its potential in alleviating oxidative stress in skeletal muscle. In this study, our aim was to elucidate the metabolic mechanisms underlying the protective effects of trehalose against hydrogen peroxide (H2O2)-induced oxidative stress in C2C12 myoblasts. Our results show that both trehalose treatment and pretreatment effectively alleviate the H2O2-induced decrease in cell viability, reduce intracellular reactive oxygen species (ROS), and attenuate lipid peroxidation. Furthermore, using NMR-based metabolomics analysis, we observed that trehalose treatment and pretreatment modulate the metabolic profile of myoblasts, specifically regulating oxidant metabolism and amino acid metabolism, contributing to their protective effects against oxidative stress. Importantly, our results reveal that trehalose treatment and pretreatment upregulate the expression levels of P62 and Nrf2 proteins, thereby activating the Nrf2-NQO1 axis and effectively reducing oxidative stress. These significant findings highlight the potential of trehalose supplementation as a promising and effective strategy for alleviating oxidative stress in skeletal muscle and provide valuable insights into its potential therapeutic applications.
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Affiliation(s)
- Shuya Zhang
- Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; (S.Z.); (X.Q.); (Y.Z.)
| | - Xu Qiu
- Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; (S.Z.); (X.Q.); (Y.Z.)
| | - Yue Zhang
- Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; (S.Z.); (X.Q.); (Y.Z.)
| | - Caihua Huang
- Research and Communication Center of Exercise and Health, Xiamen University of Technology, Xiamen 361021, China;
| | - Donghai Lin
- Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; (S.Z.); (X.Q.); (Y.Z.)
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28
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Boruta T. Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview. Comput Struct Biotechnol J 2023; 21:4021-4029. [PMID: 37649711 PMCID: PMC10462793 DOI: 10.1016/j.csbj.2023.08.011] [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: 05/14/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023] Open
Abstract
Co-cultivation is an effective method of inducing the production of specialized metabolites (SMs) in microbial strains. By mimicking the ecological interactions that take place in natural environment, this approach enables to trigger the biosynthesis of molecules which are not formed under monoculture conditions. Importantly, microbial co-cultivation may lead to the discovery of novel chemical entities of pharmaceutical interest. The experimental efforts aimed at the induction of SMs are greatly facilitated by computational techniques. The aim of this overview is to highlight the relevance of computational methods for the investigation of SM induction via microbial co-cultivation. The concepts related to the induction of SMs in microbial co-cultures are briefly introduced by addressing four areas associated with the SM induction workflows, namely the detection of SMs formed exclusively under co-culture conditions, the annotation of induced SMs, the identification of SM producer strains, and the optimization of fermentation conditions. The computational infrastructure associated with these areas, including the tools of multivariate data analysis, molecular networking, genome mining and mathematical optimization, is discussed in relation to the experimental results described in recent literature. The perspective on the future developments in the field, mainly in relation to the microbiome-related research, is also provided.
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Affiliation(s)
- Tomasz Boruta
- Lodz University of Technology, Faculty of Process and Environmental Engineering, Department of Bioprocess Engineering, ul. Wólczańska 213, 93-005 Łódź, Poland
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29
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Al-Sulaiti H, Almaliti J, Naman CB, Al Thani AA, Yassine HM. Metabolomics Approaches for the Diagnosis, Treatment, and Better Disease Management of Viral Infections. Metabolites 2023; 13:948. [PMID: 37623891 PMCID: PMC10456346 DOI: 10.3390/metabo13080948] [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: 05/31/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 08/26/2023] Open
Abstract
Metabolomics is an analytical approach that involves profiling and comparing the metabolites present in biological samples. This scoping review article offers an overview of current metabolomics approaches and their utilization in evaluating metabolic changes in biological fluids that occur in response to viral infections. Here, we provide an overview of metabolomics methods including high-throughput analytical chemistry and multivariate data analysis to identify the specific metabolites associated with viral infections. This review also focuses on data interpretation and applications designed to improve our understanding of the pathogenesis of these viral diseases.
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Affiliation(s)
- Haya Al-Sulaiti
- QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (H.A.-S.); (A.A.A.T.)
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
| | - Jehad Almaliti
- Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA P.O. Box 92093, USA;
- Department of Pharmaceutical Sciences, College of Pharmacy, The University of Jordan, Amman P.O. Box 11942, Jordan
| | - C. Benjamin Naman
- Department of Science and Conservation, San Diego Botanic Garden, Encinitas, CA P.O. Box 92024, USA;
| | - Asmaa A. Al Thani
- QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (H.A.-S.); (A.A.A.T.)
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
- College of Health Sciences, QU-Health, Qatar University, Doha P.O. Box 2713, Qatar
| | - Hadi M. Yassine
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
- College of Health Sciences, QU-Health, Qatar University, Doha P.O. Box 2713, Qatar
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30
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Ndlovu IS, Tshilwane SI, Vosloo A, Chaisi M, Mukaratirwa S. Metabolomics of Type 2 Diabetes Mellitus in Sprague Dawley Rats-In Search of Potential Metabolic Biomarkers. Int J Mol Sci 2023; 24:12467. [PMID: 37569840 PMCID: PMC10419637 DOI: 10.3390/ijms241512467] [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: 07/15/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is an expanding global health concern, closely associated with the epidemic of obesity. Individuals with diabetes are at high risk for microvascular and macrovascular complications, which include retinopathy, neuropathy, and cardiovascular comorbidities. Despite the availability of diagnostic tools for T2DM, approximately 30-60% of people with T2DM in developed countries are never diagnosed or detected. Therefore, there is a strong need for a simpler and more reliable technique for the early detection of T2DM. This study aimed to use a non-targeted metabolomic approach to systematically identify novel biomarkers from the serum samples of T2DM-induced Sprague Dawley (SD) rats using a comprehensive two-dimensional gas chromatography coupled with a time-of-flight mass spectrometry (GCxGC-TOF/MS). Fifty-four male Sprague Dawley rats weighing between 160-180 g were randomly assigned into two experimental groups, namely the type 2 diabetes mellitus group (T2DM) (n = 36) and the non-diabetic control group (n = 18). Results from this study showed that the metabolite signature of the diabetic rats was different from that of the non-diabetic control group. The most significantly upregulated metabolic pathway was aminoacyl-t-RNA biosynthesis. Metabolite changes observed between the diabetic and non-diabetic control group was attributed to the increase in amino acids, such as glycine, L-asparagine, and L-serine. Aromatic amino acids, including L-tyrosine, were associated with the risk of future hyperglycemia and overt diabetes. The identified potential biomarkers depicted a good predictive value of more than 0.8. It was concluded from the results that amino acids that were associated with impaired insulin secretion were prospectively related to an increase in glucose levels. Moreover, amino acids that were associated with impaired insulin secretion were prospectively related to an increase in glucose levels.
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Affiliation(s)
- Innocent Siyanda Ndlovu
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa; (I.S.N.); (A.V.)
| | - Selaelo Ivy Tshilwane
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa; (S.I.T.); (M.C.)
| | - Andre Vosloo
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa; (I.S.N.); (A.V.)
| | - Mamohale Chaisi
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa; (S.I.T.); (M.C.)
- Foundational Biodiversity Science, South African National Biodiversity Institute, Pretoria 0001, South Africa
| | - Samson Mukaratirwa
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa; (I.S.N.); (A.V.)
- One Health Center for Zoonoses and Tropical Veterinary Medicine, School of Veterinary Medicine, Ross University, Basseterre KN0101, Saint Kitts and Nevis
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31
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Bucheli OTM, Eyer K. Insights into the relationship between persistent antibody secretion and metabolic programming - A question for single-cell analysis. Immunol Lett 2023; 260:35-43. [PMID: 37315849 DOI: 10.1016/j.imlet.2023.06.006] [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: 11/02/2022] [Revised: 04/28/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Vaccination aims to generate a protective and persisting antibody response. Indeed, humoral vaccine-mediated protection depends on the quality and quantity of the produced antigen-specific antibodies for its initial magnitude and the persistence of the plasma cells for its duration. Therefore, understanding the mechanisms behind the generation, selection and maintenance of long-lived plasma cells secreting protective antibodies is of fundamental importance for understanding long-term immunity, vaccine responses, therapeutical approaches for autoimmune disease and multiple myeloma. Recent studies have observed correlations between the generation, function and lifespan of plasma cells and their metabolism, with metabolism being both a main driver and primary consequence of changes in cellular behavior. This review introduces how metabolic programs influence and drive immune cell functions in general and plasma cell differentiation and longevity more specifically, summarizing the current knowledge on metabolic pathways and their influences on cellular fate. In addition, available technologies to profile metabolism and their limitations are discussed, leading to the unique and open technological challenges for further advancement of this research field.
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Affiliation(s)
- Olivia T M Bucheli
- Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland
| | - Klaus Eyer
- Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
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Raclariu-Manolică AC, Mauvisseau Q, Paranaiba R, De Boer HJ, Socaciu C. Authentication of milk thistle commercial products using UHPLC-QTOF-ESI + MS metabolomics and DNA metabarcoding. BMC Complement Med Ther 2023; 23:257. [PMID: 37480124 PMCID: PMC10360273 DOI: 10.1186/s12906-023-04091-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Milk thistle is one of the most popular hepatoprotectants, and is often sold in combination with other ingredients. Botanical supplements are known to be vulnerable to contamination and adulteration, and emerging technologies show promise to improve their quality control. METHODS Untargeted and semi-targeted metabolomics based on UHPLC-QTOF-ESI+MS techniques, UV spectrometry, and DNA metabarcoding using Illumina MiSeq were used to authenticate eighteen milk thistle botanical formulations (teas, capsules, tablets, emulsion). RESULTS Untargeted metabolomics separated 217 molecules and by multivariate analysis the discrimination between the different preparations was established. The semi-targeted metabolomics focused on 63 phytochemicals, mainly silymarin flavonolignans and flavonoids, that may be considered as putative biomarkers of authenticity. All formulations contained molecules from silymarin complexes at different levels. The quantitative evaluation of silybins was done using in parallel UV spectrometry and UHPLC-QTOF-ESI+MS and their correlations were compared. DNA metabarcoding detected milk thistle in eleven out of sixteen retained preparations, whereas two others had incomplete evidence of milk thistle despite metabolomics validating specific metabolites, e.g., silymarin complex, identified and quantified in all samples. Meanwhile, the DNA metabarcoding provided insights into the total species composition allowing the interpretation of the results in a broad context. CONCLUSION Our study emphasizes that combining spectroscopic, chromatographic, and genetic techniques bring complementary information to guarantee the quality of the botanical formulations.
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Affiliation(s)
- Ancuța Cristina Raclariu-Manolică
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Alexandru cel Bun Street, 6, Piatra Neamț, 610004, Romania.
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, Oslo, 0318, Norway.
| | - Quentin Mauvisseau
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, Oslo, 0318, Norway
| | - Renato Paranaiba
- Natural Products Laboratory, School of Health Sciences, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, 70910-900, Brazil
- DNA Laboratory, National Institute of Criminalistics, Brazilian Federal Police, SAIS Quadra 7, Lote 23, Brasília, DF, 70610-200, Brazil
| | - Hugo J De Boer
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, Oslo, 0318, Norway
| | - Carmen Socaciu
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Mănăştur Street, nr. 3-5, Cluj Napoca, 400372, Romania
- BIODIATECH- Research Center for Applied Biotechnology in Diagnosis and Molecular Therapy, Trifoiului Street 12G, Cluj-Napoca, 400478, Romania
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Mattoli L, Gianni M, Burico M. Mass spectrometry-based metabolomic analysis as a tool for quality control of natural complex products. MASS SPECTROMETRY REVIEWS 2023; 42:1358-1396. [PMID: 35238411 DOI: 10.1002/mas.21773] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/16/2021] [Accepted: 02/11/2022] [Indexed: 06/07/2023]
Abstract
Metabolomics is an area of intriguing and growing interest. Since the late 1990s, when the first Omic applications appeared to study metabolite's pool ("metabolome"), to understand new aspects of the global regulation of cellular metabolism in biology, there have been many evolutions. Currently, there are many applications in different fields such as clinical, medical, agricultural, and food. In our opinion, it is clear that developments in metabolomics analysis have also been driven by advances in mass spectrometry (MS) technology. As natural complex products (NCPs) are increasingly used around the world as medicines, food supplements, and substance-based medical devices, their analysis using metabolomic approaches will help to bring more and more rigor to scientific studies and industrial production monitoring. This review is intended to emphasize the importance of metabolomics as a powerful tool for studying NCPs, by which significant advantages can be obtained in terms of elucidation of their composition, biological effects, and quality control. The different approaches of metabolomic analysis, the main and basic techniques of multivariate statistical analysis are also briefly illustrated, to allow an overview of the workflow associated with the metabolomic studies of NCPs. Therefore, various articles and reviews are illustrated and commented as examples of the application of MS-based metabolomics to NCPs.
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Affiliation(s)
- Luisa Mattoli
- Department of Metabolomics & Analytical Sciences, Aboca SpA Società Agricola, Sansepolcro, AR, Italy
| | - Mattia Gianni
- Department of Metabolomics & Analytical Sciences, Aboca SpA Società Agricola, Sansepolcro, AR, Italy
| | - Michela Burico
- Department of Metabolomics & Analytical Sciences, Aboca SpA Società Agricola, Sansepolcro, AR, Italy
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Wang W, Rong Z, Wang G, Hou Y, Yang F, Qiu M. Cancer metabolites: promising biomarkers for cancer liquid biopsy. Biomark Res 2023; 11:66. [PMID: 37391812 DOI: 10.1186/s40364-023-00507-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/27/2023] [Indexed: 07/02/2023] Open
Abstract
Cancer exerts a multitude of effects on metabolism, including the reprogramming of cellular metabolic pathways and alterations in metabolites that facilitate inappropriate proliferation of cancer cells and adaptation to the tumor microenvironment. There is a growing body of evidence suggesting that aberrant metabolites play pivotal roles in tumorigenesis and metastasis, and have the potential to serve as biomarkers for personalized cancer therapy. Importantly, high-throughput metabolomics detection techniques and machine learning approaches offer tremendous potential for clinical oncology by enabling the identification of cancer-specific metabolites. Emerging research indicates that circulating metabolites have great promise as noninvasive biomarkers for cancer detection. Therefore, this review summarizes reported abnormal cancer-related metabolites in the last decade and highlights the application of metabolomics in liquid biopsy, including detection specimens, technologies, methods, and challenges. The review provides insights into cancer metabolites as a promising tool for clinical applications.
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Affiliation(s)
- Wenxiang Wang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
- Peking University People's Hospital Thoracic Oncology Institute, Beijing, 100044, China
| | - Zhiwei Rong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, 100191, China
| | - Guangxi Wang
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yan Hou
- Department of Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
- Clinical Research Center, Peking University, Beijing, 100191, China
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
- Peking University People's Hospital Thoracic Oncology Institute, Beijing, 100044, China.
| | - Mantang Qiu
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
- Peking University People's Hospital Thoracic Oncology Institute, Beijing, 100044, China.
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Vahid F, Hajizadeghan K, Khodabakhshi A. Nutritional Metabolomics in Diet-Breast Cancer Relations: Current Research, Challenges, and Future Directions-A Review. Biomedicines 2023; 11:1845. [PMID: 37509485 PMCID: PMC10377267 DOI: 10.3390/biomedicines11071845] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 07/30/2023] Open
Abstract
Breast cancer is one of the most common types of cancer in women worldwide, and its incidence is increasing. Diet has been identified as a modifiable risk factor for breast cancer, but the complex interplay between diet, metabolism, and cancer development is not fully understood. Nutritional metabolomics is a rapidly evolving field that can provide insights into the metabolic changes associated with dietary factors and their impact on breast cancer risk. The review's objective is to provide a comprehensive overview of the current research on the application of nutritional metabolomics in understanding the relationship between diet and breast cancer. The search strategy involved querying several electronic databases, including PubMed, Scopus, Web of Science, and Google Scholar. The search terms included combinations of relevant keywords such as "nutritional metabolomics", "diet", "breast cancer", "metabolites", and "biomarkers". In this review, both in vivo and in vitro studies were included, and we summarize the current state of knowledge on the role of nutritional metabolomics in understanding the diet-breast cancer relationship, including identifying specific metabolites and metabolic pathways associated with breast cancer risk. We also discuss the challenges associated with nutritional metabolomics research, including standardization of analytical methods, interpretation of complex data, and integration of multiple-omics approaches. Finally, we highlight future directions for nutritional metabolomics research in studying diet-breast cancer relations, including investigating the role of gut microbiota and integrating multiple-omics approaches. The application of nutritional metabolomics in the study of diet-breast cancer relations, including 2-amino-4-cyano butanoic acid, piperine, caprate, rosten-3β,17β-diol-monosulfate, and γ-carboxyethyl hydrochroman, among others, holds great promise for advancing our understanding of the role of diet in breast cancer development and identifying personalized dietary recommendations for breast cancer prevention, control, and treatment.
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Affiliation(s)
- Farhad Vahid
- Nutrition and Health Research Group, Precision Health Department, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - Kimia Hajizadeghan
- Department of Nutrition, Faculty of Public Health, Kerman University of Medical Sciences, Kerman 7616913555, Iran
| | - Adeleh Khodabakhshi
- Department of Nutrition, Faculty of Public Health, Kerman University of Medical Sciences, Kerman 7616913555, Iran
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De Spiegeleer M, Plekhova V, Geltmeyer J, Schoolaert E, Pomian B, Singh V, Wijnant K, De Windt K, Paukku V, De Loof A, Gies I, Michels N, De Henauw S, De Graeve M, De Clerck K, Vanhaecke L. Point-of-care applicable metabotyping using biofluid-specific electrospun MetaSAMPs directly amenable to ambient LA-REIMS. SCIENCE ADVANCES 2023; 9:eade9933. [PMID: 37294759 PMCID: PMC10256167 DOI: 10.1126/sciadv.ade9933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/05/2023] [Indexed: 06/11/2023]
Abstract
In recent years, ambient ionization mass spectrometry (AIMS) including laser ablation rapid evaporation IMS, has enabled direct biofluid metabolome analysis. AIMS procedures are, however, still hampered by both analytical, i.e., matrix effects, and practical, i.e., sample transport stability, drawbacks that impede metabolome coverage. In this study, we aimed at developing biofluid-specific metabolome sampling membranes (MetaSAMPs) that offer a directly applicable and stabilizing substrate for AIMS. Customized rectal, salivary, and urinary MetaSAMPs consisting of electrospun (nano)fibrous membranes of blended hydrophilic (polyvinylpyrrolidone and polyacrylonitrile) and lipophilic (polystyrene) polymers supported metabolite absorption, adsorption, and desorption. Moreover, MetaSAMP demonstrated superior metabolome coverage and transport stability compared to crude biofluid analysis and was successfully validated in two pediatric cohorts (MetaBEAse, n = 234 and OPERA, n = 101). By integrating anthropometric and (patho)physiological with MetaSAMP-AIMS metabolome data, we obtained substantial weight-driven predictions and clinical correlations. In conclusion, MetaSAMP holds great clinical application potential for on-the-spot metabolic health stratification.
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Affiliation(s)
- Margot De Spiegeleer
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Vera Plekhova
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Jozefien Geltmeyer
- Department of Materials, Textiles and Chemical Engineering, Faculty of Engineering and Architecture, Ghent University, Ghent, Belgium
| | - Ella Schoolaert
- Department of Materials, Textiles and Chemical Engineering, Faculty of Engineering and Architecture, Ghent University, Ghent, Belgium
| | - Beata Pomian
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Varoon Singh
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Kathleen Wijnant
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Kimberly De Windt
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Volter Paukku
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Alexander De Loof
- Department of Public Health and Primary Care, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Inge Gies
- Department of Pediatrics, Free University of Brussels (VUB), University Hospital Brussels (UZ Brussel), Brussels, Belgium
| | - Nathalie Michels
- Department of Developmental, Personality and Social Psychology, Ghent University, Ghent, Belgium
| | - Stefaan De Henauw
- Department of Public Health and Primary Care, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Marilyn De Graeve
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
| | - Karen De Clerck
- Department of Materials, Textiles and Chemical Engineering, Faculty of Engineering and Architecture, Ghent University, Ghent, Belgium
| | - Lynn Vanhaecke
- Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Ghent, Belgium
- Institute for Global Food Security, School of Biological Sciences, Queen’s University, Belfast, UK
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37
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Nitusca D, Socaciu C, Socaciu AI, Sirbu IO, Bardan R, Cumpanas AA, Seclaman E, Marian C. Potential Diagnostic Biomarker Detection for Prostate Cancer Using Untargeted and Targeted Metabolomic Profiling. Curr Issues Mol Biol 2023; 45:5036-5051. [PMID: 37367069 DOI: 10.3390/cimb45060320] [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: 04/26/2023] [Revised: 05/27/2023] [Accepted: 06/03/2023] [Indexed: 06/28/2023] Open
Abstract
Prostate cancer (PCa) remains one of the leading causes of cancer mortality in men worldwide, currently lacking specific, early detection and staging biomarkers. In this regard, modern research focuses efforts on the discovery of novel molecules that could represent potential future non-invasive biomarkers for the diagnosis of PCa, as well as therapeutic targets. Mounting evidence shows that cancer cells express an altered metabolism in their early stages, making metabolomics a promising tool for the discovery of altered pathways and potential biomarker molecules. In this study, we first performed untargeted metabolomic profiling on 48 PCa plasma samples and 23 healthy controls using ultra-high-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-[ESI+]-MS) for the discovery of metabolites with altered profiles. Secondly, we selected five molecules (L-proline, L-tryptophan, acetylcarnitine, lysophosphatidylcholine C18:2 and spermine) for the downstream targeted metabolomics and found out that all the molecules, regardless of the PCa stage, were decreased in the PCa plasma samples when compared to the controls, making them potential biomarkers for PCa detection. Moreover, spermine, acetylcarnitine and L-tryptophan had very high diagnostic accuracy, with AUC values of 0.992, 0.923 and 0.981, respectively. Consistent with other literature findings, these altered metabolites could represent future specific and non-invasive candidate biomarkers for PCa detection, which opens novel horizons in the field of metabolomics.
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Affiliation(s)
- Diana Nitusca
- Department of Biochemistry and Pharmacology, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
- Center for Complex Networks Science, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
| | - Carmen Socaciu
- BIODIATECH, Research Center for Applied Biotechnology in Diagnosis and Molecular Therapy, 400478 Cluj-Napoca, Romania
| | - Andreea Iulia Socaciu
- Department of Occupational Health, Iuliu Hateganu University of Medicine and Pharmacy, Str. Victor Babes Nr. 8, 400347 Cluj-Napoca, Romania
| | - Ioan Ovidiu Sirbu
- Department of Biochemistry and Pharmacology, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
- Center for Complex Networks Science, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
| | - Razvan Bardan
- Department of Urology, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
- Urology Clinic, Timisoara Emergency County Hospital, 300723 Timisoara, Romania
| | - Alin Adrian Cumpanas
- Department of Urology, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
- Urology Clinic, Timisoara Emergency County Hospital, 300723 Timisoara, Romania
| | - Edward Seclaman
- Department of Biochemistry and Pharmacology, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
- Center for Complex Networks Science, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
| | - Catalin Marian
- Department of Biochemistry and Pharmacology, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
- Center for Complex Networks Science, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
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38
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Favilli L, Griffith CM, Schymanski EL, Linster CL. High-throughput Saccharomyces cerevisiae cultivation method for credentialing-based untargeted metabolomics. Anal Bioanal Chem 2023:10.1007/s00216-023-04724-5. [PMID: 37212869 DOI: 10.1007/s00216-023-04724-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/23/2023]
Abstract
Identifying metabolites in model organisms is critical for many areas of biology, including unravelling disease aetiology or elucidating functions of putative enzymes. Even now, hundreds of predicted metabolic genes in Saccharomyces cerevisiae remain uncharacterized, indicating that our understanding of metabolism is far from complete even in well-characterized organisms. While untargeted high-resolution mass spectrometry (HRMS) enables the detection of thousands of features per analysis, many of these have a non-biological origin. Stable isotope labelling (SIL) approaches can serve as credentialing strategies to distinguish biologically relevant features from background signals, but implementing these experiments at large scale remains challenging. Here, we developed a SIL-based approach for high-throughput untargeted metabolomics in S. cerevisiae, including deep-48 well format-based cultivation and metabolite extraction, building on the peak annotation and verification engine (PAVE) tool. Aqueous and nonpolar extracts were analysed using HILIC and RP liquid chromatography, respectively, coupled to Orbitrap Q Exactive HF mass spectrometry. Of the approximately 37,000 total detected features, only 3-7% of the features were credentialed and used for data analysis with open-source software such as MS-DIAL, MetFrag, Shinyscreen, SIRIUS CSI:FingerID, and MetaboAnalyst, leading to the successful annotation of 198 metabolites using MS2 database matching. Comparable metabolic profiles were observed for wild-type and sdh1Δ yeast strains grown in deep-48 well plates versus the classical shake flask format, including the expected increase in intracellular succinate concentration in the sdh1Δ strain. The described approach enables high-throughput yeast cultivation and credentialing-based untargeted metabolomics, providing a means to efficiently perform molecular phenotypic screens and help complete metabolic networks.
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Affiliation(s)
- Lorenzo Favilli
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, Belvaux, L-4367, Luxembourg.
| | - Corey M Griffith
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, Belvaux, L-4367, Luxembourg
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, Belvaux, L-4367, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, Belvaux, L-4367, Luxembourg
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Sharma H, Ozogul F. Mass spectrometry-based techniques for identification of compounds in milk and meat matrix. ADVANCES IN FOOD AND NUTRITION RESEARCH 2023; 104:43-76. [PMID: 37236734 DOI: 10.1016/bs.afnr.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Food including milk and meat is often viewed as the mixture of different components such as fat, protein, carbohydrates, moisture and ash, which are estimated using well-established protocols and techniques. However, with the advent of metabolomics, low-molecular weight substances, also known as metabolites, have been recognized as one of the major factors influencing the production, quality and processing. Therefore, different separation and detection techniques have been developed for the rapid, robust and reproducible separation and identification of compounds for efficient control in milk and meat production and supply chain. Mass-spectrometry based techniques such as GC-MS and LC-MS and nuclear magnetic resonance spectroscopy techniques have been proven successful in the detailed food component analysis owing to their associated benefits. Different metabolites extraction protocols, derivatization, spectra generated, data processing followed by data interpretation are the major sequential steps for these analytical techniques. This chapter deals with not only the detailed discussion of these analytical techniques but also sheds light on various applications of these analytical techniques in milk and meat products.
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Affiliation(s)
- Heena Sharma
- Food Technology Lab, Dairy Technology Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Fatih Ozogul
- Department of Seafood Processing Technology, Faculty of Fisheries, Cukurova University, Adana, Turkey.
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40
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Chang CW, Hsu JY, Su YH, Chen YC, Hsiao PZ, Liao PC. Monitoring long-term chemical exposome by characterizing the hair metabolome using a high-resolution mass spectrometry-based suspect screening approach. CHEMOSPHERE 2023; 332:138864. [PMID: 37156292 DOI: 10.1016/j.chemosphere.2023.138864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/20/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
Abstract
Hair has recently emerged as a biospecimen for characterizing the long-term chemical exposome in biomonitoring investigations spanning several months, as chemical compounds circulating in the bloodstream accumulate in hair. Although there has been interest in using human hair as a biospecimen for exposome studies, it has yet to be widely adopted compared to blood and urine. Here, we applied a high-resolution mass spectrometry (HRMS)-based suspect screening strategy to characterize the long-term chemical exposome in human hair. Hair samples were collected from 70 subjects and cut into 3 cm segments, which were then mixed to prepare pooled samples. The pooled hair samples underwent a sample preparation procedure, and the hair extracts were further analyzed using an HRMS-based suspect screening approach. An in-house chemical suspect list containing 1227 chemical entries from National Report on Human Exposure to Environmental Chemicals (Report) published by the U.S. CDC and the Exposome-Explorer 3.0 database developed by the WHO was subsequently used to screen and filter the suspect features against the HRMS dataset. Overall, we matched 587 suspect features in the HRMS dataset to 246 unique chemical formulas in the suspect list, and the structures of 167 chemicals were further identified through a fragmentation analysis. Among these, chemicals such as mono-2-ethylhexyl phthalate, methyl paraben, and 1-naphthol, which have been detected in the urine or blood for exposure assessment, were also identified in human hair. This suggests that hair reflects the accumulation of environmental compounds to which an individual is exposed. Exposure to exogenous chemicals may exert adverse effects on cognitive function, and we discovered 15 chemicals in human hair that may contribute to the pathogenesis of Alzheimer's disease. This finding suggests that human hair may be a promising biospecimen for monitoring long-term exposure to multiple environmental chemicals and perturbations in endogenous chemicals in biomonitoring investigations.
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Affiliation(s)
- Chih-Wei Chang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Yi Hsu
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Hsiang Su
- Division of Neurology, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City, 60002, Taiwan
| | - Yuan-Chih Chen
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Zu Hsiao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Najafova T, Dagdeviren G, Kasikci M, Sahin D, Yucel A, Ozyuncu O, Gurler M. Segmental hair metabolomics analysis in pregnant women with pregnancy complications. Metabolomics 2023; 19:45. [PMID: 37084096 DOI: 10.1007/s11306-023-02009-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 04/11/2023] [Indexed: 04/22/2023]
Abstract
INTRODUCTION Pregnancy complications, as preeclampsia (PE) and HELLP syndrome, occurring with similar pathophysiological mechanisms, have adverse effects on the health of both mother and fetus during pregnancy and thereafter, they are leading causes of maternal and fetal morbidity and mortality. The hair metabolome has been recognized as a valuable source of information in pregnancy research, as it provides stable metabolite information to be able to assist with studying biomarkers or metabolic mechanisms of pregnancy and its complications. OBJECTIVE The aim of this study was to investigate the hair metabolome profile of pregnant women with PE, HELLP syndrome and healthy women. METHOD Hair samples of new-borns' mothers (patients and controls) were investigated segmentally relevant to each trimester using a proper sample preparation and gas chromatography-mass spectrometry (GC-MS) to identify robust biomarkers that can be useful for screening, early detection, follow-up and treatment of PE and HELLP syndrome, the etiology of which are still unknown. RESULTS The results showed a significant change in the metabolome profiles of the patient and control groups regarding the trimesters. A striking decrease was observed in all 100 metabolites investigated in the patient group (p < 0.000). The metabolic pathways associated with significant metabolites have also been investigated, and the most affected pathways were observed to be the urea cycle, glycine, serine, aspartate, methionine and purine metabolism, ammonia cycle, and phosphatidylethanolamine biosynthesis. CONCLUSION The found metabolites provide us with extensive data on the ability to establish biomarkers for predicting, early detection and monitoring of PE.
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Affiliation(s)
- Tahmina Najafova
- Department of Medical Biochemistry, Faculty of Medicine, Hacettepe University, Sıhhiye, 06100, Ankara, Turkey.
| | - Gulsah Dagdeviren
- Department of Perinatology, University of Health Sciences Etlik Zubeyde Hanım Women's Health Care, Training and Research Hospital, Ankara, Turkey
| | - Merve Kasikci
- Department of Biostatistics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Dilek Sahin
- Department of Perinatology, University of Health Sciences Etlik Zubeyde Hanım Women's Health Care, Training and Research Hospital, Ankara, Turkey
| | - Aykan Yucel
- Department of Perinatology, University of Health Sciences Etlik Zubeyde Hanım Women's Health Care, Training and Research Hospital, Ankara, Turkey
| | - Ozgur Ozyuncu
- Department of Gynaecology and Obstetrics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Mukaddes Gurler
- Department of Medical Biochemistry, Faculty of Medicine, Hacettepe University, Sıhhiye, 06100, Ankara, Turkey
- Department of Medical Biochemistry and Forensic Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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42
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Nastasi JR, Daygon VD, Kontogiorgos V, Fitzgerald MA. Qualitative Analysis of Polyphenols in Glycerol Plant Extracts Using Untargeted Metabolomics. Metabolites 2023; 13:metabo13040566. [PMID: 37110224 PMCID: PMC10146371 DOI: 10.3390/metabo13040566] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Glycerol is a reliable solvent for extracting polyphenols from food and waste products. There has been an increase in the application of glycerol over benchmark alcoholic solvents such as ethanol and methanol for natural product generation because of its non-toxic nature and high extraction efficiency. However, plant extracts containing a high glycerol concentration are unsuitable for mass spectrometry-based investigation utilising electrospray ionization, inhibiting the ability to analyse compounds of interest. In this investigation, a solid phase extraction protocol is outlined for removing glycerol from plant extracts containing a high concentration of glycerol and their subsequent analysis of polyphenols using ultra-performance liquid chromatography coupled with quadrupole time of flight tandem mass spectrometry. Using this method, glycerol-based extracts of Queen Garnet Plum (Prunus salicina) were investigated and compared to ethanolic extracts. Anthocyanins and flavonoids in high abundance were found in both glycerol and ethanol extracts. The polyphenol metabolome of Queen Garnet Plum was 53% polyphenol glycoside derivatives and 47% polyphenols in their aglycone forms. Furthermore, 56% of the flavonoid derivates were found to be flavonoid glycosides, and 44% were flavonoid aglycones. In addition, two flavonoid glycosides not previously found in Queen Garnet Plum were putatively identified: Quercetin-3-O-xyloside and Quercetin-3-O-rhamnoside.
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Affiliation(s)
- Joseph Robert Nastasi
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Venea Dara Daygon
- Queensland Metabolomics and Proteomics Facility, Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Vassilis Kontogiorgos
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Melissa A Fitzgerald
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
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Porto VA, da Rocha Júnior ER, Ursulino JS, Porto RS, da Silva M, de Jesus LWO, Oliveira JMD, Crispim AC, Santos JCC, Aquino TMD. NMR-based metabolomics applied to ecotoxicology with zebrafish (Danio rerio) as a prominent model for metabolic profiling and biomarker discovery: Overviewing the most recent approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161737. [PMID: 36693575 DOI: 10.1016/j.scitotenv.2023.161737] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/28/2022] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Metabolomics is an innovative approach used in the medical, toxicological, and biological sciences. As an interdisciplinary topic, metabolomics and its relation with the environment and toxicological research are extensive. The use of substances, such as drugs and pesticides, contributes to the continuous releasing of xenobiotics into the environment, harming organisms and their habitats. In this context, fish are important bioindicators of the environmental condition and have often been used as model species. Among them, zebrafish (Danio rerio) presents itself as a versatile and straightforward option due to its unique attributes for research. Zebrafish proves to be a valuable model for toxicity assays and also for metabolomics profiling by analytical tools. Thus, NMR-based metabolomics associated with statistical analysis can reasonably assist researchers in critical factors related to discovering and validating biomarkers through accurate diagnosis. Therefore, this review aimed to report the studies that applied zebrafish as a model for (eco)toxicological assays and essentially utilized NMR-based metabolomics analysis to assess the biochemical profile and thus suggest the potential biological marker.
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Affiliation(s)
- Viviane Amaral Porto
- Research Group on Therapeutic Strategies, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, Brazil.
| | | | - Jeferson Santana Ursulino
- Research Group on Therapeutic Strategies, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, Brazil
| | - Ricardo Silva Porto
- Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, Brazil
| | - Marciliano da Silva
- Laboratory of Applied Animal Morphophysiology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, Brazil
| | - Lázaro Wender Oliveira de Jesus
- Laboratory of Applied Animal Morphophysiology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, Brazil
| | | | - Alessandre Carmo Crispim
- Research Group on Therapeutic Strategies, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, Brazil
| | | | - Thiago Mendonça de Aquino
- Research Group on Therapeutic Strategies, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, Brazil
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44
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Zhang R, Pavan E, Ross AB, Deb-Choudhury S, Dixit Y, Mungure TE, Realini CE, Cao M, Farouk MM. Molecular insights into quality and authentication of sheep meat from proteomics and metabolomics. J Proteomics 2023; 276:104836. [PMID: 36764652 DOI: 10.1016/j.jprot.2023.104836] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
Sheep meat (encompassing lamb, hogget and mutton) is an important source of animal protein in many countries, with a unique flavour and sensory profile compared to other red meats. Flavour, colour and texture are the key quality attributes contributing to consumer liking of sheep meat. Over the last decades, various factors from 'farm to fork', including production system (e.g., age, breed, feeding regimes, sex, pre-slaughter stress, and carcass suspension), post-mortem manipulation and processing (e.g., electrical stimulation, ageing, packaging types, and chilled and frozen storage) have been identified as influencing different aspects of sheep meat quality. However conventional meat-quality assessment tools are not able to elucidate the underlying mechanisms and pathways for quality variations. Advances in broad-based analytical techniques have offered opportunities to obtain deeper insights into the molecular changes of sheep meat which may become biomarkers for specific variations in quality traits and meat authenticity. This review provides an overview on how omics techniques, especially proteomics (including peptidomics) and metabolomics (including lipidomics and volatilomics) are applied to elucidate the variations in sheep meat quality, mainly in loin muscles, focusing on colour, texture and flavour, and as tools for authentication. SIGNIFICANCE: From this review, we observed that attempts have been made to utilise proteomics and metabolomics techniques on sheep meat products for elucidating pathways of quality variations due to various factors. For instance, the improvement of colour stability and tenderness could be associated with the changes to glycolysis, energy metabolism and endogenous antioxidant capacity. Several studies identify proteolysis as being important, but potentially conflicting for quality as the enhanced proteolysis improves tenderness and flavour, while reducing colour stability. The use of multiple analytical methods e.g., lipidomics, metabolomics, and volatilomics, detects a wider range of flavour precursors (including both water and lipid soluble compounds) that underlie the possible pathways for sheep meat flavour evolution. The technological advancement in omics (e.g., direct analysis-mass spectrometry) could make analysis of the proteins, lipids and metabolites in sheep meat routine, as well as enhance the confidence in quality determination and molecular-based assurance of meat authenticity.
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Affiliation(s)
- Renyu Zhang
- Food Technology & Processing, AgResearch Ltd, Palmerston North, New Zealand.
| | - Enrique Pavan
- Food Technology & Processing, AgResearch Ltd, Palmerston North, New Zealand; Unidad Integrada Balcarce (FCA, UNMdP - INTA, EEA Balcarce), Ruta 226 km 73.5, CP7620 Balcarce, Argentina
| | - Alastair B Ross
- Proteins and Metabolites, AgResearch Ltd, Lincoln, New Zealand
| | | | - Yash Dixit
- Food informatics, AgResearch Ltd, Palmerston North, New Zealand
| | | | - Carolina E Realini
- Food Technology & Processing, AgResearch Ltd, Palmerston North, New Zealand
| | - Mingshu Cao
- Data Science, AgResearch Ltd, Palmerston North, New Zealand
| | - Mustafa M Farouk
- Food Technology & Processing, AgResearch Ltd, Palmerston North, New Zealand
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Childhood Obesity and the Cryptic Language of the Microbiota: Metabolomics’ Upgrading. Metabolites 2023; 13:metabo13030414. [PMID: 36984854 PMCID: PMC10052538 DOI: 10.3390/metabo13030414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/01/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
The growing obesity epidemic in childhood is increasingly concerning for the related physical and psychological consequences, with a significant impact on health care costs in both the short and the long term. Nonetheless, the scientific community has not yet completely clarified the complex metabolic mechanisms underlying body weight alterations. In only a small percentage of cases, obesity is the result of endocrine, monogenic, or syndromic causes, while in much more cases, lifestyle plays a crucial role in obesity development. In this context, the pediatric age appears to be of considerable importance as prevention strategies together with early intervention can represent important therapeutic tools not only to counteract the comorbidities that increasingly affect children but also to hinder the persistence of obesity in adulthood. Although evidence in the literature supporting the alteration of the microbiota as a critical factor in the etiology of obesity is abundant, it is not yet fully defined and understood. However, increasingly clear evidence is emerging regarding the existence of differentiated metabolic profiles in obese children, with characteristic metabolites. The identification of specific pathology-related biomarkers and the elucidation of the altered metabolic pathways would therefore be desirable in order to clarify aspects that are still poorly understood, such as the consequences of the interaction between the host, the diet, and the microbiota. In fact, metabolomics can characterize the biological behavior of a specific individual in response to external stimuli, offering not only an eventual effective screening and prevention strategy but also the possibility of evaluating adherence and response to dietary intervention.
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46
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Wang W, Ma LH, Maletic-Savatic M, Liu Z. NMRQNet: a deep learning approach for automatic identification and quantification of metabolites using Nuclear Magnetic Resonance (NMR) in human plasma samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530642. [PMID: 36909516 PMCID: PMC10002723 DOI: 10.1101/2023.03.01.530642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Nuclear Magnetic Resonance is a powerful platform that reveals the metabolomics profiles within biofluids or tissues and contributes to personalized treatments in medical practice. However, data volume and complexity hinder the exploration of NMR spectra. Besides, the lack of fast and accurate computational tools that can handle the automatic identification and quantification of essential metabolites from NMR spectra also slows the wide application of these techniques in clinical. We present NMRQNet, a deep-learning-based pipeline for automatic identification and quantification of dominant metabolite candidates within human plasma samples. The estimated relative concentrations could be further applied in statistical analysis to extract the potential biomarkers. We evaluate our method on multiple plasma samples, including species from mice to humans, curated using three anticoagulants, covering healthy and patient conditions in neurological disorder disease, greatly expanding the metabolomics analytical space in plasma. NMRQNet accurately reconstructed the original spectra and obtained significantly better quantification results than the earlier computational methods. Besides, NMRQNet also proposed relevant metabolites biomarkers that could potentially explain the risk factors associated with the condition. NMRQNet, with improved prediction performance, highlights the limitations in the existing approaches and has shown strong application potential for future metabolomics disease studies using plasma samples.
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Affiliation(s)
- Wanli Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Graduate Program of Quantitative & Computational Biosciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Li-Hua Ma
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mirjana Maletic-Savatic
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
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47
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Su YH, Chang CW, Hsu JY, Li SW, Sung PS, Wang RH, Wu CH, Liao PC. Discovering Hair Biomarkers of Alzheimer's Disease Using High Resolution Mass Spectrometry-Based Untargeted Metabolomics. Molecules 2023; 28:molecules28052166. [PMID: 36903413 PMCID: PMC10004788 DOI: 10.3390/molecules28052166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Hair may be a potential biospecimen to discover biomarkers for Alzheimer's disease (AD) since it reflects the integral metabolic profiles of body burden over several months. Here, we described the AD biomarker discovery in the hair using a high-resolution mass spectrometry (HRMS)-based untargeted metabolomics approach. A total of 24 patients with AD and 24 age- and sex-matched cognitively healthy controls were recruited. The hair samples were collected 0.1-cm away from the scalp and further cut into 3-cm segments. Hair metabolites were extracted by ultrasonication with methanol/phosphate-buffered saline 50/50 (v/v) for 4 h. A total of 25 discriminatory chemicals in hair between the patients with AD and controls were discovered and identified. The AUC value achieved 0.85 (95% CI: 0.72~0.97) in patients with very mild AD compared to healthy controls using a composite panel of the 9 biomarker candidates, indicating high potential for the initiation or promotion phase of AD dementia in the early stage. A metabolic panel combined with the nine metabolites may be used as biomarkers for the early detection of AD. The hair metabolome can be used to reveal metabolic perturbations for biomarker discovery. Investigating perturbations of the metabolites will offer insight into the pathogenesis of AD.
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Affiliation(s)
- Yu-Hsiang Su
- Division of Neurology, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City 60002, Taiwan
| | - Chih-Wei Chang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Jen-Yi Hsu
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Shih-Wen Li
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Pi-Shan Sung
- Department of Neurology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Ru-Hsueh Wang
- Department of Family Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Chih-Hsing Wu
- Department of Family Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Institute of Gerontology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Correspondence:
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Bourgin M, Durand S, Kroemer G. Diagnostic, Prognostic and Mechanistic Biomarkers of COVID-19 Identified by Mass Spectrometric Metabolomics. Metabolites 2023; 13:metabo13030342. [PMID: 36984782 PMCID: PMC10056171 DOI: 10.3390/metabo13030342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/14/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
A number of studies have assessed the impact of SARS-CoV-2 infection and COVID-19 severity on the metabolome of exhaled air, saliva, plasma, and urine to identify diagnostic and prognostic biomarkers. In spite of the richness of the literature, there is no consensus about the utility of metabolomic analyses for the management of COVID-19, calling for a critical assessment of the literature. We identified mass spectrometric metabolomic studies on specimens from SARS-CoV2-infected patients and subjected them to a cross-study comparison. We compared the clinical design, technical aspects, and statistical analyses of published studies with the purpose to identify the most relevant biomarkers. Several among the metabolites that are under- or overrepresented in the plasma from patients with COVID-19 may directly contribute to excessive inflammatory reactions and deficient immune control of SARS-CoV2, hence unraveling important mechanistic connections between whole-body metabolism and the course of the disease. Altogether, it appears that mass spectrometric approaches have a high potential for biomarker discovery, especially if they are subjected to methodological standardization.
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Affiliation(s)
- Mélanie Bourgin
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75005 Paris, France
- Correspondence:
| | - Sylvère Durand
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75005 Paris, France
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75005 Paris, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, 75610 Paris, France
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Ali AM, Monaghan C, Muggeridge DJ, Easton C, Watson DG. LC/MS-based discrimination between plasma and urine metabolomic changes following exposure to ultraviolet radiation by using data modelling. Metabolomics 2023; 19:13. [PMID: 36781606 PMCID: PMC9925544 DOI: 10.1007/s11306-023-01977-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 01/23/2023] [Indexed: 02/15/2023]
Abstract
INTRODUCTION This study sought to compare between metabolomic changes of human urine and plasma to investigate which one can be used as best tool to identify metabolomic profiling and novel biomarkers associated to the potential effects of ultraviolet (UV) radiation. METHOD A pilot study of metabolomic patterns of human plasma and urine samples from four adult healthy individuals at before (S1) and after (S2) exposure (UV) and non-exposure (UC) were carried out by using liquid chromatography-mass spectrometry (LC-MS). RESULTS The best results which were obtained by normalizing the metabolites to their mean output underwent to principal components analysis (PCA) and Orthogonal Partial least squares-discriminant analysis (OPLS-DA) to separate pre-from post-of exposure and non-exposure of UV. This separation by data modeling was clear in urine samples unlike plasma samples. In addition to overview of the scores plots, the variance predicted-Q2 (Cum), variance explained-R2X (Cum) and p-value of the cross-validated ANOVA score of PCA and OPLS-DA models indicated to this clear separation. Q2 (Cum) and R2X (Cum) values of PCA model for urine samples were 0.908 and 0.982, respectively, and OPLS-DA model values were 1.0 and 0.914, respectively. While these values in plasma samples were Q2 = 0.429 and R2X = 0.660 for PCA model and Q2 = 0.983 and R2X = 0.944 for OPLS-DA model. LC-MS metabolomic analysis showed the changes in numerous metabolic pathways including: amino acid, lipids, peptides, xenobiotics biodegradation, carbohydrates, nucleotides, Co-factors and vitamins which may contribute to the evaluation of the effects associated with UV sunlight exposure. CONCLUSIONS The results of pilot study indicate that pre and post-exposure UV metabolomics screening of urine samples may be the best tool than plasma samples and a potential approach to predict the metabolomic changes due to UV exposure. Additional future work may shed light on the application of available metabolomic approaches to explore potential predictive markers to determine the impacts of UV sunlight.
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Affiliation(s)
- Ali Muhsen Ali
- College of Medicine, University of Kerbala, Karbala, Iraq.
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161, Cathedral Street, Glasgow, G4 0RE, Scotland, UK.
| | - Chris Monaghan
- Institute for Clinical Exercise and Health Science, University of theWest of Scotland, Almada Street, Hamilton, Blantyre, ML3 0JB, UK
| | | | - Chris Easton
- Institute for Clinical Exercise and Health Science, University of theWest of Scotland, Almada Street, Hamilton, Blantyre, ML3 0JB, UK
| | - David G Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 161, Cathedral Street, Glasgow, G4 0RE, Scotland, UK
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50
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Leiva T, Lueschow S, Burge K, Devette C, McElroy S, Chaaban H. Biomarkers of necrotizing enterocolitis in the era of machine learning and omics. Semin Perinatol 2023; 47:151693. [PMID: 36604292 PMCID: PMC9975050 DOI: 10.1016/j.semperi.2022.151693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Necrotizing enterocolitis (NEC) continues to be a major cause of morbidity and mortality in preterm infants. Despite decades of research in NEC, no reliable biomarkers can accurately diagnose NEC or predict patient prognosis. The recent emergence of multi-omics could potentially shift NEC biomarker discovery, particularly when evaluated using systems biology techniques. Furthermore, the use of machine learning and artificial intelligence in analyzing this 'big data' could enable novel interpretations of NEC subtypes, disease progression, and potential therapeutic targets, allowing for integration with personalized medicine approaches. In this review, we evaluate studies using omics technologies and machine learning in the diagnosis of NEC. Future implications and challenges inherent to the field are also discussed.
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Affiliation(s)
- Tyler Leiva
- Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Shiloh Lueschow
- Department of Microbiology and Immunology, Stead Family Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Kathryn Burge
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, 1200 N. Everett Dr., ETNP 7504, Oklahoma City, OK 73104, USA
| | - Christa Devette
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, 1200 N. Everett Dr., ETNP 7504, Oklahoma City, OK 73104, USA
| | - Steven McElroy
- Department of Pediatrics, University of California Davis, Sacramento, CA, USA
| | - Hala Chaaban
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, 1200 N. Everett Dr., ETNP 7504, Oklahoma City, OK 73104, USA.
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