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Tafazoli A, Abbaszadegan MR, Patrinos GP. Editorial: Integration of computational genomics into clinical pharmacogenomic tests: how bioinformatics may help primary care in precision medicine area. Front Genet 2023; 14:1261876. [PMID: 37600661 PMCID: PMC10436194 DOI: 10.3389/fgene.2023.1261876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, Bialystok, Poland
- Laboratory of Pharmacogenomics, Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Mohammad Reza Abbaszadegan
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - George P. Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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Tafazoli A, Mikros J, Khaghani F, Alimardani M, Rafigh M, Hemmati M, Siamoglou S, Golińska AK, Kamiński KA, Niemira M, Miltyk W, Patrinos GP. Pharmacovariome scanning using whole pharmacogene resequencing coupled with deep computational analysis and machine learning for clinical pharmacogenomics. Hum Genomics 2023; 17:62. [PMID: 37452347 PMCID: PMC10347842 DOI: 10.1186/s40246-023-00508-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND This pilot study aims to identify and functionally assess pharmacovariants in whole exome sequencing data. While detection of known variants has benefited from pharmacogenomic-dedicated bioinformatics tools before, in this paper we have tested novel deep computational analysis in addition to artificial intelligence as possible approaches for functional analysis of unknown markers within less studied drug-related genes. METHODS Pharmacovariants from 1800 drug-related genes from 100 WES data files underwent (a) deep computational analysis by eight bioinformatic algorithms (overall containing 23 tools) and (b) random forest (RF) classifier as the machine learning (ML) approach separately. ML model efficiency was calculated by internal and external cross-validation during recursive feature elimination. Protein modelling was also performed for predicted highly damaging variants with lower frequencies. Genotype-phenotype correlations were implemented for top selected variants in terms of highest possibility of being damaging. RESULTS Five deleterious pharmacovariants in the RYR1, POLG, ANXA11, CCNH, and CDH23 genes identified in step (a) and subsequent analysis displayed high impact on drug-related phenotypes. Also, the utilization of recursive feature elimination achieved a subset of 175 malfunction pharmacovariants in 135 drug-related genes that were used by the RF model with fivefold internal cross-validation, resulting in an area under the curve of 0.9736842 with an average accuracy of 0.9818 (95% CI: 0.89, 0.99) on predicting whether a carrying individuals will develop adverse drug reactions or not. However, the external cross-validation of the same model indicated a possible false positive result when dealing with a low number of observations, as only 60 important variants in 49 genes were displayed, giving an AUC of 0.5384848 with an average accuracy of 0.9512 (95% CI: 0.83, 0.99). CONCLUSION While there are some technologies for functionally assess not-interpreted pharmacovariants, there is still an essential need for the development of tools, methods, and algorithms which are able to provide a functional prediction for every single pharmacovariant in both large-scale datasets and small cohorts. Our approaches may bring new insights for choosing the right computational assessment algorithms out of high throughput DNA sequencing data from small cohorts to be used for personalized drug therapy implementation.
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Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy With the Division of Laboratory Medicine, Medical University of Bialystok, 15-089, Białystok, Poland
- Laboratory of Pharmacogenomics, Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Kraków, Poland
| | - John Mikros
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Faeze Khaghani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Guilan University of Medical Sciences, Rasht, Iran
| | - Maliheh Alimardani
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahboobeh Rafigh
- Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahboobeh Hemmati
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Stavroula Siamoglou
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | | | - Karol A Kamiński
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Białystok, Poland
- Department of Cardiology, Medical University of Bialystok, Białystok, Poland
| | - Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, Białystok, Poland
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy With the Division of Laboratory Medicine, Medical University of Bialystok, 15-089, Białystok, Poland.
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
- Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
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Tafazoli A, Kitlas Golińska A, Mnich K, Amirabadizadeh A, Clark Marquez J, Miltyk W. Toward Integration of Pharmacogenomic Tests into Daily Clinical Practice: A General Survey for Polish Healthcare Workers. Med Sci Monit 2023; 29:e940119. [PMID: 37303136 DOI: 10.12659/msm.940119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023] Open
Abstract
BACKGROUND Pharmacogenomics (PGx) has a direct influence on personalized drug therapy for various types of disorders and has been proven to have an important role in the future of medicine. The present study evaluated the awareness of PGx testing of clinicians and healthcare workers in the Republic of Poland. To the best of our knowledge, this is the first direct assessment of Polish healthcare professionals' attitudes toward introducing PGx tests into daily clinical practice. MATERIAL AND METHODS We used a comprehensive anonymous questionnaire with queries on level of education, background knowledge of PGx tests, advantages and barriers for implementation of such tests, and clinicians' desire to order the test that was distributed online to doctors, healthcare workers, related students/Ph.D. students, and administrative staff managing healthcare units. RESULTS We gathered 315 responses. According to the answers, two-thirds of participants had heard about PGx before (64.4%). An overwhelming majority of respondents appreciated the benefits of PGx (93.3%). Indeed, prior knowledge and level of education showed significant associations with positive attitudes toward PGx clinical testing (P≤0.05). However, all participants agreed there are major challenges for including such tests as part of routine clinical practice. CONCLUSIONS While the awareness and interest in PGx clinical testing in Polish healthcare providers are rising, some main barriers for implementation of these tests still need to be addressed in Poland.
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Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with The Division of Laboratory Medicine, Białystok, Poland
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | | | - Krzysztof Mnich
- Computational Center, University of Białystok, Białystok, Poland
| | - Alireza Amirabadizadeh
- Endocrine Research Center, Research Institute for Endocrine Sciences, Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with The Division of Laboratory Medicine, Białystok, Poland
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Tafazoli A, van der Lee M, Swen JJ, Zeller A, Wawrusiewicz-Kurylonek N, Mei H, Vorderman RHP, Konopko K, Zankiewicz A, Miltyk W. Development of an extensive workflow for comprehensive clinical pharmacogenomic profiling: lessons from a pilot study on 100 whole exome sequencing data. Pharmacogenomics J 2022; 22:276-283. [PMID: 35963939 PMCID: PMC9674517 DOI: 10.1038/s41397-022-00286-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
This pilot study is aimed at implementing an approach for comprehensive clinical pharmacogenomics (PGx) profiling. Fifty patients with cardiovascular diseases and 50 healthy individuals underwent whole-exome sequencing. Data on 1800 PGx genes were extracted and analyzed through deep filtration separately. Theoretical drug induced phenoconversion was assessed for the patients, using sequence2script. In total, 4539 rare variants (including 115 damaging non-synonymous) were identified. Four publicly available PGx bioinformatics algorithms to assign PGx haplotypes were applied to nine selected very important pharmacogenes (VIP) and revealed a 45-70% concordance rate. To ensure availability of the results at point-of-care, actionable variants were stored in a web-hosted database and PGx-cards were developed for quick access and handed to the study subjects. While a comprehensive clinical PGx profile could be successfully extracted from WES data, available tools to interpret these data demonstrated inconsistencies that complicate clinical application.
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Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, 15-089, Bialystok, Poland
- Clinical Research Centre, University Hospital of Bialystok, 15-276, Bialystok, Poland
| | - Maaike van der Lee
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Jesse J Swen
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Anna Zeller
- Clinical Research Centre, University Hospital of Bialystok, 15-276, Bialystok, Poland
| | | | - Hailiang Mei
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Ruben H P Vorderman
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Krzysztof Konopko
- Department of Photonics, Electronics, and Lighting Technology, Faculty of Electrical Engineering, Bialystok University of Technology, 15-351, Bialystok, Poland
| | - Andrzej Zankiewicz
- Department of Photonics, Electronics, and Lighting Technology, Faculty of Electrical Engineering, Bialystok University of Technology, 15-351, Bialystok, Poland
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, 15-089, Bialystok, Poland.
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Miltyk W, Patrinos GP, Verstuyft C, Coenen M, Tafazoli A. Editorial: Translation and implementation of pharmacogenomic testing in daily clinical practice: Considering current challenges and future needs. Front Pharmacol 2022; 13:1053027. [DOI: 10.3389/fphar.2022.1053027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022] Open
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Tafazoli A, Guchelaar HJ, Miltyk W, Kretowski AJ, Swen JJ. Applying Next-Generation Sequencing Platforms for Pharmacogenomic Testing in Clinical Practice. Front Pharmacol 2021; 12:693453. [PMID: 34512329 PMCID: PMC8424415 DOI: 10.3389/fphar.2021.693453] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Pharmacogenomics (PGx) studies the use of genetic data to optimize drug therapy. Numerous clinical centers have commenced implementing pharmacogenetic tests in clinical routines. Next-generation sequencing (NGS) technologies are emerging as a more comprehensive and time- and cost-effective approach in PGx. This review presents the main considerations for applying NGS in guiding drug treatment in clinical practice. It discusses both the advantages and the challenges of implementing NGS-based tests in PGx. Moreover, the limitations of each NGS platform are revealed, and the solutions for setting up and management of these technologies in clinical practice are addressed.
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Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, Bialystok, Poland
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands
- Leiden Network of Personalized Therapeutics, Leiden, Netherlands
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Adam J. Kretowski
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Jesse J. Swen
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands
- Leiden Network of Personalized Therapeutics, Leiden, Netherlands
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Tafazoli A, Guggilla RK, Kamel-Koleti Z, Miltyk W. Strategies to Improve the Clinical Outcomes for Direct-to-Consumer Pharmacogenomic Tests. Genes (Basel) 2021; 12:361. [PMID: 33802585 PMCID: PMC7999840 DOI: 10.3390/genes12030361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/22/2021] [Accepted: 02/27/2021] [Indexed: 12/27/2022] Open
Abstract
Direct-to-consumer genetic tests (DTC-GT) have become a bridge between marketing and traditional healthcare services. After earning FDA endorsement for such facilities, several fast-developing companies started to compete in the related area. Pharmacogenomic (PGx) tests have been introduced as potentially one of the main medical services of such companies. Most of the individuals will be interested in finding out about the phenotypic consequences of their genetic variants and molecular risk factors against diverse medicines they take or will take later. Direct-to-consumer pharmacogenomic tests (DTC-PT) is still in its young age, however it is expected to expand rapidly through the industry in the future. The result of PGx tests could be considered as the main road toward the implementation of personalized and precision medicine in the clinic. This narrative critical review study provides a descriptive overview on DTC-GT, then focuses on DTC-PT, and also introduces and suggests the potential approaches for improving the clinical related outcomes of such tests on healthcare systems.
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Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, 15-089 Bialystok, Poland;
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rama Krishna Guggilla
- Department of Population Medicine and Civilization Diseases Prevention, Faculty of Medicine with the Division of Dentistry and Division of Medical Education in English, Medical University of Bialystok, 15-269 Bialystok, Poland;
| | - Zahra Kamel-Koleti
- Department of Pathology and Medical Laboratory, Shohada Hospital, Mazandaran University of Medical Sciences, Behshahr 4851613185, Iran;
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, 15-089 Bialystok, Poland;
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Tafazoli A, Wawrusiewicz-Kurylonek N, Posmyk R, Miltyk W. Pharmacogenomics, How to Deal with Different Types of Variants in Next Generation Sequencing Data in the Personalized Medicine Area. J Clin Med 2020; 10:jcm10010034. [PMID: 33374421 PMCID: PMC7796098 DOI: 10.3390/jcm10010034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
Pharmacogenomics (PGx) is the knowledge of diverse drug responses and effects in people, based on their genomic profiles. Such information is considered as one of the main directions to reach personalized medicine in future clinical practices. Since the start of applying next generation sequencing (NGS) methods in drug related clinical investigations, many common medicines found their genetic data for the related metabolizing/shipping proteins in the human body. Yet, the employing of technology is accompanied by big obtained data, which most of them have no clear guidelines for consideration in routine treatment decisions for patients. This review article talks about different types of NGS derived PGx variants in clinical studies and try to display the current and newly developed approaches to deal with pharmacogenetic data with/without clear guidelines for considering in clinical settings.
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Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, 15-089 Białystok, Poland;
- Clinical Research Centre, Medical University of Białystok, 15-276 Bialystok, Poland
| | | | - Renata Posmyk
- Department of Clinical Genetics, Medical University of Białystok, 15-089 Białystok, Poland; (N.W.-K.); (R.P.)
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, 15-089 Białystok, Poland;
- Correspondence: ; Tel.: +48-857485845
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Parizi PK, Yarahmadi F, Tabar HM, Hosseini Z, Sarli A, Kia N, Tafazoli A, Esmaeili SA. MicroRNAs and target molecules in bladder cancer. Med Oncol 2020; 37:118. [PMID: 33216248 DOI: 10.1007/s12032-020-01435-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023]
Abstract
Bladder cancer (BC) is considered as one of the most common malignant tumors in humans with complex pathogenesis including gene expression variation, protein degradation, and changes in signaling pathways. Many studies on involved miRNAs in BC have demonstrated that they could be used as potential biomarkers in the prognosis, response to treatment, and screening before the cancerous phenotype onset. MicroRNAs (miRNAs) regulate many cellular processes through their different effects on special targets along with modifying signaling pathways, apoptosis, cell growth, and differentiation. The diverse expression of miRNAs in cancerous tissues could mediate procedures leading to the oncogenic or suppressor behavior of certain genes in cancer cells. Since a specific miRNA may have multiple targets, an mRNA could also be regulated by multiple miRNAs which further demonstrates the actual role of miRNAs in cancer. In addition, miRNAs can be utilized as biomarkers in some cancers that cannot be screened in the early stages. Hence, finding blood, urine, or tissue miRNA biomarkers by novel or routine gene expression method could be an essential step in the prognosis and control of cancer. In the present review, we have thoroughly evaluated the recent findings on different miRNAs in BC which can provide comprehensive information on better understanding the role of diverse miRNAs and better decision making regarding the new approaches in the diagnosis, prognosis, prevention, and treatment of BC.
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Affiliation(s)
- Payam Kheirmand Parizi
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.,Genome Medical Genetics Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | | | - Zohreh Hosseini
- Faculty of Veterinary Medicine, Shahid Chamran University, Ahvaz, Iran
| | - Abdolazim Sarli
- Department of Medical Genetic, Faculty of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - Nadia Kia
- Agostino Gemelli University Hospital, Torvergata University of Medical Sciences, Rome, Italy
| | - Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy With the Division of Laboratory Medicine, Medical University of Bialystok, Bialystok, Poland.,Clinical Research Center, Medical University of Bialystok, Bialystok, Poland
| | - Seyed-Alireza Esmaeili
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran. .,Immunology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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Khazeei Tabari MA, Khoshhal H, Tafazoli A, Khandan M, Bagheri A. Applying computer simulations in battling with COVID-19, using pre-analyzed molecular and chemical data to face the pandemic. Inform Med Unlocked 2020; 21:100458. [PMID: 33102687 PMCID: PMC7568469 DOI: 10.1016/j.imu.2020.100458] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has made many concerns for healthcare services especially, in finding useful therapeutic(s). Despite the scientists’ struggle to find and/or creating possible drugs, so far there is no treatment with high efficiency for the disease. During the pandemic, researchers have performed some molecular analyses to find potential therapeutics out of both the natural and synthetic available medicines. Computer simulations and related data have shown a significant role in drug discovery and development before. In this field, antiviral drugs, phytochemicals, anti-inflammatory agents, etc. were essential groups of compounds tested against COVID-19, using molecular modeling, molecular dynamics (MD), and docking tools. The results indicate promising effects of such compounds to be used in further experimental and clinical trials; Chloroquine, Chloroquine-OH, and Umifenovir as viral entry inhibitors, Remdesivir, Ribavirin, Lopinavir, Ritonavir, and Darunavir as viral replication inhibitors, and Sirolimus are the examples, which were tested clinically on patients after comprehensive assessments of the available data on molecular simulation. This review summarizes the outcomes of various computer simulations data in the battle against COVID-19. More knowledge of SARS-CoV-2 genomic and structural characterization is necessary. Computer simulation can find possible natural or synthetic compounds for COVID-19. Molecular docking compares binding affinity of drugs to COVID-19 related targets. Network drug repurposing determines COVID-19 associated target genes and pathways.
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Affiliation(s)
- Mohammad Amin Khazeei Tabari
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran.,USERN Office, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hooman Khoshhal
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran.,USERN Office, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, Białystok, Poland.,Genomics Laboratory, Clinical Research Centre, Medical University of Białystok, Bialystok, Poland
| | - Mohanna Khandan
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran.,USERN Office, Mazandaran University of Medical Sciences, Sari, Iran
| | - Abouzar Bagheri
- Department of Clinical Biochemistry and Medical Genetics, Faculty of Medicine, Molecular and Cell Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran
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Makvandi P, Ghomi M, Ashrafizadeh M, Tafazoli A, Agarwal T, Delfi M, Akhtari J, Zare EN, Padil VVT, Zarrabi A, Pourreza N, Miltyk W, Maiti TK. A review on advances in graphene-derivative/polysaccharide bionanocomposites: Therapeutics, pharmacogenomics and toxicity. Carbohydr Polym 2020; 250:116952. [PMID: 33049857 DOI: 10.1016/j.carbpol.2020.116952] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/17/2022]
Abstract
Graphene-based bionanocomposites are employed in several ailments, such as cancers and infectious diseases, due to their large surface area (to carry drugs), photothermal properties, and ease of their functionalization (owing to their active groups). Modification of graphene-derivatives with polysaccharides is a promising strategy to decrease their toxicity and improve target ability, which consequently enhances their biotherapeutic efficacy. Herein, functionalization of graphene-based materials with carbohydrate polymers (e.g., chitosan, starch, alginate, hyaluronic acid, and cellulose) are presented. Subsequently, recent advances in graphene nanomaterial/polysaccharide-based bionanocomposites in infection treatment and cancer therapy are comprehensively discussed. Pharmacogenomic and toxicity assessments for these bionanocomposites are also highlighted to provide insight for future optimized and smart investigations and researches.
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Affiliation(s)
- Pooyan Makvandi
- Istituto Italiano di Tecnologia, Centre for Micro-BioRobotics, viale Rinaldo Piaggio 34, Pontedera, Pisa, 56025, Italy; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, 14496-14535, Iran.
| | - Matineh Ghomi
- Chemistry Department, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, 6153753843, Iran
| | - Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, 51666-16471, Iran
| | - Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, Białystok, 15-089, Poland
| | - Tarun Agarwal
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, 721302, India
| | - Masoud Delfi
- Department of Chemical Sciences, University of Naples "Federico II", Naples, 80126, Italy
| | - Javad Akhtari
- Toxoplasmosis Research Center, Communicable Diseases Institute, Department of Medical Nanotechnology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Vinod V T Padil
- Department of Nanomaterials in Natural Sciences, Institute for Nanomaterials, Advanced Technologies and Innovation (CXI), Technical University of Liberec (TUL), Studentská, 1402/2, Liberec, Czech Republic
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, Istanbul, 34956, Turkey; Center of Excellence for Functional Surfaces and Interfaces (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, 34956, Turkey
| | - Nahid Pourreza
- Chemistry Department, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, 6153753843, Iran
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, Białystok, 15-089, Poland
| | - Tapas Kumar Maiti
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, 721302, India
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Hashemi-Soteh MB, Nejad AV, Ataei G, Tafazoli A, Ghasemi D, Siamy R. Knowledge and attitude toward genetic diseases and genetic tests among pre-marriage individuals: A cross-sectional study in northern Iran. Int J Reprod Biomed 2019; 17:543-550. [PMID: 31583371 PMCID: PMC6745081 DOI: 10.18502/ijrm.v17i8.4819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 02/19/2019] [Accepted: 05/12/2019] [Indexed: 11/24/2022] Open
Abstract
Background Genetic testing has been widely introduced for many hereditary disorders. While the attitudes towards these facilities have been evaluated in many countries, there are only a few reports on the knowledge of and the orientation among Iranians. Objective The current study assesses the attitudes and knowledge of pre-marriage individuals toward the availability and use of genetic tests. Materials and Methods A comprehensive questionnaire was distributed among 408 marrying individuals. The questions addressed the demographic characteristics along the registration of participant's knowledge, education, and attitude toward genetic testing. The individuals were divided into three groups based on their knowledge: 1) Scored above 80 to 100 were defined as "good" 2) 60 to 80 as "average" 3) less than 60 as "poor" knowledge. Results Most participants (86%) believed consanguineous marriages increase the risk of genetic diseases; 82.3% knew that thalassemia is a type of genetic disease, only 33.3% could distinguish prenatal diagnosis (PND) from other laboratory tests. The relationship between the participants' knowledge and their level of education was significant (r░=░0.78, p░<░0.001), age (r= -0.16, p░<░0.01), and urbanity (p░<░0.01). A prominent relationship was observed between the knowledge (r░=░0.64, p░<░0.001) or education (r░=░0.62, p░<░0.001) and people’s desire to use the genetic tests before the wedding ceremony. No significant correlations were found between the participant’s attitude and their ages/urbanity. Most of the individuals agreed to arrange a genetic counseling before marriage (0.94%). Conclusion This study revealed that most individuals were interested in using genetic counseling services and genetic tests before marriage.
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Affiliation(s)
- Mohammad Bagher Hashemi-Soteh
- Immunogenetic Research Center, Molecular and Cell Biology Research Center, Medical Faculty, Mazandaran University of Medical Sciences SariMazandaran Iran
| | - Ali Vali Nejad
- Ghaemshahr Health Center, Mazandaran University of Medical Sciences Mazandaran Iran
| | - Golamreza Ataei
- Department of Medical Physics, Faculty of Paramedicine, Babol University of Medical Sciences Babol Iran
| | - Alireza Tafazoli
- Department of Biochemistry, Biophysics and Genetics, School of Medicine, Mazandaran University of Medical Sciences Mazandaran Iran
| | - Dariush Ghasemi
- Department of Biostatistics, Faculty of Healthcare Sciences, Mazandaran University of Medical Sciences Mazandaran Iran
| | - Rita Siamy
- Ghaemshahr Health Center, Mazandaran University of Medical Sciences Mazandaran Iran
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Ebrahimzadeh MA, Tafazoli A, Akhtari J, Biparva P, Eslami S. Engineered Silver Nanoparticles, A New Nanoweapon Against Cancer. Anticancer Agents Med Chem 2019; 18:1962-1969. [PMID: 30088451 DOI: 10.2174/1871520618666180808093040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/15/2018] [Accepted: 07/14/2018] [Indexed: 11/22/2022]
Abstract
New modifications in nanoparticles changed their applications obviously. Green synthesis of nanoparticles and their biomedical utilizations have been the focus of increasing attention in recent years. Silver nanoparticles (AgNPs) demonstrated surprising effects and many advantageous features for cancer therapy. Investigations indicated the anticancer activity of AgNPs in different ways, comprising cell cycle arrest, DNA damaging and apoptosis, alteration of P53 function, up/down regulation of some important cytokine genes and so on. But some key inquiries like the ability to control the accidental effects of AgNPs, or encompassing process for parcels, which reduces the toxicological profile of nanoparticles, still remained. "Green synthesis" of nanoparticles has been shown to be a kind of approach to resolve the toxicity amounts in a range of 10-18 times. Using distinctive properties of this approach, i.e. as green synthesized silver nanoparticles (G-AgNPs), in order to raise potential therapeutic efficacy, even up to two-fold higher than cis-platin, is going to play a crucial role in cancer treatment and could be considered as a new insight in this field. The current review focuses on the antioxidant activity of G-AgNPs and potential impacts on cancer cells.
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Affiliation(s)
- Mohammad A Ebrahimzadeh
- Pharmaceutical Sciences Research Center, Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Tafazoli
- Department of Endocrinology, Diabetology and Internal Medicine, Clinical Research Center, Medical University of Bialystok, 15-276 Bialystok, Poland.,Department of Pharmaceutical Analysis, Faculty of Pharmacy, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Javad Akhtari
- Immunogenetics Research Center, Department of Physiology and Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Pourya Biparva
- Department of Basic Sciences, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran
| | - Shahram Eslami
- Pharmaceutical Sciences Research Center, Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
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14
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Shekarriz R, Faghani S, Tafazoli A, Hashemi-Soteh MB. The Correlation between Phospholipase C Epsilon (PLCE1) Gene Polymorphisms and Risk of Gastric Adenocarcinoma in Iranian Population. Int J Hematol Oncol Stem Cell Res 2019. [DOI: 10.18502/ijhoscr.v13i3.1268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background: Phospholipase C epsilon 1 (PLCE1) gene harbors different single nucleotide polymorphisms (SNPs), which can be correlated with the risk of different types of cancers. In this case-control study, the relationship between rs2274223 (A>G), a single nucleotide polymorphism in phospholipase C epsilon gene, (PLCE1) and gastric cancer was evaluated among Iranian patients.
Materials and Methods: The PLCE1 rs2274223 polymorphism was genotyped in 60 patients with gastric cancer and 69 control subjects using polymerase chain reaction and restriction fragment length polymorphisms (PCR-RFLP) methods. Clinical and pathologic parameters such as tumor characteristics and disease stage were also recorded.
Results: There were 48 (80%) male patients and 45 (65.5%) healthy male individuals (p=0.077). About 34 (56.6%) patients were smokers. A family history of gastric cancer was found in 21 (35%) cases. GG genotype was observed among 15% of patients and 8.7% of normals, respectively. There was no significant difference between the AA and AG genotypes. Also, there were no significant correlations between AA, AG or GG genotypes and the risk of gastric cancer, gender, tumor size, tumor stage, grade, as well as tumor location and metastasis.
Conclusion: The PLCE1 rs2274223 polymorphism was not correlated with gastric cancer in Iranian population. However, a further comprehensive study with larger sample sizes is needed.
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Shekarriz R, Faghani S, Tafazoli A, Hashemi-Soteh MB. The Correlation between Phospholipase C Epsilon (PLCE1) Gene Polymorphisms and Risk of Gastric Adenocarcinoma in Iranian Population. Int J Hematol Oncol Stem Cell Res 2019; 13:108-115. [PMID: 31649800 PMCID: PMC6801326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
Background: Phospholipase C epsilon 1 (PLCE1) gene harbors different single nucleotide polymorphisms (SNPs), which can be correlated with the risk of different types of cancers. In this case-control study, the relationship between rs2274223 (A>G), a single nucleotide polymorphism in phospholipase C epsilon gene, (PLCE1) and gastric cancer was evaluated among Iranian patients. Materials and Methods: The PLCE1 rs2274223 polymorphism was genotyped in 60 patients with gastric cancer and 69 control subjects using polymerase chain reaction and restriction fragment length polymorphisms (PCR-RFLP) methods. Clinical and pathologic parameters such as tumor characteristics and disease stage were also recorded. Results: There were 48 (80%) male patients and 45 (65.5%) healthy male individuals (p=0.077). About 34 (56.6%) patients were smokers. A family history of gastric cancer was found in 21 (35%) cases. GG genotype was observed among 15% of patients and 8.7% of normals, respectively. There was no significant difference between the AA and AG genotypes. Also, there were no significant correlations between AA, AG or GG genotypes and the risk of gastric cancer, gender, tumor size, tumor stage, grade, as well as tumor location and metastasis. Conclusion: The PLCE1 rs2274223 polymorphism was not correlated with gastric cancer in Iranian population. However, a further comprehensive study with larger sample sizes is needed.
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Affiliation(s)
- Ramin Shekarriz
- Department of Hematology and Oncology, Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sahar Faghani
- Department of Internal Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Tafazoli
- Department of Biochemistry, Biophysics and Genetics, Faculty of Medicine, Mazandaran University of Medical Sciences, sari, Iran
| | - Mohammad Bagher Hashemi-Soteh
- Immunogenetic Research Center, Cell and Molecular Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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16
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Akbari Kordkheyli V, Khonakdar Tarsi A, Mishan MA, Tafazoli A, Bardania H, Zarpou S, Bagheri A. Effects of quercetin on microRNAs: A mechanistic review. J Cell Biochem 2019; 120:12141-12155. [PMID: 30957271 DOI: 10.1002/jcb.28663] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/10/2019] [Accepted: 02/14/2019] [Indexed: 12/21/2022]
Abstract
MicroRNA (miRNA)-dependent pathways are one of the newest gene regulation mechanisms in various diseases, particularly in cancers. miRNAs are endogenous noncoding RNAs with about 18 to 25 nucleotide length, which can regulate the expression of at least 60% of human total genome posttranscriptionally. Quercetin is the most abundant flavonoid in a variety of fruits, flowers, and medical herbs, known as a strong free radical scavenger that could show antioxidant, anti-inflammatory, and antitumor activities. Recent studies also reported its strong impact on various miRNA expressions in different abnormalities. In this review, we aimed to summarize the studies focused on the effects of quercetin on different miRNA expressions to more clear the main possible mechanisms of quercetin influences and introduce it as a beneficial agent for regulation of miRNAs in various biological directions.
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Affiliation(s)
- Vahid Akbari Kordkheyli
- Department of Clinical Biochemistry-Biophysics and Genetics, Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Abbas Khonakdar Tarsi
- Department of Clinical Biochemistry-Biophysics and Genetics, Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad A Mishan
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, 15-089 Bialystok, Poland.,Department of Endocrinology, Diabetology and Internal Medicine, Clinical Research Center, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Hassan Bardania
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Setareh Zarpou
- Department of Clinical Biochemistry-Biophysics and Genetics, Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Abouzar Bagheri
- Department of Clinical Biochemistry-Biophysics and Genetics, Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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17
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Akhtari J, Tafazoli A, Mehrad-Majd H, Mahrooz A. Nanovehicle-based Small Interfering RNA (siRNA) Delivery for Therapeutic Purposes: A New Molecular Approach in Pharmacogenomics. ACTA ACUST UNITED AC 2018; 13:173-182. [DOI: 10.2174/1574884713666180709152610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/14/2018] [Accepted: 06/27/2018] [Indexed: 11/22/2022]
Affiliation(s)
- Javad Akhtari
- Immunogenetics Research Center, Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Tafazoli
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hassan Mehrad-Majd
- Clinical Research Unit, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abdolkarim Mahrooz
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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18
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Tafazoli A, Eshraghi P, Pantaleoni F, Vakili R, Moghaddassian M, Ghahraman M, Muto V, Paolacci S, Golyan FF, Abbaszadegan MR. Novel mutations and their genotype-phenotype correlations in patients with Noonan syndrome, using next-generation sequencing. Adv Med Sci 2018; 63:87-93. [PMID: 28957739 DOI: 10.1016/j.advms.2017.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 06/29/2017] [Accepted: 07/07/2017] [Indexed: 11/18/2022]
Abstract
PURPOSE Noonan Syndrome (NS) is an autosomal dominant disorder with many variable and heterogeneous conditions. The genetic basis for 20-30% of cases is still unknown. This study evaluates Iranian Noonan patients both clinically and genetically for the first time. MATERIALS/METHODS Mutational analysis of PTPN11 gene was performed in 15 Iranian patients, using PCR and Sanger sequencing at phase one. Then, as phase two, Next Generation Sequencing (NGS) in the form of targeted resequencing was utilized for analysis of exons from other related genes. Homology modelling for the novel founded mutations was performed as well. The genotype, phenotype correlation was done according to the molecular findings and clinical features. RESULTS Previously reported mutation (p.N308D) in some patients and a novel mutation (p.D155N) in one of the patients were identified in phase one. After applying NGS methods, known and new variants were found in four patients in other genes, including: CBL (p. V904I), KRAS (p. L53W), SOS1 (p. I1302V), and SOS1 (p. R552G). Structural studies of two deduced novel mutations in related genes revealed deficiencies in the mutated proteins. Following genotype, phenotype correlation, a new pattern of the presence of intellectual disability in two patients was registered. CONCLUSIONS NS shows strong variable expressivity along the high genetic heterogeneity especially in distinct populations and ethnic groups. Also possibly unknown other causative genes may be exist. Obviously, more comprehensive and new technologies like NGS methods are the best choice for detection of molecular defects in patients for genotype, phenotype correlation and disease management.
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Affiliation(s)
- Alireza Tafazoli
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Peyman Eshraghi
- Department of Pediatrics, Imam Reza Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Francesca Pantaleoni
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy; Research Center, Genetic and Rare Diseases, Ospedale Pediatrico Bambino Gesù, IRCSS, Rome, Italy
| | - Rahim Vakili
- Department of Pediatrics, Imam Reza Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Morteza Moghaddassian
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, Faculty of Applied Science and Engineering, University of Toronto, ON, Canada
| | - Martha Ghahraman
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Razavi Cancer Research Center, Razavi Hospital, Imam Reza International University, Mashhad, Iran
| | - Valentina Muto
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Paolacci
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Fatemeh Fardi Golyan
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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19
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Zeynalzadeh M, Tafazoli A, Aarabi A, Moghaddassian M, Ashrafzadeh F, Houshmand M, Taghehchian N, Abbaszadegan MR. Four novel mutations of the BCKDHA, BCKDHB and DBT genes in Iranian patients with maple syrup urine disease. J Pediatr Endocrinol Metab 2018; 31:205-212. [PMID: 29306928 DOI: 10.1515/jpem-2017-0305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 12/04/2017] [Indexed: 11/15/2022]
Abstract
BACKGROUND Maple syrup urine disease (MSUD) is a rare metabolic autosomal recessive disorder caused by dysfunction of the branched-chain α-ketoacid dehydrogenase (BCKDH) complex. Mutations in the BCKDHA, BCKDHB and DBT genes are responsible for MSUD. The current study analyzed seven Iranian MSUD patients genetically and explored probable correlations between their genotype and phenotype. METHODS The panel of genes, including BCKDHA, BCKDHB and DBT, was evaluated, using routine the polymerase chain reaction (PCR)-sequencing method. In addition, protein modeling (homology and threading modeling) of the deduced novel mutations was performed. The resulting structures were then analyzed, using state-of-the-art bioinformatics tools to better understand the structural and functional effects caused by mutations. RESULTS Seven mutations were detected in seven patients, including four novel pathogenic mutations in BCKDHA (c.1198delA, c.629C>T), BCKDHB (c.652C>T) and DBT (c.1150A>G) genes. Molecular modeling of the novel mutations revealed clear changes in the molecular energy levels and stereochemical traits of the modeled proteins, which may be indicative of strong correlations with the functional modifications of the genes. Structural deficiencies were compatible with the observed phenotypes. CONCLUSIONS Any type of MSUD can show heterogeneous clinical manifestations in different ethnic groups. Comprehensive molecular investigations would be necessary for differential diagnosis.
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Affiliation(s)
- Monica Zeynalzadeh
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Alireza Tafazoli
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Azadeh Aarabi
- Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Morteza Moghaddassian
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, Faculty of Applied Science and Engineering, University of Toronto, Ontario, Canada
| | - Farah Ashrafzadeh
- Department of Pediatric Neurology, Qaem Medical Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Massoud Houshmand
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Negin Taghehchian
- Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center and Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad 9196773117, Iran
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20
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Hashemi-Soteh MB, Mousavi SS, Tafazoli A. Haplotypes inside the beta-globin gene: use as new biomarkers for beta-thalassemia prenatal diagnosis in north of Iran. J Biomed Sci 2017; 24:92. [PMID: 29202846 PMCID: PMC5713070 DOI: 10.1186/s12929-017-0396-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/21/2017] [Indexed: 11/18/2022] Open
Abstract
Background Beta-thalassemia is common in the Mediterranean area as well as the Middle East and India. Official report in Iran revealed the average prevalence rate of carriers about 4%. More than 20 restriction fragment length polymorphisms (RFLPs) are known in the beta-globin gene cluster and used in the prenatal diagnosis (PND) services. Some of these locations may have low allele frequency and are not informative in the prenatal diagnosis. The current study aims to find new haplotypes and polymorphisms with high allele frequency in the local population. Methods Two thousand three hundred fifty samples (1,321 male and 1,029 female) from the northern Iran, whom suspected to be the carriers either for alpha or beta thalassemia and referred to the local diagnostic laboratory as a routine services were investigated during five years, (2010–2015). The beta-globin gene was sequenced for all samples. Results Heterozygosity for five SNPs in the beta-globin gene was calculated separately. 383 individuals (16.29%) showed no sign of nucleotide change in the beta-globin gene sequence. In total, codon2 (C/T) 31.72%, IVSII-16 (C/G) 31.72%, IVSII-74 (G/T) 54.71%, IVSII-81 (C/T) 19.47%, and IVSII-666 (T/C) 31.72% were seen respectively. Although all five polymorphisms showed reasonably high heterozygosity, IVSII-74 (G/T) [GG wild type (36.5%), G/T (54.71%) and TT (8.8%)] revealed the highest heterozygosity rate. Four combinations of these five SNPs were defined as new haplotypes named M1 to M4. ARMS-PCR also were designed and applied to detect IVSII-74 (G/T) nucleotide position. Conclusions This study represents an intragenic polymorphism, IVSII-74, a reliable position with high heterozygosity rates in Iranian population for PND analysis. Trial registration Retrospectively registered.
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Affiliation(s)
- Mohammad Bagher Hashemi-Soteh
- Immunogenetic Research Center, Molecular and Cell biology Research Center, Medical Faculty, Mazandaran University of Medical Sciences, Sari, Mazandaran, Iran. .,Department of Biochemistry, Biophysics and Genetics, School of Medicine, Mazandaran University of Medical Sciences, Farahabad Road, P.O. Box. 481751665, Sari, Mazandaran, Iran.
| | - Seyed Saeed Mousavi
- Novin Genetics diagnostic laboratory, Farah Abad 4, Farah Abad Boulevard, Sari, Mazandaran, Iran
| | - Alireza Tafazoli
- Department of Biochemistry, Biophysics and Genetics, School of Medicine, Mazandaran University of Medical Sciences, Farahabad Road, P.O. Box. 481751665, Sari, Mazandaran, Iran.,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Abstract
Noonan syndrome (NS) is an autosomal dominant disorder with vast heterogeneity in clinical and genetic features. Various symptoms have been reported for this abnormality such as short stature, unusual facial characteristics, congenital heart abnormalities, developmental complications, and an elevated tumor incidence rate. Noonan syndrome shares clinical features with other rare conditions, including LEOPARD syndrome, cardio-facio-cutaneous syndrome, Noonan-like syndrome with loose anagen hair, and Costello syndrome. Germline mutations in the RAS-MAPK (mitogen-activated protein kinase) signal transduction pathway are responsible for NS and other related disorders. Noonan syndrome diagnosis is primarily based on clinical features, but molecular testing should be performed to confirm it in patients. Due to the high number of genes associated with NS and other RASopathy disorders, next-generation sequencing is the best choice for diagnostic testing. Patients with NS also have higher risk for leukemia and specific solid tumors. Age-specific guidelines for the management of NS are available.
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Affiliation(s)
- Alireza Tafazoli
- Medical Genetics Research Center, Medical School, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Peyman Eshraghi
- Department of Pediatrics, Imam Reza Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Kamel Koleti
- Department of Pathology and Medical laboratory, Shohada Hospital, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammadreza Abbaszadegan
- Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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22
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Khaledi A, Bahador A, Esmaeili D, Tafazoli A, Ghazvini K, Mansury D. Prevalence of nontuberculous mycobacteria isolated from environmental samples in Iran: A meta-analysis. J Res Med Sci 2016; 21:58. [PMID: 27904603 PMCID: PMC5121994 DOI: 10.4103/1735-1995.187306] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/14/2016] [Accepted: 07/02/2016] [Indexed: 11/04/2022]
Abstract
BACKGROUND While the most nontuberculous mycobacteria (NTMs) species are considered as opportunistic pathogens, some of them are related to several human infections. It is believed that environment is the main source for these infections. Distribution and scattering pattern of NTMs has not been well studied in Iran and a few studies about this subject have been done, so the aim of this study was to determine prevalence of NTMs in environmental samples from Iran. MATERIALS AND METHODS Data about prevalence of NTMs in environmental samples from Iran were obtained by searching databases. The studies presenting cross-sectional or cohort and the papers with sample size ≥30 were included. Then, the meta-analysis was performed using Comprehensive Meta-Analysis software and Cochran's Q and I2 tests. The strategy search was based PRISMA protocol is available online (PRISMA, http://www.prisma-statement.org). RESULTS The results of this meta-analysis showed that overall combined prevalence of NTMs in environmental samples from Iran was 38.3%. The frequency of NTM was higher in the north of Iran (73.2%). The most prevalent rapid-growing mycobacterium was Mycobacterium fortuitum (19.8%), and the most dominant slow-growing mycobacterium was Mycobacterium flavescens (16.8%). CONCLUSION In regard to increasing incidence of disease in immunocompromised patients and existence of different types of mycobacteria species in environmental samples, efforts should be focused on measures that will specifically remove NTMs from habitats where susceptible individuals are exposed.
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Affiliation(s)
- Azad Khaledi
- Department of Microbiology and Virology, Antimicrobial Resistance Research Center, Avicenna Research Institute, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abbas Bahador
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Davood Esmaeili
- Department of Microbiology, Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Alireza Tafazoli
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kiarash Ghazvini
- Department of Microbiology and Virology, Antimicrobial Resistance Research Center, Avicenna Research Institute, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Davood Mansury
- Department of Microbiology and Virology, Antimicrobial Resistance Research Center, Avicenna Research Institute, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Aghdam MN, Abbaszadegan MR, Tafazoli A, Aslzare M, Mosavi Z. Presence of the RET Cys634Tyr mutation and Gly691Ser functional polymorphism in Iranian families with multiple endocrine neoplasia type 2A. Hormones (Athens) 2016; 15:65-72. [PMID: 26732158 DOI: 10.14310/horm.2002.1611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/30/2015] [Indexed: 11/20/2022]
Abstract
PURPOSE Multiple Endocrine Neoplasia type 2A (MEN2A) is a complex autosomal dominant inherited syndrome characterized by medullary thyroid carcinoma (MTC), pheochromocytoma and primary parathyroid hyperplasia. In patients with only one or two clinical features, identification of a germ line RET (REarranged in Transfection) mutation is required to make the diagnosis and initiate genetic counseling. METHODS We analyzed blood DNA from three Iranian families with three generations of MEN2A including 20 affected individuals with MTC and four with pheochromocytoma. RET hotspots were amplified in probands and sequenced for mutation detection. RESULT The causative mutation in all families was found to be the Cys634Tyr missense substitution. The presence of a functional SNP resulting in Gly691Ser was also detected in exon 11 of 15 affected cases. Four patients showed both of these RET variations. CONCLUSION Our study shows that the Cys634Tyr missense substitution and the Gly691Ser polymorphism are recurrent in Iranian patients, since our families are unrelated. All asymptomatic carriers of the Cys634Tyr high-risk activating mutation were referred for prophylactic thyroidectomy.
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Affiliation(s)
- Maryam Nasiri Aghdam
- Medical Genetics Research Center, Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Abbaszadegan
- Division of Human Genetics, Immunology Research Center, Avicena Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Tafazoli
- Medical Genetics Research Center, Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Aslzare
- Endocrine Research Center, Imam Reza/Ghaem Hospital, School of Medicine, Mashhad University of Medical Sciences; Mashhad, Iran
| | - Zohreh Mosavi
- Endocrine Research Center, Imam Reza/Ghaem Hospital, School of Medicine, Mashhad University of Medical Sciences; Mashhad, Iran
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