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Wadapurkar R, Singh S, Singh A. Leveraging the immunoinformatics approach for designing the SARS-CoV-2 omicron-specific antigenic cassette of mRNA vaccine. Vaccine 2024; 42:1630-1647. [PMID: 38336561 DOI: 10.1016/j.vaccine.2024.01.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 01/10/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]
Abstract
Emergence of SARS-CoV-2 Omicron variant has presented a significant challenge to global health, demanding rapid development of mRNA-based vaccines. The mRNA-guided vaccine platforms offer various advantages over traditional vaccine platforms. The mRNA by nature is a short-lived molecule that guides the cells to manufacture antigenic proteins. In the present work, we have created an omicron spike antigenic protein sequence characterized by base composition analysis, modeling, and docking with the ACE-2 receptor. Further, we predicted the B-cell and T-cell epitopes followed by antigenicity, toxicity, and allergenicity. Finally, the protein was reverse translated, codon-optimized, and encoding mRNA sequence was checked for its stability by predicting the secondary structures. A comprehensive examination of in-silico data revealed 628.2 as a potent antigenic candidate that was finally used in Gemcovac®-OM, a heterologous booster mRNA vaccine for COVID-19.
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Affiliation(s)
- Rucha Wadapurkar
- Gennova Biopharmaceuticals Ltd., ITBT Park, Hinjewadi Phase 2 Rd, Hinjewadi Rajiv Gandhi Infotech Park, Hinjewadi, Pune, Maharashtra 411057, India
| | - Sanjay Singh
- Gennova Biopharmaceuticals Ltd., ITBT Park, Hinjewadi Phase 2 Rd, Hinjewadi Rajiv Gandhi Infotech Park, Hinjewadi, Pune, Maharashtra 411057, India
| | - Ajay Singh
- Gennova Biopharmaceuticals Ltd., ITBT Park, Hinjewadi Phase 2 Rd, Hinjewadi Rajiv Gandhi Infotech Park, Hinjewadi, Pune, Maharashtra 411057, India.
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2
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Fattahi M, Alamdari-Palangi V, Rahimi Jaberi K, Ehtiati S, Ojaghi S, Rahimi-Jaberi A, Samavarchi Tehrani S, Dang P, Movahedpour A, Hossein Khatami S. Exosomal long non-coding RNAs in glioblastoma. Clin Chim Acta 2024; 553:117705. [PMID: 38086498 DOI: 10.1016/j.cca.2023.117705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
Glioblastoma multiforme (GBM) is the most prevalent primary tumor found in the central nervous system, accounting for 70% of all adult brain tumors. The median overall survival rate is one year post-diagnosis with treatment, and only four months without treatment. Current GBM diagnostic methods, such as magnetic resonance imaging (MRI), surgery, and brain biopsies, have limitations. These include difficulty distinguishing between tumor recurrence and post-surgical necrotic regions, and operative risks associated with obtaining histological samples through direct surgery or biopsies. Consequently, there is a need for rapid, inexpensive, and minimally invasive techniques for early diagnosis and improved subsequent treatment. Research has shown that tumor-derived exosomes containing various long non-coding RNAs (lncRNAs) play critical regulatory roles in immunomodulation, cancer metastasis, cancer development, and drug resistance in GBM. They regulate genes that enhance cancer growth and progression and alter the expression of several key signaling pathways. Due to the specificity and sensitivity of exosomal lncRNAs, they have the potential to be used as biomarkers for early diagnosis and prognosis, as well as to monitor a patient's response to chemotherapy for GBM. In this review, we discuss the role of exosomal lncRNAs in the pathogenesis of GBM and their potential clinical applications for early diagnosis.
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Affiliation(s)
- Mehdi Fattahi
- Institute of Research and Development, Duy Tan University, Da Nang, Viet Nam; School of Engineering & Technology, Duy Tan University, Da Nang, Viet Nam
| | - Vahab Alamdari-Palangi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Khojaste Rahimi Jaberi
- Department of Neuroscience, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sajad Ehtiati
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sara Ojaghi
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Rahimi-Jaberi
- Department of Neurology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Clinical Neurology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sadra Samavarchi Tehrani
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Science, Tehran, Iran
| | - Phuyen Dang
- Institute of Research and Development, Duy Tan University, Da Nang, Viet Nam; School of Engineering & Technology, Duy Tan University, Da Nang, Viet Nam
| | | | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Shaterabadi D, Zamani Sani M, Rahdan F, Taghizadeh M, Rafiee M, Dorosti N, Dianatinasab A, Taheri-Anganeh M, Asadi P, Khatami SH, Movahedpour A. MicroRNA biosensors in lung cancer. Clin Chim Acta 2024; 552:117676. [PMID: 38007056 DOI: 10.1016/j.cca.2023.117676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Lung cancer has been one of the leading causes of death over the past century. Unfortunately, the reliance on conventional methods to diagnose the phenotypic properties of tumors hinders early-stage cancer diagnosis. However, recent advancements in identifying disease-specific nucleotide biomarkers, particularly microRNAs, have brought us closer to early-stage detection. The roles of miR-155, miR-197, and miR-182 have been established in stage I lung cancer. Recent progress in synthesizing nanomaterials with higher conductivity has enhanced the diagnostic sensitivity of electrochemical biosensors, which can detect low concentrations of targeted biomarkers. Therefore, this review article focuses on exploring electrochemical biosensors based on microRNA in lung cancer.
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Affiliation(s)
- Donya Shaterabadi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Zamani Sani
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fereshteh Rahdan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Taghizadeh
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maedeh Rafiee
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, WY 82070, USA
| | - Nafiseh Dorosti
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aria Dianatinasab
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Peyman Asadi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Taheri-Anganeh M, Nezafat N, Gharibi S, Khatami SH, Vahedi F, Shabaninejad Z, Asadi M, Savardashtaki A, Movahedpour A, Ghasemi H. Designing a Secretory form of RTX-A as an Anticancer Toxin: An In Silico Approach. Recent Pat Biotechnol 2024; 18:332-343. [PMID: 38817010 DOI: 10.2174/0118722083267796231210060150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/29/2023] [Accepted: 11/17/2023] [Indexed: 06/01/2024]
Abstract
BACKGROUND Cancer is a leading cause of death and a significant public health issue worldwide. Standard treatment methods such as chemotherapy, radiotherapy, and surgery are only sometimes effective. Therefore, new therapeutic approaches are needed for cancer treatment. Sea anemone actinoporins are pore-forming toxins (PFTs) with membranolytic activities. RTX-A is a type of PFT that interacts with membrane phospholipids, resulting in pore formation. The synthesis of recombinant proteins in a secretory form has several advantages, including protein solubility and easy purification. In this study, we aimed to discover suitable signal peptides for producing RTX-A in Bacillus subtilis in a secretory form. METHODS Signal peptides were selected from the Signal Peptide Web Server. The probability and secretion pathways of the selected signal peptides were evaluated using the SignalP server. ProtParam and Protein-sol were used to predict the physico-chemical properties and solubility. AlgPred was used to predict the allergenicity of RTX-A linked to suitable signal peptides. Non-allergenic, stable, and soluble signal peptides fused to proteins were chosen, and their secondary and tertiary structures were predicted using GOR IV and I-TASSER, respectively. The PROCHECK server performed the validation of 3D structures. RESULTS According to bioinformatics analysis, the fusion forms of OSMY_ECOLI and MALE_ECOLI linked to RTX-A were identified as suitable signal peptides. The final proteins with signal peptides were stable, soluble, and non-allergenic for the human body. Moreover, they had appropriate secondary and tertiary structures. CONCLUSION The signal above peptides appears ideal for rationalizing secretory and soluble RTX-A. Therefore, the signal peptides found in this study should be further investigated through experimental researches and patents.
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Affiliation(s)
- Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saba Gharibi
- School of Exercise and Nutrition Sciences, Faculty of Health, Deakin University, Melbourne, Australia
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzaneh Vahedi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Marzieh Asadi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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Khatami SH, Vakili O, Movahedpour A, Ghesmati Z, Ghasemi H, Taheri-Anganeh M. Laccase: Various types and applications. Biotechnol Appl Biochem 2022; 69:2658-2672. [PMID: 34997643 DOI: 10.1002/bab.2313] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/03/2022] [Indexed: 12/27/2022]
Abstract
Laccase belongs to the polyphenol oxidase family and is very important in removing environmental pollutants due to its structural and functional properties. Recently, the ability of laccase to oxidize phenolic and nonphenolic substances has been considered by many researchers. This enzyme's application scope includes a broad range of chemical processes and industrial usages, such as bioremediation, nanobiotechnology, woodworking industries, bleaching of paper pulp, dyeing in the textile industry, biotechnological uses in food industries, biorefining, detoxification from wastewater, production of organic matter from phenolic and amine substrates, and biofuels. Although filamentous fungi produce large amounts of laccase, high-yield industrial-scale production of laccase is still faced with many problems. At present, researchers are trying to increase the efficiency and productivity and reduce the final price of laccase by finding suitable microorganisms and improving the process of production and purification of laccase. This article reviews the introduction of laccase, its properties, production processes, and the effect of various factors on the enzyme's stability and activity, and some of its applications in various industries.
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Affiliation(s)
- Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Zeinab Ghesmati
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mortaza Taheri-Anganeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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Designing a Humanized Immunotoxin Based on HER2 Specific scFv and DFF40 Toxin Against Breast Cancer: An In-Silico Study. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10443-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Dastjerd NT, Valibeik A, Rahimi Monfared S, Goodarzi G, Moradi Sarabi M, Hajabdollahi F, Maniati M, Amri J, Samavarchi Tehrani S. Gene therapy: A promising approach for breast cancer treatment. Cell Biochem Funct 2021; 40:28-48. [PMID: 34904722 DOI: 10.1002/cbf.3676] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 02/06/2023]
Abstract
Breast cancer (BC) is the most prevalent malignancy and the second leading cause of death among women worldwide that is caused by numerous genetic and environmental factors. Hence, effective treatment for this type of cancer requires new therapeutic approaches. The traditional methods for treating this cancer have side effects, therefore so much research have been performed in last decade to find new methods to alleviate these problems. The study of the molecular basis of breast cancer has led to the introduction of gene therapy as an effective therapeutic approach for this cancer. Gene therapy involves sending genetic material through a vector into target cells, which is followed by a correction, addition, or suppression of the gene. In this technique, it is necessary to target tumour cells without affecting normal cells. In addition, clinical trial studies have shown that this approach is less toxic than traditional therapies. This study will review various aspects of breast cancer, gene therapy strategies, limitations, challenges and recent studies in this area.
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Affiliation(s)
- Niloufar Tavakoli Dastjerd
- Department of Medical Biotechnology, School of Allied Medical Sciences, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Ali Valibeik
- Department of Clinical Biochemistry, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Sobhan Rahimi Monfared
- Department of Clinical Biochemistry, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Golnaz Goodarzi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mostafa Moradi Sarabi
- Department of Biochemistry and Genetics, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Faezeh Hajabdollahi
- Department of Anatomical Sciences, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahmood Maniati
- English Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Jamal Amri
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sadra Samavarchi Tehrani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
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Ghalamfarsa F, Khatami SH, Vakili O, Taheri-Anganeh M, Tajbakhsh A, Savardashtaki A, Fazli Y, Uonaki LR, Shabaninejad Z, Movahedpour A, Ghalamfarsa G. Bispecific antibodies in colorectal cancer therapy: recent insights and emerging concepts. Immunotherapy 2021; 13:1355-1367. [PMID: 34641708 DOI: 10.2217/imt-2021-0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Colorectal cancer (CRC) is identified as a life-threatening malignancy. Despite several efforts and proceedings available for CRC therapy, it is still a health concern. Among a vast array of novel therapeutic procedures, employing bispecific antibodies (BsAbs) is currently considered to be a promising approach for cancer therapy. BsAbs, as a large family of molecules designed to realize two distinct epitopes or antigens, can be beneficial microgadgets to target the tumor-associated antigen pairs. On the other hand, applying the immune system's capabilities to attack malignant cells has been proven as a tremendous development in cancer therapeutic projects. The current study has attempted to overview some of the approved BsAbs in CRC therapy and those under clinical trials. For this purpose, reputable scientific search engines and databases, such as PubMed, ScienceDirect, Google Scholar, Scopus, etc., were explored using the keywords 'bispecific antibodies', 'colorectal cancer', 'immunotherapy' and 'tumor markers'.
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Affiliation(s)
- Farideh Ghalamfarsa
- Department of Medical Biotechnology, School of Advanced Medical Sciences & Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy & Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mortaza Taheri-Anganeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences & Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Tajbakhsh
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences & Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yousef Fazli
- Dena Clinical Diagnostic Laboratory, Yasuj, Iran
| | - Leila Rezaei Uonaki
- Department of Biotechnology, School of Science, Shahrekord University, Shahrekord, Iran
| | - Zahra Shabaninejad
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences & Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ghasem Ghalamfarsa
- Department of Microbiology & Immunology, School of Medicine, Yasuj University of Medical Sciences, Yasuj, Iran
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