1
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Pang L, Xu K, Qi L, Chatzisymeon E, Liu X, Yang P. Response behavior of antibiotic resistance genes to zinc oxide nanoparticles in cattle manure thermophilic anaerobic digestion process: A metagenomic analysis. BIORESOURCE TECHNOLOGY 2022; 347:126709. [PMID: 35033645 DOI: 10.1016/j.biortech.2022.126709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
This work investigated the metagenomics-based behavior of antibiotic resistance genes (ARGs) during cattle manure anaerobic digestion with zinc oxide nanoparticles (ZnO NPs) that are commonly used as animal feed additives. The 6.6% decrease in total ARGs abundance while remained unchanged ARGs diversity with ZnO NPs (5 mg/g total solid), suggested ZnO NPs may mitigate ARGs risk by abundance. Also, ZnO NPs affected ARGs with mechanisms specifically of antibiotic inactivation and antibiotic target change, and declined potential hosts' abundance (bacterial genus Ruminiclostridium, Riminococcus, and Paenibacillus) which mainly contributed to the decreased ARGs' abundance. Besides, microbial chemotaxis decreased by 17% with ZnO NPs compared to that without nanoparticles indicated a depression on potential hosts, who could develop the mechanism to adapt to altered digestion conditions, which probably inhibited the ARGs' propagation. These findings are important to promote understanding of the potential ARGs risks in treatments of livestock wastes containing animal feed additives.
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Affiliation(s)
- Lina Pang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Kalin Xu
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Luqing Qi
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China; Department of Environment Systems, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8563, Japan
| | - Efthalia Chatzisymeon
- Institute for Infrastructure and Environment, School of Engineering, The University of Edinburgh, Edinburgh EH9 3JL, United Kingdom
| | - Xuna Liu
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ping Yang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China.
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2
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CRISPR-Cas, a Revolution in the Treatment and Study of ESKAPE Infections: Pre-Clinical Studies. Antibiotics (Basel) 2021; 10:antibiotics10070756. [PMID: 34206474 PMCID: PMC8300728 DOI: 10.3390/antibiotics10070756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/14/2022] Open
Abstract
One of the biggest threats we face globally is the emergence of antimicrobial-resistant (AMR) bacteria, which runs in parallel with the lack in the development of new antimicrobials. Among these AMR bacteria pathogens belonging to the ESKAPE group can be highlighted (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) due to their profile of drug resistance and virulence. Therefore, innovative lines of treatment must be developed for these bacteria. In this review, we summarize the different strategies for the treatment and study of molecular mechanisms of AMR in the ESKAPE pathogens based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins’ technologies: loss of plasmid or cellular viability, random mutation or gene deletion as well directed mutations that lead to a gene’s loss of function.
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3
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Kouhpayeh S, Shariati L, Boshtam M, Rahimmanesh I, Mirian M, Esmaeili Y, Najaflu M, Khanahmad N, Zeinalian M, Trovato M, Tay FR, Khanahmad H, Makvandi P. The Molecular Basis of COVID-19 Pathogenesis, Conventional and Nanomedicine Therapy. Int J Mol Sci 2021; 22:5438. [PMID: 34064039 PMCID: PMC8196740 DOI: 10.3390/ijms22115438] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 12/12/2022] Open
Abstract
In late 2019, a new member of the Coronaviridae family, officially designated as "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2), emerged and spread rapidly. The Coronavirus Disease-19 (COVID-19) outbreak was accompanied by a high rate of morbidity and mortality worldwide and was declared a pandemic by the World Health Organization in March 2020. Within the Coronaviridae family, SARS-CoV-2 is considered to be the third most highly pathogenic virus that infects humans, following the severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV). Four major mechanisms are thought to be involved in COVID-19 pathogenesis, including the activation of the renin-angiotensin system (RAS) signaling pathway, oxidative stress and cell death, cytokine storm, and endothelial dysfunction. Following virus entry and RAS activation, acute respiratory distress syndrome develops with an oxidative/nitrosative burst. The DNA damage induced by oxidative stress activates poly ADP-ribose polymerase-1 (PARP-1), viral macrodomain of non-structural protein 3, poly (ADP-ribose) glycohydrolase (PARG), and transient receptor potential melastatin type 2 (TRPM2) channel in a sequential manner which results in cell apoptosis or necrosis. In this review, blockers of angiotensin II receptor and/or PARP, PARG, and TRPM2, including vitamin D3, trehalose, tannins, flufenamic and mefenamic acid, and losartan, have been investigated for inhibiting RAS activation and quenching oxidative burst. Moreover, the application of organic and inorganic nanoparticles, including liposomes, dendrimers, quantum dots, and iron oxides, as therapeutic agents for SARS-CoV-2 were fully reviewed. In the present review, the clinical manifestations of COVID-19 are explained by focusing on molecular mechanisms. Potential therapeutic targets, including the RAS signaling pathway, PARP, PARG, and TRPM2, are also discussed in depth.
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Affiliation(s)
- Shirin Kouhpayeh
- Erythron Genetics and Pathobiology Laboratory, Department of Immunology, Isfahan 8164776351, Iran;
| | - Laleh Shariati
- Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran;
- Biosensor Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran;
| | - Maryam Boshtam
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan 8158388994, Iran;
| | - Ilnaz Rahimmanesh
- Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran;
| | - Mina Mirian
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran;
| | - Yasaman Esmaeili
- Biosensor Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran;
| | - Malihe Najaflu
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran; (M.N.); (M.Z.)
| | - Negar Khanahmad
- School of Medicine, Isfahan University of Medical Sciences, Isfahan 817467346, Iran;
| | - Mehrdad Zeinalian
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran; (M.N.); (M.Z.)
| | - Maria Trovato
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), 80131 Naples, Italy;
| | - Franklin R Tay
- The Graduate School, Augusta University, Augusta, GA 30912, USA;
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran; (M.N.); (M.Z.)
| | - Pooyan Makvandi
- Istituto Italiano di Tecnologia, Centre for Materials Interface, viale Rinaldo Piaggio 34, 56025 Pisa, Italy
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4
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Dailey KM, Allgood JE, Johnson PR, Ostlie MA, Schaner KC, Brooks BD, Brooks AE. The next frontier of oncotherapy: accomplishing clinical translation of oncolytic bacteria through genetic engineering. Future Microbiol 2021; 16:341-368. [PMID: 33754804 DOI: 10.2217/fmb-2020-0245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The development of a 'smart' drug capable of distinguishing tumor from host cells has been sought for centuries, but the microenvironment of solid tumors continues to confound therapeutics. Solid tumors present several challenges for current oncotherapeutics, including aberrant vascularization, hypoxia, necrosis, abnormally high pH and local immune suppression. While traditional chemotherapeutics are limited by such an environment, oncolytic microbes are drawn to it - having an innate ability to selectively infect, colonize and eradicate solid tumors. Development of an oncolytic species would represent a shift in the cancer therapeutic paradigm, with ramifications reaching from the medical into the socio-economic. Modern genetic engineering techniques could be implemented to customize 'Frankenstein' bacteria with advantageous characteristics from several species.
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Affiliation(s)
- Kaitlin M Dailey
- Cellular & Molecular Biology Program, North Dakota State University, Fargo, ND 58103, USA.,Pharmaceutical Sciences Department, North Dakota State University, Fargo, ND 58103, USA
| | - JuliAnne E Allgood
- Department of Neuroscience, University of Wyoming, Laramie, WY 82071, USA
| | - Paige R Johnson
- Pharmaceutical Sciences Department, North Dakota State University, Fargo, ND 58103, USA
| | - Mackenzie A Ostlie
- Pharmaceutical Sciences Department, North Dakota State University, Fargo, ND 58103, USA
| | - Kambri C Schaner
- Pharmaceutical Sciences Department, North Dakota State University, Fargo, ND 58103, USA
| | | | - Amanda E Brooks
- Cellular & Molecular Biology Program, North Dakota State University, Fargo, ND 58103, USA.,Pharmaceutical Sciences Department, North Dakota State University, Fargo, ND 58103, USA.,Office of Research & Scholarly Activity. Rocky Vista University, Ivins, UT 84738, USA
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5
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Hosseini N, Khanahmad H, Esfahani BN, Bandehpour M, Shariati L, Zahedi N, Kazemi B. Targeting of cholera toxin A ( ctxA) gene by zinc finger nuclease: pitfalls of using gene editing tools in prokaryotes. Res Pharm Sci 2020; 15:182-190. [PMID: 32582358 PMCID: PMC7306252 DOI: 10.4103/1735-5362.283818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/22/2019] [Accepted: 04/29/2020] [Indexed: 01/14/2023] Open
Abstract
Background and purpose: The study was launched to use zinc finger nuclease (ZFN) technology to disrupt the cholera toxin gene (ctxA) for inhibiting CT toxin production in Vibrio cholera (V. cholera). Experimental approach: An engineered ZFN was designed to target the catalytic site of the ctxA gene. The coding sequence of ZFN was cloned to pKD46, pTZ57R T/A vector, and E2-crimson plasmid and transformed to Escherichia coli (E. coli) Top10 and V. cholera. The efficiency of ZFN was evaluated by colony counting. Findings/Results: No expression was observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and western blotting in transformed E. coli. The ctxA gene sequencing did not show any mutation. Polymerase chain reaction on pKD46-ZFN plasmid had negative results. Transformation of E. coli Top10 with T/A vectors containing whole ZFN sequence led to 7 colonies all of which contained bacteria with self-ligated vector. Transformation with left array ZFN led to 24 colonies of which 6 contained bacteria with self-ligated vector and 18 of them contained bacteria with vector/left array. Transformation of V. cholera with E2-crimson vectors containing whole ZFN did not produce any colonies. Transformation with left array vectors led to 17 colonies containing bacteria with vector/left array. Left array protein band was captured using western blot assay. Conclusions and implications: ZFN might have off target on bacterial genome causing lethal double-strand DNA break due to lack of non-homologous end joining (NHEJ) mechanism. It is recommended to develop ZFNs against bacterial genes, engineered packaging host with NHEJ repair system is essential.
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Affiliation(s)
- Nafiseh Hosseini
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Mojgan Bandehpour
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
| | - Laleh Shariati
- Biosensor Research Center, Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Nushin Zahedi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Bahram Kazemi
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran.,Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
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6
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Gholizadeh P, Köse Ş, Dao S, Ganbarov K, Tanomand A, Dal T, Aghazadeh M, Ghotaslou R, Ahangarzadeh Rezaee M, Yousefi B, Samadi Kafil H. How CRISPR-Cas System Could Be Used to Combat Antimicrobial Resistance. Infect Drug Resist 2020; 13:1111-1121. [PMID: 32368102 PMCID: PMC7182461 DOI: 10.2147/idr.s247271] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/31/2020] [Indexed: 12/26/2022] Open
Abstract
Rapid emergence of antibiotic-resistant bacteria has made it harder for us to combat infectious diseases and to develop new antibiotics. The clustered regularly interspaced short palindromic repeats - CRISPR-associated (CRISPR-Cas) system, as a bacterial adaptive immune system, is recognized as one of the new strategies for controlling antibiotic-resistant strains. The programmable Cas nuclease of this system used against bacterial genomic sequences could be lethal or could help reduce resistance of bacteria to antibiotics. Therefore, this study aims to review using the CRISPR-Cas system to promote sensitizing bacteria to antibiotics. We envision that CRISPR-Cas approaches may open novel ways for the development of smart antibiotics, which could eliminate multidrug-resistant (MDR) pathogens and differentiate between beneficial and pathogenic microorganisms. These systems can be exploited to quantitatively and selectively eliminate individual bacterial strains based on a sequence-specific manner, creating opportunities in the treatment of MDR infections, the study of microbial consortia, and the control of industrial fermentation.
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Affiliation(s)
- Pourya Gholizadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Şükran Köse
- Department of Infectious Diseases and Clinical Microbiology, University of Health Sciences, Tepecik Training and Research Hospital, İzmir, Turkey
| | - Sounkalo Dao
- Faculté de Médecine, de Pharmacie et d’Odonto-Stomatologie (FMPOS), University of Bamako, Bamako, Mali
| | - Khudaverdi Ganbarov
- Department of Microbiology, Baku State University, Baku, Republic of Azerbaijan
| | - Asghar Tanomand
- Department of Basic Sciences, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Tuba Dal
- Department of Clinical Microbiology, Faculty of Medicine, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - Mohammad Aghazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghotaslou
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Bahman Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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7
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Jiang W, Yang W, Zhao X, Wang N, Ren H. Klebsiella pneumoniae presents antimicrobial drug resistance for β-lactam through the ESBL/PBP signaling pathway. Exp Ther Med 2020; 19:2449-2456. [PMID: 32256721 PMCID: PMC7086219 DOI: 10.3892/etm.2020.8498] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
Overuse and misuse of antibiotics leads to antibiotic resistance which has become a significant public health concern. Klebsiella pneumoniae is the most common pathogenic bacteria underlying nosocomial infections due to the expression of virulence factors and occurrence of antibiotic resistance. Evidence indicates that β-lactamase is involved in the antibiotic resistance of Klebsiella pneumoniae to β-lactam antibiotics. The aim of the present study was to investigate the association between the molecular biological mechanisms of antibiotic resistance of Klebsiella pneumoniae and extended-spectrum β-lactamase (ESBL). In order to assess temporal trends in prevalence and antimicrobial susceptibility, Klebsiella pneumoniae bacteria were isolated and the ESBL expression level was analyzed. Susceptibility tests were performed using automated systems. The β-lactam-resistance in Klebsiella pneumoniae was assessed by the β-lactam agar screen plate and respective MIC values were evaluated using E-test strips. The confirmatory disk diffusion methods were applied for phenotypic identification of the ESBL production of Klebsiella pneumoniae. The results showed that Klebsiella pneumoniae bacteria exhibited higher ESBL production after treatment with β-lactam compared to the control. The ESBL gene expression was upregulated in Klebsiella pneumoniae after treatment with β-lactam. Results identified that penicillin-binding proteins (PBPs) were associated with the growth and resistance to β-lactams. Zinc finger nuclease markedly inhibited the antibiotic resistance of Klebsiella pneumoniae to β-lactam. PBP knockdown abolished the inhibitory effects of zinc finger nuclease on the growth of Klebsiella pneumoniae induced by β-lactam antibiotic treatment. In conclusion, these results suggest that the resistance of Klebsiella pneumoniae bacteria to antimicrobial drugs is through the ESBL signaling pathway, which indicates that ESBL may be a potential target for abolishing resistance to β-lactam.
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Affiliation(s)
- Wei Jiang
- Department of Infectious Disease, Tianjin First Central Hospital, Tianjin 300000, P.R. China
| | - Wenjie Yang
- Department of Transplantation, Tianjin First Central Hospital, Tianjin 300000, P.R. China
| | - Xuequn Zhao
- Department of Transplantation, Tianjin First Central Hospital, Tianjin 300000, P.R. China
| | - Na Wang
- Department of Infectious Disease, Tianjin First Central Hospital, Tianjin 300000, P.R. China
| | - Haixia Ren
- Department of Pharmaceutical Preparation, Tianjin First Central Hospital, Tianjin 300000, P.R. China
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8
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Jamalvandi M, Khanahmad H, Irani S, Bastaminezhad S. Selection and characterization of single-stranded DNA aptamers against interleukin-5. Res Pharm Sci 2019; 14:515-523. [PMID: 32038731 PMCID: PMC6937751 DOI: 10.4103/1735-5362.272560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Asthma as a chronic inflammatory disorder is associated with many cytokines like interleukin-5 (IL-5) which plays essential role in eosinophil differentiation and maturation. Accordingly, blockage of IL-5 using mepalizumab has been considered as a promising therapeutic approach for asthma. Despite the monocolonal antibody advantages, some restrictions provided an acceptable background for alternative agents like aptamers which could replace with antibodies. In the current study, aptamer isolation against IL-5 molecule was intended, according to the valuable benefits of aptamers over antibodies. HEK-293T/IL-5 cell was constructed to select aptamer using cell-systematic evolution of ligands by exponential enrichment (SELEX) method. Integration of the IL-5 fragment to genome of the HEK-293T was verified by polymerase chain reaction on the genomic DNA of the transfected cells. Moreover, IL-5 protein expression on the cell surface was confirmed using flow cytometry analysis. Then, cell SELEX was carried out in 12 rounds and isolated aptamers were evaluated by flow cytometry analysis. The selected clones were then sequenced and assessed for any possible secondary structure. The results of this study led to the selection of 19 different single-stranded DNA clones after 12 rounds of selection which were clustered to five groups based on common structural motifs. In conclusion, the findings revealed the isolation of IL-5-specific single-stranded DNA aptamers, which can further be substituted with mepolizumab.
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Affiliation(s)
- Mina Jamalvandi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, I.R. Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, I.R. Iran
| | - Sayad Bastaminezhad
- Department of Medicine and Genetics, School of Medicine, Ilam University of Medical Sciences, Ilam, I.R. Iran
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9
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Kouhpayeh S, Hejazi Z, Boshtam M, Mirian M, Rahimmanesh I, Darzi L, Rezaei A, Shariati L, Khanahmad H. Development of α4 integrin DNA aptamer as a potential therapeutic tool for multiple sclerosis. J Cell Biochem 2019; 120:16264-16272. [PMID: 31111537 DOI: 10.1002/jcb.28907] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/03/2019] [Accepted: 02/14/2019] [Indexed: 12/25/2022]
Abstract
One of the most important molecules for multiple sclerosis pathogenesis is α4 integrin, which is responsible for autoreactive leukocytes migration into the brain. The monoclonal antibody, natalizumab, was introduced to market for blocking the extravasation of autoreactive leukocytes via inhibition of α4 integrin. However, the disadvantages of antibodies provided a suitable background for other agents to be replaced with antibodies. Considering the profound advantages of aptamers over antibodies, aptamer isolation against α4 integrin was intended in the current study. The α4 integrin-specific aptamers were selected using cell-systematic evolution of ligands by exponential enrichment (SELEX) method with human embryonic kidney (HEK)-293T overexpressing α4 integrin and HEK-293T as target and control cells, respectively. Evaluation of selected aptamer was performed through flow cytometric analysis. The selected clones were then sequenced and analyzed for any possible secondary structure and affinity. The results of this study led to isolation of 13 different single-stranded DNA clones in 11 rounds of selection which were categorized to three clusters based on common structural motifs and the equilibrium dissociation constant (K d ) of the most stable structure was calculated. The evaluation of SELEX progress showed growth in aptamer affinity with increasing of the number of cycles. Taken together, the findings of this study demonstrated the isolation of α4-specific single-stranded DNA aptamers with suitable affinity for ligand, which can further be replaced with natalizumab.
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Affiliation(s)
- Shirin Kouhpayeh
- Department of Immunology, Erythron Pathobiology and Genetics Laboratory, Isfahan, Islamic Republic of Iran
| | - Zahra Hejazi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Maryam Boshtam
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Mina Mirian
- Department of Pharmaceutical Biotechnology, Isfahan Pharmaceutical Science Research Center, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Ilnaz Rahimmanesh
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Leila Darzi
- Department of Medical Biotechnology, Faculty of Medical Science, Tarbiat Modares University, Tehran, Islamic Republic of Iran
| | - Abbas Rezaei
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Laleh Shariati
- Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran.,Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
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10
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Shariati L, Modarressi MH, Tabatabaiefar MA, Kouhpayeh S, Hejazi Z, Shahbazi M, Sabzehei F, Salehi M, Khanahmad H. Engineered zinc-finger nuclease to generate site-directed modification in the KLF1 gene for fetal hemoglobin induction. J Cell Biochem 2019; 120:8438-8446. [PMID: 30556211 DOI: 10.1002/jcb.28130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/31/2018] [Indexed: 01/24/2023]
Abstract
Elevation of hemoglobin F (HbF) ameliorates symptoms of β-thalassemia, as a common autosomal recessive disorder. In this study, the ability of an engineered zinc-finger nuclease (ZFN) system was assesed to disrupt the KLF1 gene to inhibit the γ to β hemoglobin switching in K562 cells. This study was performed using a second generation integration-deficient lentiviral vector assigned to transient gene targeting. The sequences coding for zinc finger protein arrays were designed and subcloned in TDH plus as a transfer vector. Transduction of K562 cells was performed with the integrase minus lentivirus containing ZFN. The indel percentage of the transducted cells with lentivirus containing ZFN was about 29%. Differentiation of K562 cell line into erythroid cell lineage was induced with cisplatin concentration of 15 µg/mL. After differentiation, γ-globin and HbF expression were evaluated using real-time reverse-transcription polymerase chain reaction and hemoglobin electrophoresis methods. The levels of γ-globin messenger RNA were nine-fold higher in the ZFN treated cells compared with untreated cells 5 days after differentiation. Hemoglobin electrophoresis method showed the same results for HbF level measurement. Application of the ZFN tool to induce KLF1 gene mutation in adult erythroid progenitors might be a candidate to stimulate HbF expression in β-thalassemia patients.
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Affiliation(s)
- Laleh Shariati
- Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran.,Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shirin Kouhpayeh
- Department of Immunology, Erythron Genetics and Pathobiology Laboratory, Isfahan, Iran
| | - Zahra Hejazi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoureh Shahbazi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Faezeh Sabzehei
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoor Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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11
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Shariati L, Rohani F, Heidari Hafshejani N, Kouhpayeh S, Boshtam M, Mirian M, Rahimmanesh I, Hejazi Z, Modarres M, Pieper IL, Khanahmad H. Disruption of
SOX6
gene using CRISPR/Cas9 technology for gamma‐globin reactivation: An approach towards gene therapy of β‐thalassemia. J Cell Biochem 2018; 119:9357-9363. [DOI: 10.1002/jcb.27253] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/20/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Laleh Shariati
- Applied Physiology Research Center Cardiovascular Research Institute, Isfahan University of Medical Sciences Isfahan Iran
- Isfahan Cardiovascular Research Center Cardiovascular Research Institute, Isfahan University of Medical Sciences Isfahan Iran
| | - Fattah Rohani
- Department of Clinical Sciences Faculty of Veterinary Medicine, University of Shahrekord Shahrekord Iran
| | - Nahid Heidari Hafshejani
- Department of Genetics and Molecular Biology School of Medicine, Isfahan University of Medical Sciences Isfahan Iran
| | - Shirin Kouhpayeh
- Isfahan Neurosciences Research Center, Alzahra Research Institute Isfahan University of Medical Sciences Isfahan Iran
| | - Maryam Boshtam
- Isfahan Cardiovascular Research Center Cardiovascular Research Institute, Isfahan University of Medical Sciences Isfahan Iran
| | - Mina Mirian
- Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Science Research Center, School of Pharmacy and Pharmaceutical Science Isfahan University of Medical Sciences Isfahan Iran
| | - Ilnaz Rahimmanesh
- Department of Genetics and Molecular Biology School of Medicine, Isfahan University of Medical Sciences Isfahan Iran
| | - Zahra Hejazi
- Department of Genetics and Molecular Biology School of Medicine, Isfahan University of Medical Sciences Isfahan Iran
| | - Mehran Modarres
- Department of Genetics and Molecular Biology School of Medicine, Isfahan University of Medical Sciences Isfahan Iran
| | - Ina Laura Pieper
- Institute of Life Science, College of Medicine Swansea University Medical School Swansea United Kingdom
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology School of Medicine, Isfahan University of Medical Sciences Isfahan Iran
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Modares Sadeghi M, Shariati L, Hejazi Z, Shahbazi M, Tabatabaiefar MA, Khanahmad H. Inducing indel mutation in the SOX6 gene by zinc finger nuclease for gamma reactivation: An approach towards gene therapy of beta thalassemia. J Cell Biochem 2017; 119:2512-2519. [PMID: 28941328 DOI: 10.1002/jcb.26412] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 09/22/2017] [Indexed: 02/04/2023]
Abstract
β-thalassemia is a common autosomal recessive disorder characterized by a deficiency in the synthesis of β-chains. Evidences show that increased HbF levels improve the symptoms in patients with β-thalassemia or sickle cell anemia. In this study, ZFN technology was applied to induce a mutation in the binding domain region of SOX6 to reactivate γ-globin expression. The sequences coding for ZFP arrays were designed and sub cloned in TDH plus as a transfer vector. The ZFN expression was confirmed using Western blot analysis. In the next step, using the site-directed mutagenesis strategy through the overlap PCR, a missense mutation (D64V) was induced in the catalytic domain of the integrase gene in the packaging plasmid and verified using DNA sequencing. Then, the integrase minus lentivirus containing ZFN cassette was packaged. Transduction of K562 cells with this virus was performed. Mutation detection assay was performed. The indel percentage of the cells transducted with lenti virus containing ZFN was 31%. After 5 days of erythroid differentiation with 15 μg/mL cisplatin, the levels of γ-globin mRNA were sixfold in the cells treated with ZFN compared to untreated cells. In the meantime, the measurement of HbF expression levels was carried out using hemoglobin electrophoresis and showed the same results. Integrase minus lentivirus can provide a useful tool for efficient transient gene expression and helps avoid disadvantages of gene targeting using the native virus. The ZFN strategy applied here to induce indel on SOX6 gene in adult erythroid progenitors may provide a method to activate fetal hemoglobin expression in individuals with β-thalassemia.
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Affiliation(s)
- Mehran Modares Sadeghi
- Department of Genetics and Molecular biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Laleh Shariati
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zahra Hejazi
- Department of Genetics and Molecular biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoureh Shahbazi
- Department of Genetics and Molecular biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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13
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Shatzkes K, Singleton E, Tang C, Zuena M, Shukla S, Gupta S, Dharani S, Onyile O, Rinaggio J, Connell ND, Kadouri DE. Predatory Bacteria Attenuate Klebsiella pneumoniae Burden in Rat Lungs. mBio 2016; 7:e01847-16. [PMID: 27834203 PMCID: PMC5101354 DOI: 10.1128/mbio.01847-16] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/11/2016] [Indexed: 12/26/2022] Open
Abstract
Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus are predatory bacteria that naturally-and obligately-prey on other Gram-negative bacteria, and their use has been proposed as a potential new approach to control microbial infection. The ability of predatory bacteria to prey on Gram-negative human pathogens in vitro is well documented; however, the in vivo safety and efficacy of predatory bacteria have yet to be fully assessed. In this study, we examined whether predatory bacteria can reduce bacterial burden in the lungs in an in vivo mammalian system. Initial safety studies were performed by intranasal inoculation of rats with predatory bacteria. No adverse effects or lung pathology were observed in rats exposed to high concentrations of predatory bacteria at up to 10 days postinoculation. Enzyme-linked immunosorbent assay (ELISA) of the immune response revealed a slight increase in inflammatory cytokine levels at 1 h postinoculation that was not sustained by 48 h. Additionally, dissemination experiments showed that predators were efficiently cleared from the host by 10 days postinoculation. To measure the ability of predatory bacteria to reduce microbial burden in vivo, we introduced sublethal concentrations of Klebsiella pneumoniae into the lungs of rats via intranasal inoculation and followed with multiple doses of predatory bacteria over 24 h. Predatory bacteria were able to reduce K. pneumoniae bacterial burden, on average, by more than 3.0 log10 in the lungs of most rats as measured by CFU plating. The work presented here provides further support for the idea of developing predatory bacteria as a novel biocontrol agent. IMPORTANCE A widely held notion is that antibiotics are the greatest medical advance of the last 50 years. However, the rise of multidrug-resistant (MDR) bacterial infections has become a global health crisis over the last decade. As we enter the postantibiotic era, it is crucial that we begin to develop new strategies to combat bacterial infection. Here, we report one such new approach: the use of predatory bacteria (Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus) that naturally-and obligately-prey on other Gram-negative bacteria. To our knowledge, this is the first study that demonstrated the ability of predatory bacteria to attenuate the bacterial burden of a key human pathogen in an in vivo mammalian system. As the prevalence of MDR infections continues to rise each year, our results may represent a shift in how we approach treating microbial infections in the future.
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Affiliation(s)
- Kenneth Shatzkes
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Eric Singleton
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Chi Tang
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Michael Zuena
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Sean Shukla
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Shilpi Gupta
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
| | - Sonal Dharani
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
| | - Onoyom Onyile
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Joseph Rinaggio
- Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, New Jersey, USA
| | - Nancy D Connell
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
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