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Pandita D, Pandita A. Omics Technology for the Promotion of Nutraceuticals and Functional Foods. Front Physiol 2022; 13:817247. [PMID: 35634143 PMCID: PMC9136416 DOI: 10.3389/fphys.2022.817247] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/23/2022] [Indexed: 12/24/2022] Open
Abstract
The influence of nutrition and environment on human health has been known for ages. Phytonutrients (7,000 flavonoids and phenolic compounds; 600 carotenoids) and pro-health nutrients—nutraceuticals positively add to human health and may prevent disorders such as cancer, diabetes, obesity, cardiovascular diseases, and dementia. Plant-derived bioactive metabolites have acquired an imperative function in human diet and nutrition. Natural phytochemicals affect genome expression (nutrigenomics and transcriptomics) and signaling pathways and act as epigenetic modulators of the epigenome (nutri epigenomics). Transcriptomics, proteomics, epigenomics, miRNomics, and metabolomics are some of the main platforms of complete omics analyses, finding use in functional food and nutraceuticals. Now the recent advancement in the integrated omics approach, which is an amalgamation of multiple omics platforms, is practiced comprehensively to comprehend food functionality in food science.
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Affiliation(s)
- Deepu Pandita
- Government Department of School Education, Jammu, India
- *Correspondence: Deepu Pandita,
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Banecka-Majkutewicz Z, Kadziński L, Grabowski M, Bloch S, Kaźmierkiewicz R, Jakóbkiewicz-Banecka J, Gabig-Cimińska M, Węgrzyn G, Węgrzyn A, Banecki B. Evidence for interactions between homocysteine and genistein: insights into stroke risk and potential treatment. Metab Brain Dis 2017; 32:1855-1860. [PMID: 28748495 DOI: 10.1007/s11011-017-0078-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 07/19/2017] [Indexed: 01/06/2023]
Abstract
Elevated plasma homocysteine (2-amino-4-sulfanylbutanoic acid) level is a risk factor for stroke. Moreover, it has been suggested that high levels of homocysteine in the acute phase of an ischemic stroke can predict mortality, especially in stroke patients with the large-vessel atherosclerosis subtype. In clinical studies, supplementation with genistein (5, 7-dihydroxy-3- (4-hydroxyphenyl)-4H-1-benzopyran-4-one) decreased plasma homocysteine levels considerably. Therefore, genistein could be considered as a potential drug for prevention and/or treatment of stroke. However, the mechanism of the effect of genistein on homocysteine level remains to be elucidated. In this report, direct functional interactions between homocysteine and genistein are demonstrated in in vitro experimental systems for determination of methylenetetrahydrofolate reductase (MetF) and glutathione peroxidase (GPx) activities, reconstructed with purified compounds, and in a simple in vivo system, based on measurement of growth rate of Vibrio harveyi and Bacillus subtilis cultures. Results of molecular modelling indicated that homocysteine can directly interact with genistein. Therefore, genistein-mediated decrease in plasma levels of homocysteine, and alleviation of biochemical and physiological effects of one of these compounds by another, might be ascribed to formation of homocysteine-genistein complexes in which biological activities of these molecules are abolished or alleviated.
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Affiliation(s)
| | - Leszek Kadziński
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Michał Grabowski
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Sylwia Bloch
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Rajmund Kaźmierkiewicz
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | | | - Magdalena Gabig-Cimińska
- Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Alicja Węgrzyn
- Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Bogdan Banecki
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland.
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Song X, Zeng R, Ni L, Liu C. The effect of soy or isoflavones on homocysteine levels: a meta-analysis of randomised controlled trials. J Hum Nutr Diet 2016; 29:797-804. [PMID: 27214197 DOI: 10.1111/jhn.12383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND The present study aimed to evaluate the effect of soy or isoflavones on blood homocysteine levels via a systematic review and meta-analysis. METHODS Pubmed, Embase, Web of Science and the Cochrane Library (up to 16 December 2015) were used for the literature review. Only randomised controlled trials were included. The primary outcome was the standard mean difference (SMD) of blood homocysteine levels between the experimental and control groups. RESULTS Nineteen randomised controlled studies were included for qualitative analysis. Eighteen studies were included in the data synthesis. Soy or isoflavones were found to have no effect on homocysteine levels, with a SMD of -0.21 (95% confidence interval = -0.43 to 0.00, I2 =67.7%, random effect model). No publication bias was found among those studies (P = 0.296 for Egger's test, and P = 0.198 for Begg's test). CONCLUSIONS Soy or isoflavones were not found to be associated with a reduction in homocysteine levels. Further studies might still be needed in carefully selected populations.
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Affiliation(s)
- X Song
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - R Zeng
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - L Ni
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - C Liu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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Han S, Wu H, Li W, Gao P. Protective effects of genistein in homocysteine-induced endothelial cell inflammatory injury. Mol Cell Biochem 2015; 403:43-9. [PMID: 25626894 DOI: 10.1007/s11010-015-2335-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/16/2015] [Indexed: 11/29/2022]
Abstract
Hyperhomocysteinemia is a risk factor for cardiovascular disease and the mechanism of homocysteine (HCY)-induced vascular endothelial cell injury has been intensively studied for many years. Recently, a large number of studies have shown inhibitory effects of genistein (GEN), a soy isoflavone, in the process of endothelial cell injury. In the present study, the protective effects of GEN in HCY-induced endothelial cell inflammatory injury were investigated. A model of HCY-induced endothelial cell (ECV-304) inflammatory injury was established in vitro, and the protective effect of GEN in this procession was explored. According to our results, GEN protected HCY-induced endothelial cell from viability decreases, meanwhile prevented the changes of cell morphology and the production of reactive oxygen species (ROS). The expression of NF-kB P-65, IL-6, and ICAM-1 was all down-regulated. During the HCY-induced endothelial cell injury, the endothelial cell apoptosis and proliferation disorder were alleviated. Therefore, we conclude that HCY-induced endothelial cell inflammatory injury could be blocked by GEN. The present findings suggest that GEN protects HCY-induced endothelial cell inflammatory injury may through reducing the release of ROS, inhibiting NF-kB activation, down-regulating the expression of cytokine IL-6 and adhesion molecules ICAM-1, avoiding inflammatory cells and platelet adhesion, accordingly, leading to a balance of endothelial cell proliferation and apoptosis.
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Affiliation(s)
- Shengbo Han
- Clinical Laboratory of Zhengzhou Traditional Chinese Medicine Hospital, Wenhuagong Road 65, Zhengzhou, 450007, China,
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Genistein attenuates vascular endothelial impairment in ovariectomized hyperhomocysteinemic rats. J Biomed Biotechnol 2012; 2012:730462. [PMID: 23226943 PMCID: PMC3511852 DOI: 10.1155/2012/730462] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 10/14/2012] [Accepted: 10/15/2012] [Indexed: 01/18/2023] Open
Abstract
Hyperhomocysteinemia (HHcy) is a well-known independent risk factor for vascular diseases in the general population. This study was to explore the effect of genistein (GST), a natural bioactive compound derived from legumes, on HHcy-induced vascular endothelial impairment in ovariectomized rats in vivo. Thirty-two adult female Wistar rats were assigned randomly into four groups (n = 8): (a) Con: control; (b) Met: 2.5% methionine diet; (c) OVX + Met: ovariectomy + 2.5% methionine diet; (d) OVX + Met + GST: ovariectomy + 2.5% methionine diet + supplementation with genistein. After 12 wk of different treatment, the rats' blood, toracic aortas and liver samples were collected for analysis. Results showed that high-methionine diet induced both elevation of plasma Hcy and endothelial dysfunction, and ovariectomy deteriorated these injuries. Significant improvement of both functional and morphological changes of vascular endothelium was observed in OVX + Met + GST group; meanwhile the plasma Hcy levels decreased remarkably. There were significant elevations of plasma ET-1 and liver MDA levels in ovariectomized HHcy rats, and supplementation with genistein could attenuate these changes. These results implied that genistein could lower the elevated Hcy levels, and prevent the development of endothelial impairment in ovariectomized HHcy rats. This finding may shed a novel light on the anti-atherogenic activities of genistein in HHcy patients.
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Romagnolo DF, Milner JA. Opportunities and challenges for nutritional proteomics in cancer prevention. J Nutr 2012; 142:1360S-9S. [PMID: 22649262 DOI: 10.3945/jn.111.151803] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Knowledge gaps persist about the efficacy of cancer prevention strategies based on dietary food components. Adaptations to nutrient supply are executed through tuning of multiple protein networks that include transcription factors, histones, modifying enzymes, translation factors, membrane and nuclear receptors, and secreted proteins. However, the simultaneous quantitative and qualitative measurement of all proteins that regulate cancer processes is not practical using traditional protein methodologies. Proteomics offers an attractive opportunity to fill this knowledge gap and unravel the effects of dietary components on protein networks that impinge on cancer. The articles presented in this supplement are from talks proffered in the "Nutrition Proteomics and Cancer Prevention" session at the American Institute for Cancer Research Annual Research Conference on Food, Nutrition, Physical Activity and Cancer held in Washington, DC on October 21 and 22, 2010. Recent advances in MS technologies suggest that studies in nutrition and cancer prevention may benefit from the adoption of proteomic tools to elucidate the impact on biological processes that govern the transition from normal to malignant phenotype; to identify protein changes that determine both positive and negative responses to food components; to assess how protein networks mediate dose-, time-, and tissue-dependent responses to food components; and, finally, for predicting responders and nonresponders. However, both the limited accessibility to proteomic technologies and research funding appear to be hampering the routine adoption of proteomic tools in nutrition and cancer prevention research.
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Affiliation(s)
- Donato F Romagnolo
- Department of Nutritional Sciences and The University of Arizona Cancer Center, The University of Arizona, Tucson, AZ, USA.
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Protective effect of isoflavones against homocysteine-mediated neuronal degeneration in SH-SY5Y cells. Amino Acids 2010; 39:785-94. [DOI: 10.1007/s00726-010-0523-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 02/10/2010] [Indexed: 01/02/2023]
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Cheng KW, Wong CC, Wang M, He QY, Chen F. Identification and characterization of molecular targets of natural products by mass spectrometry. MASS SPECTROMETRY REVIEWS 2010; 29:126-155. [PMID: 19319922 DOI: 10.1002/mas.20235] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Natural products, and their derivatives and mimics, have contributed to the development of important therapeutics to combat diseases such as infections and cancers over the past decades. The value of natural products to modern drug discovery is still considerable. However, its development is hampered by a lack of a mechanistic understanding of their molecular action, as opposed to the emerging molecule-targeted therapeutics that are tailored to a specific protein target(s). Recent advances in the mass spectrometry-based proteomic approaches have the potential to offer unprecedented insights into the molecular action of natural products. Chemical proteomics is established as an invaluable tool for the identification of protein targets of natural products. Small-molecule affinity selection combined with mass spectrometry is a successful strategy to "fish" cellular targets from the entire proteome. Mass spectrometry-based profiling of protein expression is also routinely employed to elucidate molecular pathways involved in the therapeutic and possible toxicological responses upon treatment with natural products. In addition, mass spectrometry is increasingly utilized to probe structural aspects of natural products-protein interactions. Limited proteolysis, photoaffinity labeling, and hydrogen/deuterium exchange in conjunction with mass spectrometry are sensitive and high-throughput strategies that provide low-resolution structural information of non-covalent natural product-protein complexes. In this review, we provide an overview on the applications of mass spectrometry-based techniques in the identification and characterization of natural product-protein interactions, and we describe how these applications might revolutionize natural product-based drug discovery.
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Affiliation(s)
- Ka-Wing Cheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Wang L, Zheng X, Xiang HL, Fu XH, Cao JG. 7-difluoromethyl-5,4'-dimethoxygenistein, a novel agent protecting against vascular endothelial injury caused by oxidative stress. Clin Exp Pharmacol Physiol 2009; 36:e90-5. [PMID: 19793105 DOI: 10.1111/j.1440-1681.2009.05305.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
1. Genistein is known to protect the vascular endothelium. However, genistein exhibits poor bioavailability, which limits its use in the treatment of cardiovascular diseases. 7-Difluoromethyl-5,4'-dimethoxygenistein (dFMGEN), prepared by the difluoromethylation and alkylation of genistein, is a new active chemical entity. The protective effects of dFMGEN against vascular endothelial injury caused by oxidative stress were investigated in the present study. 2. Human umbilical vein endothelial cells were treated with either genistein (10 micromol/L) or various concentrations of dFMGEN (0.1, 0.3, 1, 3 and 10 micromol/L) for 30 min before exposure to 1 mmol/L H(2)O(2) for 24 h. The generation of reactive oxygen species (ROS) was assessed by fluorescence flow cytometry, the release of lactate dehydrogenase (LDH) was examined by biochemical assay, cell viability was measured by the 3-(4,5-dimethyl-2 thiazoyl)-2,5-diphenyl-2H-tetrazolium bromide assay, cell apoptosis was detected by flow cytometry and the expression of caspase 3 was examined by western blot analysis. 3. Pretreatment with 0.1, 0.3, 1, 3 and 10 micromol/L dFMGEN decreased the generation of ROS and the release of LDH in H(2)O(2)-exposed vascular endothelial cells, enhanced cell viability in a concentration-dependent manner over the concentration range 0.1-10 micromol/L, suppressed H(2)O(2)-induced apoptosis of vascular endothelial cells and downregulated the expression of caspase 3. The protective effect of 10 micromol/L dFMGEN against oxidative stress-induced endothelial injury was stronger than that of 10 micromol/L genistein. 4. The results of the present study suggest that dFMGEN can protect against vascular endothelial injury caused by oxidative stress.
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Affiliation(s)
- Li Wang
- College of Medicine, University of South China, Hengyang, China
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García-Cañas V, Simó C, León C, Cifuentes A. Advances in Nutrigenomics research: novel and future analytical approaches to investigate the biological activity of natural compounds and food functions. J Pharm Biomed Anal 2009; 51:290-304. [PMID: 19467817 DOI: 10.1016/j.jpba.2009.04.019] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 04/06/2009] [Accepted: 04/09/2009] [Indexed: 01/03/2023]
Abstract
In recent years, nutrition research has moved from classical epidemiology and physiology to molecular biology and genetics. Following this trend, Nutrigenomics has emerged as a novel and multidisciplinary research field in nutritional science that aims to elucidate how diet can influence human health. It is already well known that bioactive food compounds can interact with genes affecting transcription factors, protein expression and metabolite production. The study of these complex interactions requires the development of advanced analytical approaches combined with bioinformatics. Thus, to carry out these studies Transcriptomics, Proteomics and Metabolomics approaches are employed together with an adequate integration of the information that they provide. In this article, an overview of the current methodologies and a thorough revision of the advances in analytical technologies and their possibilities for future developments and applications in the field of Nutrigenomics is provided.
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Affiliation(s)
- V García-Cañas
- Institute of Industrial Fermentations (CSIC), Juan de la Cierva 3, Madrid, Spain
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Huang G, Liu Y, Chang H, Zhang X, Ren D, Wilson JX, Cao X. Effects of genistein on oxidative injury in endothelial cells. J Nutr Sci Vitaminol (Tokyo) 2009; 54:402-8. [PMID: 19001773 DOI: 10.3177/jnsv.54.402] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The aim of this study was to test the hypothesis that genistein protects vascular endothelial cells against the pro-atherosclerotic stressor, oxidized low-density lipoprotein (ox-LDL), by inducing antioxidant enzymes and preventing apoptosis. Human umbilical cord-derived endothelial cells (ECV 304) were incubated with genistein (10-100 micromol/L), the radical scavenging antioxidant vitamin E (alpha-tocopherol, 50 micromol/L), or vehicle for 24 h and then were incubated with ox-LDL for an additional 24 h. Subsequently, antioxidant enzyme activities, lipid peroxidation, adhesion to monocytes, cell morphology, viability and apoptotic index were assessed. Ox-LDL decreased superoxide dismutase and glutathione peroxidase activities in endothelial cells and caused lipid peroxidation, adhesion to monocytes, morphological injury and apoptosis (p<0.05). These effects were prevented by vitamin E and dose-dependently by genistein (p<0.05). Further, this effect of genistein is associated with maintenance of antioxidant enzyme activities and inhibition of lipid peroxidation.
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Affiliation(s)
- Guowei Huang
- Tianjin Key Laboratory of Food Nutrition and Safety, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, China
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Wang L, Zheng X, Xiang HL, Fu XH, Cao JG. 7-Difluoromethyl-5,4′-dimethoxygenistein inhibits oxidative stress induced adhesion between endothelial cells and monocytes via NF-κB. Eur J Pharmacol 2009; 605:31-5. [DOI: 10.1016/j.ejphar.2009.01.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Abstract
Após seqüenciamento do genoma humano, os estudos genômicos têm se voltado à elucidação das funções de todos os genes, bem como à caracterização de suas interações com fatores ambientais. A nutrigenômica surgiu no contexto do pós-genoma humano e é considerada área-chave para a nutrição nesta década. Seu foco de estudo baseia-se na interação gene-nutriente. Esta ciência recente tem como objetivo principal o estabelecimento de dietas personalizadas, com base no genótipo, para a promoção da saúde e a redução do risco de doenças crônicas não transmissíveis como as cardiovasculares, o câncer, o diabetes, entre outras. Nesse contexto, é fundamental a aplicação na área de nutrição das ferramentas de genômica funcional para análise do transcritoma (transcritômica), do proteoma (proteômica) e do metaboloma (metabolômica). As aplicabilidades dessas metodologias em estudos nutricionais parecem ilimitadas, pois podem ser conduzidas em cultura de células, modelos de experimentação em animais, estudos pré-clinicos e clínicos. Tais técnicas apresentam potencial para identificar biomarcadores que respondem especificamente a um determinado nutriente ou composto bioativo dos alimentos e para estabelecer as melhores recomendações dietéticas individuais para redução do risco das doenças crônicas não transmissíveis e promoção da saúde.
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de Roos B, Duthie SJ, Polley ACJ, Mulholland F, Bouwman FG, Heim C, Rucklidge GJ, Johnson IT, Mariman EC, Daniel H, Elliott RM. Proteomic methodological recommendations for studies involving human plasma, platelets, and peripheral blood mononuclear cells. J Proteome Res 2008; 7:2280-90. [PMID: 18489134 DOI: 10.1021/pr700714x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This study was designed to develop, optimize and validate protocols for blood processing prior to proteomic analysis of plasma, platelets and peripheral blood mononuclear cells (PBMC) and to determine analytical variation of a single sample of depleted plasma, platelet and PBMC proteins within and between four laboratories each using their own standard operating protocols for 2D gel electrophoresis. Plasma depleted either using the Beckman Coulter IgY-12 proteome partitioning kit or the Amersham albumin and IgG depletion columns gave good quality gels, but reproducibility appeared better with the single-use immuno-affinity column. The use of the Millipore Filter Device for protein concentration gave a 16% ( p < 0.005) higher recovery of protein in flow-through sample compared with acetone precipitation. The use of OptiPrep gave the lowest level of platelet contamination (1:0.8) during the isolation of PBMC from blood. Several proteins (among which are alpha-tropomyosin, fibrinogen and coagulation factor XIII A) were identified that may be used as biomarkers of platelet contamination in future studies. When identifying preselected spots, at least three out of the four centers found similar identities for 10 out of the 10 plasma proteins, 8 out of the 10 platelet proteins and 8 out of the 10 PBMC proteins. The discrepancy in spot identifications has been described before and may be explained by the mis-selection of spots due to laboratory-to-laboratory variation in gel formats, low scores on the peptide analysis leading to no or only tentative identifications, or incomplete resolution of different proteins in what appears as a single abundant spot. The average within-laboratory coefficient of variation (CV) for each of the matched spots after automatic matching using either PDQuest or ProteomWeaver software ranged between 18 and 69% for depleted plasma proteins, between 21 and 55% for platelet proteins, and between 22 and 38% for PBMC proteins. Subsequent manual matching improved the CV with on average between 1 and 16%. The average between laboratory CV for each of the matched spots after automatic matching ranged between 4 and 54% for depleted plasma proteins, between 5 and 60% for platelet proteins, and between 18 and 70% for PBMC proteins. This variation must be considered when designing sufficiently powered studies that use proteomics tools for biomarker discovery. The use of tricine in the running buffer for the second dimension appears to enhance the resolution of proteins especially in the high molecular weight range.
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Kussmann M, Rezzi S, Daniel H. Profiling techniques in nutrition and health research. Curr Opin Biotechnol 2008; 19:83-99. [DOI: 10.1016/j.copbio.2008.02.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Revised: 02/13/2008] [Accepted: 02/14/2008] [Indexed: 12/13/2022]
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Zhang X, Yap Y, Wei D, Chen G, Chen F. Novel omics technologies in nutrition research. Biotechnol Adv 2008; 26:169-76. [DOI: 10.1016/j.biotechadv.2007.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 11/07/2007] [Accepted: 11/07/2007] [Indexed: 01/05/2023]
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Winkelmann I, Näßl AM, Daniel H, Wenzel U. Proteome response in HT-29 human colorectal cancer cells to two apoptosis-inducing compounds with different mode of action. Int J Cancer 2008; 122:2223-32. [DOI: 10.1002/ijc.23387] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Astle J, Ferguson JT, German JB, Harrigan GG, Kelleher NL, Kodadek T, Parks BA, Roth MJ, Singletary KW, Wenger CD, Mahady GB. Characterization of proteomic and metabolomic responses to dietary factors and supplements. J Nutr 2007; 137:2787-93. [PMID: 18029500 DOI: 10.1093/jn/137.12.2787] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Over the past decade there has been a renewed interest in research and development of both dietary and nutritional supplements. Significant advancements have been made in the scientific assessment of the quality, safety, and efficacy of these products because of the strong interest in and financial support of these projects. As research in both fields continues to advance, opportunities to use new and innovative research technologies and methodologies, such as proteomics and metabolomics, are critical for the future progress of the science. The purpose of the symposium was to begin the process of communicating new innovative proteomic and metabolomic methodologies that may be applied by researchers in both the nutrition and the natural product communities. This symposium highlighted 2 proteomic approaches, protein fingerprinting in complex mixtures with peptoid microarrays and top-down mass spectrometry for annotation of gene products. Likewise, an overview of the methodologies used in metabolomic profiling of natural products was presented, and an illustration of an integrated metabolomics approach in nutrition research was highlighted.
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Affiliation(s)
- John Astle
- University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
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Kuhla S, Rudolph PE, Albrecht D, Schoenhusen U, Zitnan R, Tomek W, Huber K, Voigt J, Metges CC. A Milk Diet Partly Containing Soy Protein Does Not Change Growth but Regulates Jejunal Proteins in Young Goats. J Dairy Sci 2007; 90:4334-45. [PMID: 17699054 DOI: 10.3168/jds.2007-0022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Soy protein is known to alter intestinal function and structure. We determined in young goats whether a diet partly containing soy protein differently affects intestinal morphology and the jejunal and hepatic proteome as compared with a milk diet. Fourteen male 2-wk-old White German dairy goat kids were fed comparable diets based on whole cow's milk in which 35% of the crude protein was casein (milk protein group; MP) or soy protein supplemented by indispensable AA (SPAA) for 34 d (n = 7/group). Body weight gain and food efficiency were not different. Jejunal and hepatic tissue was collected to determine intestinal morphology by microscopy and protein repertoire by 2-dimensional gel electrophoresis and mass spectrometry. Jejunal crypt depth was reduced and villus height to crypt depth ratio was higher in SPAA than in milk protein. Out of 131 proteins identified, 32 proteins were found to be differently expressed in both groups. In SPAA, down-regulated jejunal proteins were involved in processes related to cytoskeleton generation, protein, lipid, and energy metabolism. Downregulated hepatic proteins were related to glycolysis and Krebs cycle. Thirteen proteins were upregulated in SPAA. Among these, 2 hepatic proteins were related to carbohydrate breakdown. The other 11 jejunal proteins were involved in cytoskeleton assembly, proteolysis, and carbohydrate breakdown. In addition, glutathione-S-transferase was found to be upregulated in the medial jejunum. In conclusion, a SPAA diet as compared with a milk diet was related to changes in jejunal morphology and jejunal proteins relevant for protein turnover, energy metabolism, and cytoskeleton assembly with no apparent impact on animal BW gain.
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Affiliation(s)
- S Kuhla
- Research Unit Nutritional Physiology Oskar Kellner, Research Institute for the Biology of Farm Animals (FBN), D-18196 Dummerstorf, Germany
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Dietary isoflavones in the prevention of cardiovascular disease--a molecular perspective. Food Chem Toxicol 2007; 46:1308-19. [PMID: 17689850 DOI: 10.1016/j.fct.2007.06.029] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 06/21/2007] [Indexed: 12/24/2022]
Abstract
The Food and Drugs Administration has approved a health claim for soy based on clinical trials and epidemiological data indicating that high soy consumption is associated with a lower risk of coronary artery disease. Soy products contain a group of compounds called isoflavones, with genistein and daidzein being the most abundant. A number of cardioprotective benefits have been attributed to dietary isoflavones including a reduction in LDL cholesterol, an inhibition of pro-inflammatory cytokines, cell adhesion proteins and inducible nitric oxide production, potential reduction in the susceptibility of the LDL particle to oxidation, inhibition of platelet aggregation and an improvement in vascular reactivity. There is increasing interest in the use of nutrigenomic methods to understand the mechanisms by which isoflavones induce these changes, and in the use of nutrigenetics to understand why the effects vary between individuals. Nutrigenomics is a rapidly growing field making use of molecular biology methodologies, such as microarray technology and proteomics, to study how specific nutrients or diets affect gene expression and cellular protein levels. The analysis of differential gene expression and protein levels in endothelial cells, macrophages and smooth muscle cells is critical to elucidating the sequence of events leading to the formation of atherosclerotic lesions, and to understanding the potential anti-atherogenic properties of soy isoflavones. An increasing number of studies demonstrate a significant impact of genetic variation on changes in cardiovascular risk factors in response to dietary intervention. Nutrigenetic effects of this type have recently been reported for dietary isoflavones, and may help to explain some of the disparities in the current literature concerning isoflavones and cardiovascular health.
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Fuchs D, Dirscherl B, Schroot JH, Daniel H, Wenzel U. Proteome analysis suggests that mitochondrial dysfunction in stressed endothelial cells is reversed by a soy extract and isolated isoflavones. J Proteome Res 2007; 6:2132-42. [PMID: 17503794 DOI: 10.1021/pr060547y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Apoptosis is a driving force in atherosclerosis development. A soy extract or a combination of the soy isoflavones genistein and daidzein inhibited apoptosis induced by oxidized LDL in endothelial cells. Proteome analysis revealed that the LDL-induced alterations of numerous proteins were reversed by the extract and the genistein/daidzein mixture but only three protein entities, all functionally linked to mitochondrial dysfunction, were regulated in common by both treatments.
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Affiliation(s)
- Dagmar Fuchs
- Department of Food and Nutrition, Molecular Nutrition Unit, Technical University of Munich, Am Forum 5, D-85350 Freising, Germany
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Fuchs D, Winkelmann I, Johnson IT, Mariman E, Wenzel U, Daniel H. Proteomics in nutrition research: principles, technologies and applications. Br J Nutr 2007; 94:302-14. [PMID: 16176599 DOI: 10.1079/bjn20051458] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The global profiling of the whole protein complement of the genome expressed in a particular cell or organ, or in plasma or serum, makes it possible to identify biomarkers that respond to alterations in diet or to treatment, and that may have predictive value for the modelling of biological processes. Proteomics has not yet been applied on a large scale in nutritional studies, yet it has advantages over transcriptome profiling techniques in that it directly assesses the entities that carry out the biological functions. The present review summarizes the different approaches in proteomics research, with special emphasis on the current technical ‘workhorses’: two-dimensional (2D)-PAGE with immobilized pH gradients and protein identification by MS. Using a work-flow approach, we provide information and advice on sample handling and preparation, protein solubilization and pre-fractionation, protein separation by 2D-PAGE, detection and quantification via computer-assisted analysis of gels, and protein identification and characterization techniques by means of MS. Examples from nutritional studies employing proteomics are provided to demonstrate not only the advantages but also the limitations of current proteome analysis platforms.
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Affiliation(s)
- Dagmar Fuchs
- Molecular Nutrition Unit, Technical University of Munich, Am Forum 5, D-85 350 Freising-Weihenstephan, Germany
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23
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Frey IM, Rubio-Aliaga I, Siewert A, Sailer D, Drobyshev A, Beckers J, de Angelis MH, Aubert J, Bar Hen A, Fiehn O, Eichinger HM, Daniel H. Profiling at mRNA, protein, and metabolite levels reveals alterations in renal amino acid handling and glutathione metabolism in kidney tissue ofPept2−/−mice. Physiol Genomics 2007; 28:301-10. [PMID: 17077276 DOI: 10.1152/physiolgenomics.00193.2006] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
PEPT2 is an integral membrane protein in the apical membrane of renal epithelial cells that operates as a rheogenic transporter for di- and tripeptides and structurally related drugs. Its prime role is thought to be the reabsorption of filtered di- and tripeptides contributing to amino acid homeostasis. To elucidate the role of PEPT2 in renal amino acid metabolism we submitted kidney tissues of wild-type and a Pept2−/−mouse line to a comprehensive transcriptome, proteome and metabolome profiling and analyzed urinary amino acids and dipeptides. cDNA microarray analysis identified 147 differentially expressed transcripts in transporter-deficient animals, and proteome analysis by 2D-PAGE and MALDI-TOF-MS identified 37 differentially expressed proteins. Metabolite profiling by GC-MS revealed predominantly altered concentrations of amino acids and derivatives. Urinary excretion of amino acids demonstrated increased glycine and cysteine/cystine concentrations and dipeptides in urine were assessed by amino acid analysis of urine samples before and after in vitro dipeptidase digestion. Dipeptides constituted a noticeable fraction of urinary amino acids in Pept2−/−animals, only, and dipeptide-bound glycine and cystine were selectively increased in Pept2−/−urine samples. These findings were confirmed by a drastically increased excretion of cysteinyl-glycine (cys-gly). Urinary loss of cys-gly together with lower concentrations of cysteine, glycine, and oxoproline in kidney tissue and altered expression of mRNA and proteins involved in glutathione (GSH) metabolism suggests that PEPT2 is predominantly a system for reabsorption of cys-gly originating from GSH break-down, thus contributing to resynthesis of GSH.
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Affiliation(s)
- Isabelle M Frey
- Molecular Nutrition Unit, Technical University of Munich, Freising, Germany
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Konstantakopoulos N, Larsen MR, Campbell IG, Quinn MA, Baker MS, Georgiou HM, Rice GE. Genistein-induced proteome changes in the human endometrial carcinoma cell line, ishikawa. Clin Proteomics 2006. [DOI: 10.1007/bf02752498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Abstract
Epidemiological studies have shown that Asian populations display a lower incidence of hormone-dependant cancers, cardiovascular disease, osteoporosis, and menopausal ailments compared to Western societies. Available data support the proposal that lower incidence is associated with the high dietary consumption of isoflavones, such as genistein. This study used two-dimensional electrophoresis to characterize the effect of genistein on the proteome of an endometrial tumor cell model, namely the Ishikawa cell line. Proteome maps displaying approx 1800 proteins were obtained from cells treated with vehicle or genistein at physiologically attainable concentrations of 0.5, 5, or 50 μM or supra-physiological concentration, 500 μM. The effects of genistein on protein expression were characterized using image analysis software. A total 65 protein spots displayed a significant decrease in expression and 32 proteins displayed a significant increase in expression. Of these protein spots, 29 were randomly selected for characterization by matrix assisted laser desorption/ionization tandem mass spectrometry, yielding 18 different proteins. This type of analysis enabled the characterization of a wide range of cellular proteins and allowed for the identification of functional and biochemical pathways that may be regulated or affected by genistein, including cellular transcription, cell proliferation, stress response, or modulation of oncogenic pathways.
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Mayr M, Zhang J, Greene AS, Gutterman D, Perloff J, Ping P. Proteomics-based Development of Biomarkers in Cardiovascular Disease. Mol Cell Proteomics 2006; 5:1853-64. [PMID: 16733263 DOI: 10.1074/mcp.r600007-mcp200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Manuel Mayr
- Cardiovascular Division, King's College, University of London, London SE59 NU, United Kingdom
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Rist MJ, Wenzel U, Daniel H. Nutrition and food science go genomic. Trends Biotechnol 2006; 24:172-8. [PMID: 16488035 DOI: 10.1016/j.tibtech.2006.02.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 11/09/2005] [Accepted: 02/02/2006] [Indexed: 11/20/2022]
Abstract
The wealth of genomic information and high-throughput profiling technologies are now being exploited by scientists in the disciplines of nutrition and food science. Diet and food components are prime environmental factors that affect the genome, transcriptome, proteome and metabolome, and this life-long interaction defines the health or disease state of an individual. For the first time the interaction of foods, and individual food constituents, with the biological systems can be defined on a molecular basis. Profiling technologies are used in basic-science applications for identifying the mode of action of foods or particular ingredients, and are similarly taken into the science-driven development of foods with a defined biofunctionality. Biomarker profiles and patterns derived from genomics applications in humans should guide nutrition and food science in developing evidence-based dietary recommendations and health-promoting foods.
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Affiliation(s)
- Manuela J Rist
- Molecular Nutrition Unit, Department Food and Nutrition, Technical University of Munich, Am Forum 5, D-85350 Freising-Weihenstephan, Germany
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Fuchs D, Dirscherl B, Schroot JH, Daniel H, Wenzel U. Soy extract has different effects compared with the isolated isoflavones on the proteome of homocysteine-stressed endothelial cells. Mol Nutr Food Res 2006; 50:58-69. [PMID: 16502433 DOI: 10.1002/mnfr.200500133] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Epidemiological studies suggest that soy consumption may provide a protection in the development and progression of atherosclerosis. It is under debate, however, whether the soy isoflavones or other compounds are the "active principle". As apoptosis is a driving force in the process of atherosclerosis, we tested whether a soy extract or a combination of the two predominant isoflavones genistein and daidzein, in concentrations as found in the extract, exert similar or different effects on apoptosis in EA.hy 926 endothelial cells after exposure to the endothelial stressor homocysteine. Plasma membrane disintegration and nuclear fragmentation served as relevant apoptosis markers. To assess whether the extract and the genistein/daidzein mixture differently affect cellular target proteins changed in amount by homocysteine treatment, proteome analysis was performed by two-dimensional gel-electrophoresis and peptide mass fingerprinting of regulated protein spots. Homocysteine induced apoptosis in the cells, and both extract and genistein/daidzein inhibited apoptosis to a comparable extent. Whereas the extract prevented for 10 proteins the changes in expression levels as caused by homocysteine, the genistein/daidzein mixture reversed the homocysteine effects on the proteome for 13 proteins. The cytoskeletal protein matrin 3 and a U5 snRNP-specific 40-kDa protein were the only protein entities where both extract and genistein/daidzein reversed the homocysteine-induced changes in a common way. In conclusion, our studies provide evidence that an isoflavone containing soy extract and isolated isoflavones, despite similar effects on inhibition of homocysteine-induced apoptosis in endothelial cells, affect a quite different spectrum of cellular target proteins.
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Affiliation(s)
- Dagmar Fuchs
- Department of Food and Nutrition, Molecular Nutrition Unit, Technical University of Munich, Freising, Germany
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