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Sieminska J, Miniewska K, Mroz R, Sierko E, Naumnik W, Kisluk J, Michalska-Falkowska A, Reszec J, Kozlowski M, Nowicki L, Moniuszko M, Kretowski A, Niklinski J, Ciborowski M, Godzien J. First insight about the ability of specific glycerophospholipids to discriminate non-small cell lung cancer subtypes. Front Mol Biosci 2024; 11:1379631. [PMID: 38725870 PMCID: PMC11079276 DOI: 10.3389/fmolb.2024.1379631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/05/2024] [Indexed: 05/12/2024] Open
Abstract
Introduction: Discrimination between adenocarcinoma (ADC) and squamous cell carcinoma (SCC) subtypes in non-small cell lung cancer (NSCLC) patients is a significant challenge in oncology. Lipidomics analysis provides a promising approach for this differentiation. Methods: In an accompanying paper, we explored oxPCs levels in a cohort of 200 NSCLC patients. In this research, we utilized liquid chromatography coupled with mass spectrometry (LC-MS) to analyze the lipidomics profile of matching tissue and plasma samples from 25 NSCLC patients, comprising 11 ADC and 14 SCC cases. This study builds upon our previous findings, which highlighted the elevation of oxidised phosphatidylcholines (oxPCs) in NSCLC patients. Results: We identified eight lipid biomarkers that effectively differentiate between ADC and SCC subtypes using an untargeted approach. Notably, we observed a significant increase in plasma LPA 20:4, LPA 18:1, and LPA 18:2 levels in the ADC group compared to the SCC group. Conversely, tumour PC 16:0/18:2, PC 16:0/4:0; CHO, and plasma PC 16:0/18:2; OH, PC 18:0/20:4; OH, PC 16:0/20:4; OOH levels were significantly higher in the ADC group. Discussion: Our study is the first to report that plasma LPA levels can distinguish between ADC and SCC patients in NSCLC, suggesting a potential role for LPAs in NSCLC subtyping. This finding warrants further investigation into the mechanisms underlying these differences and their clinical implications.
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Affiliation(s)
- Julia Sieminska
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Katarzyna Miniewska
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Robert Mroz
- 2nd Department of Lung Diseases and Tuberculosis, Medical University of Bialystok, Bialystok, Poland
| | - Ewa Sierko
- Department of Oncology, Medical University of Bialystok, Bialystok, Poland
| | - Wojciech Naumnik
- 1st Department of Lung Diseases and Tuberculosis, Medical University of Bialystok, Bialystok, Poland
| | - Joanna Kisluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | | | - Joanna Reszec
- Department of Medical Patomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Miroslaw Kozlowski
- Department of Thoracic Surgery, Medical University of Bialystok, Bialystok, Poland
| | | | - Marcin Moniuszko
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
| | - Adam Kretowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Michal Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Joanna Godzien
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
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2
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Godzien J, Lopez-Lopez A, Sieminska J, Jablonowski K, Pietrowska K, Kisluk J, Mojsak M, Dzieciol-Anikiej Z, Barbas C, Reszec J, Kozlowski M, Moniuszko M, Kretowski A, Niklinski J, Ciborowski M. Exploration of oxidized phosphocholine profile in non-small-cell lung cancer. Front Mol Biosci 2024; 10:1279645. [PMID: 38288337 PMCID: PMC10824250 DOI: 10.3389/fmolb.2023.1279645] [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: 08/18/2023] [Accepted: 12/20/2023] [Indexed: 01/31/2024] Open
Abstract
Introduction: Lung cancer is one of the most frequently studied types of cancer and represents the most common and lethal neoplasm. Our previous research on non-small cell lung cancer (NSCLC) has revealed deep lipid profile reprogramming and redox status disruption in cancer patients. Lung cell membranes are rich in phospholipids that are susceptible to oxidation, leading to the formation of bioactive oxidized phosphatidylcholines (oxPCs). Persistent and elevated levels of oxPCs have been shown to induce chronic inflammation, leading to detrimental effects. However, recent reports suggest that certain oxPCs possess anti-inflammatory, pro-survival, and endothelial barrier-protective properties. Thus, we aimed to measure the levels of oxPCs in NSCLC patients and investigate their potential role in lung cancer. Methods: To explore the oxPCs profiles in lung cancer, we performed in-depth, multi-level metabolomic analyses of nearly 350 plasma and lung tissue samples from 200 patients with NSCLC, including adenocarcinoma (ADC) and squamous cell carcinoma (SCC), the two most prevalent NSCLC subtypes and COPD patients as a control group. First, we performed oxPC profiling of plasma samples. Second, we analyzed tumor and non-cancerous lung tissues collected during the surgical removal of NSCLC tumors. Because of tumor tissue heterogeneity, subsequent analyses covered the surrounding healthy tissue and peripheral and central tumors. To assess whether the observed phenotypic changes in the patients were associated with measured oxPC levels, metabolomics data were augmented with data from medical records. Results: We observed a predominance of long-chain oxPCs in plasma samples and of short-chain oxPCs in tissue samples from patients with NSCLC. The highest concentration of oxPCs was observed in the central tumor region. ADC patients showed higher levels of oxPCs compared to the control group, than patients with SCC. Conclusion: The detrimental effects associated with the accumulation of short-chain oxPCs suggest that these molecules may have greater therapeutic utility than diagnostic value, especially given that elevated oxPC levels are a hallmark of multiple types of cancer.
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Affiliation(s)
- Joanna Godzien
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Angeles Lopez-Lopez
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Julia Sieminska
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Kacper Jablonowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Karolina Pietrowska
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Joanna Kisluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Malgorzata Mojsak
- Independent Laboratory of Molecular Imaging, Medical University of Bialystok, Bialystok, Poland
| | | | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Joanna Reszec
- Department of Medical Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Miroslaw Kozlowski
- Department of Thoracic Surgery, Medical University of Bialystok, Bialystok, Poland
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
| | - Adam Kretowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Michal Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
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Morel Y, Jones JW. Utilization of LC-MS/MS and Drift Tube Ion Mobility for Characterizing Intact Oxidized Arachidonate-Containing Glycerophosphatidylethanolamine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37369083 DOI: 10.1021/jasms.3c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Lipid peroxidation is a key component in the pathogenesis of numerous disease states, where the oxidative damage of lipids frequently leads to membrane dysfunction and subsequent cellular death. Glycerophosphoethanolamine (PE) is the second most abundant phospholipid found in cellular membranes and, when oxidized, has been identified as an executor of ferroptotic cell death. PE commonly exists in the plasmalogen form, where the presence of the vinyl ether bond and its enrichment in polyunsaturated fatty acids make it especially susceptible to oxidative degradation. This results in a multitude of oxidized products complicating identification and often requiring several analytical techniques for interpretation. In the present study, we outline an analytical approach for the structural characterization of intact oxidized products of arachidonate-containing diacyl and plasmalogen PE. Intact oxidized PE structures, including structural and positional isomers, were identified using complementary liquid chromatography techniques, drift tube ion mobility, and high-resolution tandem mass spectrometry. This work establishes a comprehensive method for the analysis of intact lipid peroxidation products and provides an important pathway to investigate how lipid peroxidation initially impacts glycerophospholipids and their role in redox biology.
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Affiliation(s)
- Yulemni Morel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Jace W Jones
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
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Delgado Dolset MI, Obeso D, Rodriguez-Coira J, Villaseñor A, González Cuervo H, Arjona A, Barbas C, Barber D, Carrillo T, Escribese MM. Contribution of allergy in the acquisition of uncontrolled severe asthma. Front Med (Lausanne) 2022; 9:1009324. [PMID: 36213665 PMCID: PMC9532527 DOI: 10.3389/fmed.2022.1009324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/22/2022] [Indexed: 12/02/2022] Open
Abstract
Asthma is a multifactorial, heterogeneous disease that has a challenging management. It can be divided in non-allergic and allergic (usually associated with house dust mites (HDM) sensitization). There are several treatments options for asthma (corticosteroids, bronchodilators, antileukotrienes, anticholinergics,…); however, there is a subset of patients that do not respond to any of the treatments, who can display either a T2 or a non-T2 phenotype. A deeper understanding of the differential mechanisms underlying each phenotype will help to decipher the contribution of allergy to the acquisition of this uncontrolled severe phenotype. Here, we aim to elucidate the biological pathways associated to allergy in the uncontrolled severe asthmatic phenotype. To do so, twenty-three severe uncontrolled asthmatic patients both with and without HDM-allergy were recruited from Hospital Universitario de Gran Canaria Dr. Negrin. A metabolomic fingerprint was obtained through liquid chromatography coupled to mass spectrometry, and identified metabolites were associated with their pathways. 9/23 patients had uncontrolled HDM-allergic asthma (UCA), whereas 14 had uncontrolled, non-allergic asthma (UCNA). 7/14 (50%) of the UCNA patients had Aspirin Exacerbated Respiratory Disease. There were no significant differences regarding gender or body mass index; but there were significant differences in age and onset age, which were higher in UCNA patients; and in total IgE, which was higher in UCA. The metabolic fingerprint revealed that 103 features were significantly different between UCNA and UCA (p < 0.05), with 97 being increased in UCA and 6 being decreased. We identified lysophosphocholines (LPC) 18:2, 18:3 and 20:4 (increased in UCA patients); and deoxycholic acid and palmitoleoylcarnitine (decreased in UCA). These metabolites were related with a higher activation of phospholipase A2 (PLA2) and other phospholipid metabolism pathways. Our results show that allergy induces the activation of specific inflammatory pathways, such as the PLA2 pathway, which supports its role in the development of an uncontrolled asthma phenotype. There are also clinical differences, such as higher levels of IgE and earlier onset ages for the allergic asthmatic group, as expected. These results provide evidences to better understand the contribution of allergy to the establishment of a severe uncontrolled phenotype.
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Affiliation(s)
- María Isabel Delgado Dolset
- Institute for Applied Molecular Medicine Nemesio Díez, School of Medicine, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - David Obeso
- Institute for Applied Molecular Medicine Nemesio Díez, School of Medicine, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
- Centre of Metabolomics and Bioanalysis (CEMBIO), School of Pharmacy, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Juan Rodriguez-Coira
- Institute for Applied Molecular Medicine Nemesio Díez, School of Medicine, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
- Centre of Metabolomics and Bioanalysis (CEMBIO), School of Pharmacy, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Alma Villaseñor
- Institute for Applied Molecular Medicine Nemesio Díez, School of Medicine, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
- Centre of Metabolomics and Bioanalysis (CEMBIO), School of Pharmacy, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Heleia González Cuervo
- Allergy Service, Hospital Universitario de Gran Canaria Doctor Negrin, Las Palmas de Gran Canaria, Spain
| | - Ana Arjona
- Allergy Service, Hospital Universitario de Gran Canaria Doctor Negrin, Las Palmas de Gran Canaria, Spain
| | - Coral Barbas
- Centre of Metabolomics and Bioanalysis (CEMBIO), School of Pharmacy, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Domingo Barber
- Institute for Applied Molecular Medicine Nemesio Díez, School of Medicine, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Teresa Carrillo
- Allergy Service, Hospital Universitario de Gran Canaria Doctor Negrin, Las Palmas de Gran Canaria, Spain
- Department of Medical and Surgical Sciences, School of Health Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - María M. Escribese
- Institute for Applied Molecular Medicine Nemesio Díez, School of Medicine, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
- Department of Basic Medical Sciences, School of Medicine, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
- *Correspondence: María M. Escribese
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Villaseñor A, Godzien J, Barker-Tejeda TC, Gonzalez-Riano C, López-López Á, Dudzik D, Gradillas A, Barbas C. Analytical approaches for studying oxygenated lipids in the search of potential biomarkers by LC-MS. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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6
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Manzi M, Palazzo M, Knott ME, Beauseroy P, Yankilevich P, Giménez MI, Monge ME. Coupled Mass-Spectrometry-Based Lipidomics Machine Learning Approach for Early Detection of Clear Cell Renal Cell Carcinoma. J Proteome Res 2020; 20:841-857. [PMID: 33207877 DOI: 10.1021/acs.jproteome.0c00663] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A discovery-based lipid profiling study of serum samples from a cohort that included patients with clear cell renal cell carcinoma (ccRCC) stages I, II, III, and IV (n = 112) and controls (n = 52) was performed using ultraperformance liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry and machine learning techniques. Multivariate models based on support vector machines and the LASSO variable selection method yielded two discriminant lipid panels for ccRCC detection and early diagnosis. A 16-lipid panel allowed discriminating ccRCC patients from controls with 95.7% accuracy in a training set under cross-validation and 77.1% accuracy in an independent test set. A second model trained to discriminate early (I and II) from late (III and IV) stage ccRCC yielded a panel of 26 compounds that classified stage I patients from an independent test set with 82.1% accuracy. Thirteen species, including cholic acid, undecylenic acid, lauric acid, LPC(16:0/0:0), and PC(18:2/18:2), identified with level 1 exhibited significantly lower levels in samples from ccRCC patients compared to controls. Moreover, 3α-hydroxy-5α-androstan-17-one 3-sulfate, cis-5-dodecenoic acid, arachidonic acid, cis-13-docosenoic acid, PI(16:0/18:1), PC(16:0/18:2), and PC(O-16:0/20:4) contributed to discriminate early from late ccRCC stage patients. The results are auspicious for early ccRCC diagnosis after validation of the panels in larger and different cohorts.
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Affiliation(s)
- Malena Manzi
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina.,Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD Buenos Aires, Argentina
| | - Martín Palazzo
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France.,Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Elena Knott
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - Pierre Beauseroy
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France
| | - Patricio Yankilevich
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Isabel Giménez
- Departamento de Diagnóstico y Tratamiento, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190, C1199ABB CABA, Argentina
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
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7
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Oxidized lipids in the metabolic profiling of neuroendocrine tumors - Analytical challenges and biological implications. J Chromatogr A 2020; 1625:461233. [PMID: 32709312 DOI: 10.1016/j.chroma.2020.461233] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 02/08/2023]
Abstract
Untargeted metabolomics can be a great tool for exploring new scientific areas; however, wrong metabolite annotation questions the credibility and puts the success of the entire research at risk. Therefore, an effort should be made to improve the quality and robustness of the annotation despite of the challenges, especially when final identification with standards is not possible. Through non-targeted analysis of human plasma samples, from a large cancer cohort study using RP-LC-ESI-QTOF-MS/MS, we have resolved MS/MS annotation through spectral matching, directed to hydroxyeicosatetraenoic acids (HETEs) and, MS/MS structural elucidation for newly annotated oxidized lyso-phosphatidylcholines (oxLPCs). The annotation of unknowns is supported with structural information from fragmentation spectra as well as the fragmentation mechanisms involved, necessarily including data from both polarity modes and different collision energies. In this work, we present evidences that various oxidation products show significant differences between cancer patients and control individuals and we establish a workflow to help identify such modifications. We report here the upregulation of HETEs and oxLPCs in patients with neuroendocrine tumors (NETs). To our knowledge, this is the first attempt to determine HETEs in NETs and one of very few studies where oxLPCs are annotated. The obtained results provide an important insight regarding lipid oxidation in NETs, although their physiological functions still have to be established and require further research.
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8
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Lam KL, Cheng WY, Yang F, Lin S, You L, Chiou J, Kwan HS, Cheung PCK. Framework as a Service, FaaS: Personalized Prebiotic Development for Infants with the Elements of Time and Parametric Modelling of in vitro Fermentation. Microorganisms 2020; 8:microorganisms8050623. [PMID: 32344924 PMCID: PMC7285508 DOI: 10.3390/microorganisms8050623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/09/2020] [Accepted: 04/23/2020] [Indexed: 11/17/2022] Open
Abstract
We proposed a framework with parametric modeling to obtain biological relevant parameters from the total probiotic growth pattern and metabolite production curves. The lag phase, maximum increase rate, and maximum capacity were obtained via a 205-h exploratory In vitro fermentation of a library of 13 structural-characterized prebiotic candidates against an exclusively breastfed infant fecal inoculum. We also conducted 16S rRNA amplicon sequencing of the infant fecal inoculum. Moreover, we introduce a robust composite metabolite-based indicator that reflects the eubiosis/dysbiosis of microbiota to complement the conventional microbial markers. In terms of short-chain fatty acid, we discovered that polymeric beta-glucans from barley demonstrated potential as prebiotic candidates, while alpha-glucans as glycogen showed the least dissolved ammonia production. In terms of total probiotic, beta-glucans from oat and mushroom sclerotia of Pleurotus tuber-regium showed comparable sustainability when compared to alpha-glucans after 48 h. Being classical prebiotic, galacto-oligosaccharides gave the second-highest metabolite-based indicator, followed by lactose. While limited improvement could be made to lactose and oligosaccharides, polymeric beta-glucans from barley avails more capacity for novel prebiotic development, such as structural modification. We anticipate that more similar parallel screening with the element of time and parametric modeling will provide more novel insights.
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Affiliation(s)
- Ka-Lung Lam
- Food and Nutritional Sciences, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 000000, China; (K.-L.L.); (W.-Y.C.); (F.Y.); (H.-S.K.)
| | - Wai-Yin Cheng
- Food and Nutritional Sciences, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 000000, China; (K.-L.L.); (W.-Y.C.); (F.Y.); (H.-S.K.)
| | - Fan Yang
- Food and Nutritional Sciences, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 000000, China; (K.-L.L.); (W.-Y.C.); (F.Y.); (H.-S.K.)
| | - Shaoling Lin
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Lijun You
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, Guangdong, China;
| | - Jiachi Chiou
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China;
| | - Hoi-Shan Kwan
- Food and Nutritional Sciences, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 000000, China; (K.-L.L.); (W.-Y.C.); (F.Y.); (H.-S.K.)
| | - Peter Chi-Keung Cheung
- Food and Nutritional Sciences, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 000000, China; (K.-L.L.); (W.-Y.C.); (F.Y.); (H.-S.K.)
- Correspondence: ; Tel.: +852-39436144
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9
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Zhang W, Chen Y, Jiang H, Yang J, Wang Q, Du Y, Xu H. Integrated strategy for accurately screening biomarkers based on metabolomics coupled with network pharmacology. Talanta 2020; 211:120710. [PMID: 32070601 DOI: 10.1016/j.talanta.2020.120710] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 01/10/2023]
Abstract
Screening diagnostic biomarkers can be challenging due to the complexity of traditional Chinese medicine (TCM) and ambiguous pharmacological mechanisms. In this study, we reported an integrated strategy for accurately screening diagnostic biomarkers based on metabolomics coupled with network pharmacology. First, a feasible pharmacological model was established through systems pharmacology and based on metabolomics-based techniques to explore diagnostic biomarkers. While the components satisfying the q-value < 0.05, fold change (FC) ≥ 1.2 or FC ≤ 0.8, coefficient of variance (CV) ≤ 30%(QC) and the variable importance in the project (VIP) value > 1 are considered to be diagnostic biomarkers. Second, the ingredients were retained only when oral bioavailability (OB), Caco-2 permeability, drug half-life, TPSA and drug likeness (DL) satisfied the criteria (OB ≥ 40%; Caco-2 ≥ -0.4; HL ≥ 4 h; TPSA˂140; DL ≥ 0.18) suggested by the TCMSP database. Moreover, ingredients that exhibit extensive biological activity in TCM are also retained. Third, the effect targets of TCM were screened using the TCMSP database, Swiss Target Prediction and STICH online software. Disease targets were gathered from the therapeutic target database (TTD), PharmGkb and TCMSP database. Hub genes were screened by potential protein-protein interaction (PPI) network pharmacology analysis. Finally, a metabolic network pathway is established between the diagnostic biomarker and the hub gene. In the network analysis of metabolic pathways, most of the genes involved in this pathway are the second-step-obtained hub genes, which can explain the accuracy of the identified biomarkers. The proposed integrated strategy was successfully applied to explore the mechanism of action of Pulsatilla decoction (PD) in the treatment of acute ulcerative colitis (UC). Based on this integrated strategy, 23 potential biomarkers of acute UC treated with PD were identified. In conclusion, the integrated strategy provides novel insights into network pharmacology and metabolomics as effective tools to illuminate the mechanism of action of TCM.
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Affiliation(s)
- Wendan Zhang
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Yu Chen
- Department of Ultrasound, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, PR China
| | - Honghong Jiang
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Jianxi Yang
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Qiao Wang
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Yingfeng Du
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Huijun Xu
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, PR China.
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10
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Ni Z, Goracci L, Cruciani G, Fedorova M. Computational solutions in redox lipidomics - Current strategies and future perspectives. Free Radic Biol Med 2019; 144:110-123. [PMID: 31035005 DOI: 10.1016/j.freeradbiomed.2019.04.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 12/31/2022]
Abstract
The high chemical diversity of lipids allows them to perform multiple biological functions ranging from serving as structural building blocks of biological membranes to regulation of metabolism and signal transduction. In addition to the native lipidome, lipid species derived from enzymatic and non-enzymatic modifications (the epilipidome) make the overall picture even more complex, as their functions are still largely unknown. Oxidized lipids represent the fraction of epilipidome which has attracted high scientific attention due to their apparent involvement in the onset and development of numerous human disorders. Development of high-throughput analytical methods such as liquid chromatography coupled on-line to mass spectrometry provides the possibility to address epilipidome diversity in complex biological samples. However, the main bottleneck of redox lipidomics, the branch of lipidomics dealing with the characterization of oxidized lipids, remains the lack of optimal computational tools for robust, accurate and specific identification of already discovered and yet unknown modified lipids. Here we discuss the main principles of high-throughput identification of lipids and their modified forms and review the main software tools currently available in redox lipidomics. Different levels of confidence for software assisted identification of redox lipidome are defined and necessary steps toward optimal computational solutions are proposed.
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Affiliation(s)
- Zhixu Ni
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, Leipzig, Germany
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy; Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy; Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, Leipzig, Germany.
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Godzien J, Kalaska B, Adamska-Patruno E, Siroka J, Ciborowski M, Kretowski A, Barbas C. Oxidized glycerophosphatidylcholines in diabetes through non-targeted metabolomics: Their annotation and biological meaning. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1120:62-70. [DOI: 10.1016/j.jchromb.2019.04.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 02/07/2023]
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Li SZ, Zeng SL, Wu Y, Zheng GD, Chu C, Yin Q, Chen BZ, Li P, Lu X, Liu EH. Cultivar differentiation of Citri Reticulatae Pericarpium by a combination of hierarchical three-step filtering metabolomics analysis, DNA barcoding and electronic nose. Anal Chim Acta 2019; 1056:62-69. [PMID: 30797461 DOI: 10.1016/j.aca.2019.01.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 12/29/2018] [Accepted: 01/04/2019] [Indexed: 12/11/2022]
Abstract
The traditional Chinese medicine Citri Reticulatae Pericarpium (CRP) was mainly originated from the dried pericarp of Citrus reticulata 'Chachi' (Crc), Citrus reticulata 'Dahongpao' (Crd), Citrus reticulata 'Unshiu' (Cru) and Citrus reticulata 'Tangerina' (Crt) in China. Since these four cultivars have great similarities in morphology, reliable methods to differentiate CRP cultivars have rarely been reported. To discriminate the differences of these CRP cultivars, herein an efficient and reliable method by combining metabolomics, DNA barcoding and electronic nose was first established. The hierarchical three-step filtering metabolomics analysis based on liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) indicated that 9 species-specific chemical markers including 6 flavanone glycosides and 3 polymethoxyflavones could be considered as marker metabolites for discrimination of the geoherb Crc from other cultivars. A total of 19 single nucleotide polymorphism (SNP) sites were found in nuclear internal transcribed spacer 2 (ITS2) of CRP, and three stable SNP sites (33, 128 and 174) in the ITS2 region can distinguish the four CRP cultivars. The electronic nose coupled with chemometrics could also be used to effectively distinguish Crc from other CRP cultivars. Therefore, our results indicated that the integrated method will be an effective strategy for discrimination of similar herbal medicines.
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Affiliation(s)
- Shang-Zhen Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing, 210009, China
| | - Su-Ling Zeng
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing, 210009, China
| | - Yan Wu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing, 210009, China
| | - Guo-Dong Zheng
- Department of Pharmacy, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, PR China
| | - Chu Chu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Qiang Yin
- Department of Management, Xinjiang Uygur Pharmaceutical Co., Ltd, Wulumuqi, Xinjiang, 830001, PR China
| | - Bai-Zhong Chen
- Guangdong Xinbaotang Biological Technology Co., Ltd, Guangdong, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing, 210009, China
| | - Xu Lu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing, 210009, China.
| | - E-Hu Liu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing, 210009, China.
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Gil-de-la-Fuente A, Godzien J, Saugar S, Garcia-Carmona R, Badran H, Wishart DS, Barbas C, Otero A. CEU Mass Mediator 3.0: A Metabolite Annotation Tool. J Proteome Res 2018; 18:797-802. [PMID: 30574788 DOI: 10.1021/acs.jproteome.8b00720] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
CEU Mass Mediator (CMM, http://ceumass.eps.uspceu.es ) is an online tool that has evolved from a simple interface to query different metabolomic databases (CMM 1.0) to a tool that unifies the compounds from these databases and, using an expert system with knowledge about the experimental setup and the compounds properties, filters and scores the query results (CMM 2.0). Since this last major revision, CMM has continued to grow, expanding the knowledge base of its expert system and including new services to support researchers in the metabolite annotation and identification process. The information from external databases has been refreshed, and an in-house library with oxidized lipids not present in other sources has been added. This has increased the number of experimental metabolites up 332,665 and the number of predicted metabolites to 681,198. Furthermore, new taxonomy and ontology metadata have been included. CMM has expanded its functionalities with a service for the annotation of oxidized glycerophosphocholines, a service for spectral comparison from MS2 data, and a spectral quality-assessment service to determine the reliability of a spectrum for compound identification purposes. To facilitate the collaboration and integration of CMM with external tools and metabolomic platforms, a RESTful API has been created, and it has already been integrated into the HMDB (Human Metabolome Database). This paper will present the novel functionalities incorporated into version 3.0 of CMM.
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Affiliation(s)
- Alberto Gil-de-la-Fuente
- Department of Information Technology, Escuela Politécnica Superior , Universidad San Pablo-CEU, CEU Universities, Campus Montepríncipe , Boadilla del Monte, Madrid 28668 , Spain.,Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia , Universidad San Pablo-CEU, CEU Universities, Campus Montepríncipe , Boadilla del Monte, Madrid 28668 , Spain
| | - Joanna Godzien
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia , Universidad San Pablo-CEU, CEU Universities, Campus Montepríncipe , Boadilla del Monte, Madrid 28668 , Spain
| | - Sergio Saugar
- Department of Information Technology, Escuela Politécnica Superior , Universidad San Pablo-CEU, CEU Universities, Campus Montepríncipe , Boadilla del Monte, Madrid 28668 , Spain
| | - Rodrigo Garcia-Carmona
- Department of Information Technology, Escuela Politécnica Superior , Universidad San Pablo-CEU, CEU Universities, Campus Montepríncipe , Boadilla del Monte, Madrid 28668 , Spain
| | - Hasan Badran
- Department of Biological Sciences University of Alberta , Edmonton , Alberta T6G 2E9 , Canada
| | - David S Wishart
- Department of Biological Sciences University of Alberta , Edmonton , Alberta T6G 2E9 , Canada.,Department of Computing Science , University of Alberta , Edmonton , Alberta T6G 2E8 , Canada.,Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , Alberta T6G 2N8 , Canada
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia , Universidad San Pablo-CEU, CEU Universities, Campus Montepríncipe , Boadilla del Monte, Madrid 28668 , Spain
| | - Abraham Otero
- Department of Information Technology, Escuela Politécnica Superior , Universidad San Pablo-CEU, CEU Universities, Campus Montepríncipe , Boadilla del Monte, Madrid 28668 , Spain.,Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia , Universidad San Pablo-CEU, CEU Universities, Campus Montepríncipe , Boadilla del Monte, Madrid 28668 , Spain
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