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کاربرد نوع شرط:
- جایگاه : پژوهشی
- مجله: Research Journal of Pharmacognosy
- نوع مقاله: Journal Article
- کلمات کلیدی: Rats,Protein,Non-Alcoholic fatty liver disease,protein interaction maps
- چکیده:
- چکیده انگلیسی: Background and objectives: Non-alcoholic fatty liver disease (NAFLD) is a common liver condition. On the other hand, coffee consumption has shown promising for gastrointestinal diseases. Detection of the most valuable biomarkers of decaffeinated coffee treatment in healthy and non-alcoholic fatty liver disease conditions was the aim of the present study. Methods: A previous proteomics study about effect of decaffeinated coffee (1.5 mL daily drinking coffee for two months) on protein expression change of rat liver was selected for protein-protein interaction (PPI) network analysis via Cytoscape v.3.7.1 and the related applications. The most central proteins with regards to a high degree and betweenness centralities in the coffee treatment condition of healthy and NAFLD were then analyzed by ClueGO for biological process (BP) derivation. Results: HSPA5, HSPA4, HSPA9, HSPA7, PARK7, HSP90AA1, P4HB, PRDX1, and PDIA3 were introduced as central proteins, which are involved in folding and antioxidant activities. Conclusion: There is a complicated combination of the components in coffee; some elements are involved in liver protection against NAFLD and the others are in contrast.
- انتشار مقاله: 11-04-1398
- نویسندگان: Majid Rezaei-Tavirani,Mostafa Rezaei Tavirani,Mona Zamanian Azodi*,Zahra Akbari,Homa Hajimehdipoor
- مشاهده
- جایگاه : پژوهشی
- مجله: Iranian Journal of Basic Medical Sciences
- نوع مقاله: Journal Article
- کلمات کلیدی: NMR,Thyroid cancer,Serum,Metabolomics,Multinodular goiter
- چکیده:
- چکیده انگلیسی: Objective(s): As the most prevalent endocrine system malignancy, papillary thyroid carcinoma had a very fast rising incidence in recent years for unknown reasons besides the fact that the current methods in thyroid cancer diagnosis still hold some limitations. Therefore, the aim of this study was to improve the potential molecular markers for diagnosis of benign and malignant thyroid nodules to prevent unnecessary surgeries for benign tumors.
Materials and Methods: In this study, 1H-NMR metabolomics platform was used to seek the discriminating serum metabolites in malignant papillary thyroid carcinoma (PTC) compared to benign multinodular goiter (MNG) and healthy subjects and also to better understand the disease mechanisms using bioinformatics analysis. Multivariate statistical analysis showed that PTC and MNG samples could be successfully discriminated in PCA and OPLS-DA score plots.
Results: Significant metabolites that differentiated malignant and benign thyroid lesions included citrate, acetylcarnitine, glutamine, homoserine, glutathione, kynurenine, nicotinic acid, hippurate, tyrosine, tryptophan, β-alanine, and xanthine. The significant metabolites in the PTC group compared to healthy subjects also included scyllo- and myo-inositol, tryptophan, propionate, lactate, homocysteine, 3-methyl glutaric acid, asparagine, aspartate, choline, and acetamide. The metabolite sets enrichment analysis demonstrated that aspartate metabolism and urea cycle were the most important pathways in papillary thyroid cancer progression.
Conclusion: The study results demonstrated that serum metabolic fingerprinting could serve as a viable method for differentiating various thyroid lesions and for proposing novel potential markers for thyroid cancers. Obviously, further studies are needed for the validation of the results.- انتشار مقاله: 15-12-1396
- نویسندگان: Reyhaneh Farrokhi Yekta,Mostafa Rezaei Tavirani,Afsaneh Arefi Oskuie,Mohamad Reza Mohajeri Tehrani,Ahmad Reza Soroush,Alireza Akbarzadeh Baghban
- مشاهده
- جایگاه : پژوهشی
- مجله: Iranian Journal of Basic Medical Sciences
- نوع مقاله: Journal Article
- کلمات کلیدی: NMR,Thyroid cancer,Serum,Metabolomics,Multinodular goiter
- چکیده:
- چکیده انگلیسی: Objective(s): As the most prevalent endocrine system malignancy, papillary thyroid carcinoma had a very fast rising incidence in recent years for unknown reasons besides the fact that the current methods in thyroid cancer diagnosis still hold some limitations. Therefore, the aim of this study was to improve the potential molecular markers for diagnosis of benign and malignant thyroid nodules to prevent unnecessary surgeries for benign tumors.
Materials and Methods: In this study, 1H-NMR metabolomics platform was used to seek the discriminating serum metabolites in malignant papillary thyroid carcinoma (PTC) compared to benign multinodular goiter (MNG) and healthy subjects and also to better understand the disease mechanisms using bioinformatics analysis. Multivariate statistical analysis showed that PTC and MNG samples could be successfully discriminated in PCA and OPLS-DA score plots.
Results: Significant metabolites that differentiated malignant and benign thyroid lesions included citrate, acetylcarnitine, glutamine, homoserine, glutathione, kynurenine, nicotinic acid, hippurate, tyrosine, tryptophan, β-alanine, and xanthine. The significant metabolites in the PTC group compared to healthy subjects also included scyllo- and myo-inositol, tryptophan, propionate, lactate, homocysteine, 3-methyl glutaric acid, asparagine, aspartate, choline, and acetamide. The metabolite sets enrichment analysis demonstrated that aspartate metabolism and urea cycle were the most important pathways in papillary thyroid cancer progression.
Conclusion: The study results demonstrated that serum metabolic fingerprinting could serve as a viable method for differentiating various thyroid lesions and for proposing novel potential markers for thyroid cancers. Obviously, further studies are needed for the validation of the results.- انتشار مقاله: 15-12-1396
- نویسندگان: Reyhaneh Farrokhi Yekta,Mostafa Rezaei Tavirani,Afsaneh Arefi Oskuie,Mohamad Reza Mohajeri Tehrani,Ahmad Reza Soroush,Alireza Akbarzadeh Baghban
- مشاهده
- جایگاه : پژوهشی
- مجله: Asian Pacific Journal of Cancer Prevention
- نوع مقاله: Journal Article
- کلمات کلیدی: oral cancer,Biomarker,Protein-protein interaction,hub-bottleneck,Cluster
- چکیده:
- چکیده انگلیسی: Background: Oral cancer is a frequently encountered neoplasm of the head and neck region, being the eight most
common type of human malignancy worldwide. Despite improvement in its control, morbidity and mortality rates have
improved little in the past decades. Therefore, prevention and/or early detection are a high priority. Proteomics with
network analysis have emerged as a powerful tool to identify important proteins associated with cancer development
and progression that can be potential targets for early diagnosis. In the present study, network- based protein- protein
interactions (PPI) for oral cancer were identified and then analyzed for use as key proteins/potential biomarkers.
Material and Methods: Gene expression data in articles which focused on saliva proteomics of oral cancer were
collected and 74 candidate genes or proteins were extracted. Related protein networks of differentially expressed proteins
were explored and visualized using cytoscape software. Further PPI analysis was performed by Molecular Complex
Detection (MCODE) and BiNGO methods. Results: Network analysis of genes/proteins related to oral cancer identified
kininogen-1, angiotensinogen, annexin A1, IL-8, IgG heavy variable and constant chains, CRP, collagen alpha-1 and
fibronectin as 9 hub-bottleneck proteins. In addition, based on clustering with the MCODE tool, vitronectin, collagen
alpha-2, IL-8 and integrin alpha-v were established as 5 distinct seed proteins. Conclusion: A hub-bottleneck protein
panel may offer a potential /candidate biomarker pattern for diagnosis and treatment of oral cancer disease. Further
investigation and validation of these proteins are warranted.- انتشار مقاله: 28-09-1396
- نویسندگان: Nasrin Amiri Dash Atan,Mehdi Koushki,Mostafa Rezaei Tavirani,Nayeb Ali Ahmadi
- مشاهده
- جایگاه : پژوهشی
- مجله: Asian Pacific Journal of Cancer Prevention
- نوع مقاله: Journal Article
- کلمات کلیدی: Nasopharyngeal carcinoma,Protein-protein interaction network analysis,Topological Analysis,Gene ontology
- چکیده:
- چکیده انگلیسی: Nasopharyngeal carcinoma (NPC), although not very common in many parts of the world, is a major concern in
some countries, including Iran. Molecular studies are very helpful to provide essential information regarding underlying
carcinogenetic mechanisms. Here, considering NPC proteomic approaches, established biomarkers were designated for
protein-protein interaction network construction and analysis with corresponding plug-ins. A network of reported protein
markers was constructed and topological and biological process features were investigated. Centrality analysis showed
that JUN, CALM1, HSB1, and SOD1 are more important than other differentially expressed proteins in an interacting
pattern. What is more, by extending the network, Tp53, PRDM10, AKT1, ALB, HSP90AA1, and EGFR achieved the
highest values for NPC network strength. It can be concluded that these proteins as well as their contributing processes,
particularly in a second network, may be important for NPC onset and development. Targeting these candidate proteins
may allow novel treatment approaches following appropriate validation.- انتشار مقاله: 21-08-1396
- نویسندگان: Mona Zamanian Azodi,Majid Rezaei Tavirani,Mostafa Rezaei Tavirani,Reza Vafaee,Mohammad Rostami-Nejad
- مشاهده