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Rikhtehgaran R, Shamsi K, Renani EM, Arab A, Nouri F, Mohammadifard N, Marateb HR, Mansourian M, Sarrafzadegan N. Population food intake clusters and cardiovascular disease incidence: a Bayesian quantifying of a prospective population-based cohort study in a low and middle-income country. Front Nutr 2023; 10:1150481. [PMID: 37521422 PMCID: PMC10374205 DOI: 10.3389/fnut.2023.1150481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Aims This study was designed to explore the relationship between cardiovascular disease incidence and population clusters, which were established based on daily food intake. Methods The current study examined 5,396 Iranian adults (2,627 males and 2,769 females) aged 35 years and older, who participated in a 10-year longitudinal population-based study that began in 2001. The frequency of food group consumption over the preceding year (daily, weekly, or monthly) was assessed using a 49-item qualitative food frequency questionnaire (FFQ) administered via a face-to-face interview conducted by an expert dietitian. Participants were clustered based on their dietary intake by applying the semi-parametric Bayesian approach of the Dirichlet Process. In this approach, individuals with the same multivariate distribution based on dietary intake were assigned to the same cluster. The association between the extracted population clusters and the incidence of cardiovascular diseases was examined using Cox proportional hazard models. Results In the 10-year follow-up, 741 participants (401 men and 340 women) were diagnosed with cardiovascular diseases. Individuals were categorized into three primary dietary clusters: healthy, unhealthy, and mixed. After adjusting for potential confounders, subjects in the unhealthy cluster exhibited a higher risk for cardiovascular diseases [Hazard Ratio (HR): 2.059; 95% CI: 1.013, 4.184] compared to those in the healthy cluster. In the unadjusted model, individuals in the mixed cluster demonstrated a higher risk for cardiovascular disease than those in the healthy cluster (HR: 1.515; 95% CI: 1.097, 2.092). However, this association was attenuated after adjusting for potential confounders (HR: 1.145; 95% CI: 0.769, 1.706). Conclusion The results have shown that individuals within an unhealthy cluster have a risk that is twice as high for the incidence of cardiovascular diseases. However, these associations need to be confirmed through further prospective investigations.
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Affiliation(s)
- Reyhaneh Rikhtehgaran
- Department of Mathematical Sciences, Isfahan University of Technology, Isfahan, Iran
| | - Khadijeh Shamsi
- Student Research Committee, Department of Epidemiology and Biostatistics, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elnaz Mojoudi Renani
- Department of Mathematical Sciences, Isfahan University of Technology, Isfahan, Iran
| | - Arman Arab
- Department of Community Nutrition, School of Nutrition and Food Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Nouri
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Noushin Mohammadifard
- Hypertension Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamid Reza Marateb
- Department of Biomedical Engineering, Faculty of Engineering, University of Isfahan, Isfahan, Iran
| | - Marjan Mansourian
- Pediatric Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Nizal Sarrafzadegan
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
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Afshari Z, Rasaee MJ, Paknejad M, Khalili S, Baradaran-Rafii A. The Ability of Antibody against Truncated Matrix Metalloproteinase 9 Peptide to Evaluate the Native Protein on Tear Drops of Dry Eye Disease Patients by a Point-of-Care Diagnostic System. J Curr Ophthalmol 2023; 35:170-176. [PMID: 38250498 PMCID: PMC10795817 DOI: 10.4103/joco.joco_320_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 06/17/2023] [Accepted: 06/18/2023] [Indexed: 01/23/2024] Open
Abstract
Purpose To obtain a reactive and specific antibody against truncated matrix metalloproteinase 9 (MMP-9), that has reactivity toward the native protein. Precision, accuracy, specificity, and sensitivity were evaluated using a point-of-care test. Methods An in silico study was used to confirm the anti peptide truncated MMP-9 is against native MMP-9. After an antibody titer assessment, purification, and characterization, the anti MMP-9 was assessed. The cut-off value was determined using the purified gelatinases of the supernatant HCT 116 cell line. The supernatant was purified by preparative native-polyacrylamide gel electrophoresis based on charge and size of the proteins. Furthermore, quality control (QC) of the results were performed following standard densitometry methods. Results A truncated MMP-9 is the major epitope peptide that can trigger the immune system to scavenge for a specific and reactive antibody against the native MMP-9. The MMP-9 native protein is purified from the supernatant of the HCT 116 cell line and the commercially available, full-length MMP-9. The cut-off value was estimated at 30 μg/mL. QC results indicated that the specificity was 80%, sensitivity was 96.7%, accuracy was 91%, and precision was 91.66%. The area under curve was 0.827 (P < 0.001). The positive predictive value was 83%, and the negative predictive value was 96%. Conclusions The antibody against the synthetic epitope peptide can detect the native MMP-9. Native MMP-9 is considered the main biomarker in an immunoassay POCT and is used to diagnose dry eye disease (DED). In accordance with QC results, MMP-9 point of care test can be utilized for screening patients suffering from DED.
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Affiliation(s)
- Zahra Afshari
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Javad Rasaee
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Maliheh Paknejad
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Faculty of Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Alireza Baradaran-Rafii
- Department of Ophthalmology, Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Shi D, Chen Y, Chen M, Zhou T, Xu F, Zhang C, Wang C, Li Z. Bioinformatics analysis of Omp19 and Omp25 proteins for designing multi-epitope vaccines against Brucella. Medicine (Baltimore) 2023; 102:e33182. [PMID: 36930131 PMCID: PMC10019172 DOI: 10.1097/md.0000000000033182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023] Open
Abstract
Brucellosis is a zoonotic disease caused by Brucella. There is no effective vaccine against human brucellosis. Omp19 and Omp25 are the outer membrane proteins of Brucella. They are widely expressed and highly conserved in Brucella and have high immunogenicity. Herein, we aim to identify multi-epitope vaccine candidates based on Omp19 and Omp25. We analyzed the physicochemical properties and protein structure of Omp19 and Omp25, and predicted the corresponding B cell and T cell epitopes using bioinformatics analysis. Omp19 and Omp25 were composed of 177 amino acids and 213 amino acids, respectively. They were both stable hydrophilic proteins. The instability indices were 44.8 and 23, respectively. The hydrophilicity was -0.1 and -0.317, respectively. In the secondary structure of Omp19 and Omp25 proteins, the α-helix accounted for 12.43% and 23.94%, the β-sheet was 18.64% and 23.47%, the β-turn was 6.78% and 4.23%, and the random coil was 62.15% and 48.36%. Finally, 5 B cell epitopes, 3 Th-cell epitopes and 5 CTL cell epitopes of Omp19 protein, and 4 B cell epitopes, 3 Th-cell epitopes, and 5 CTL cell epitopes of Omp25 protein were selected as vaccine candidates. In conclusion, we obtained potential B cell and T cell epitopes of the Brucella outer membrane Omp19 and Omp25 proteins. This lays the foundation for the further design of multi-epitope vaccine of Brucella.
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Affiliation(s)
- Donghao Shi
- Clinical Laboratory Center, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, P.R. China
| | - Yuan Chen
- Clinical Laboratory Center, People`s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, P.R. China
| | - Muzhi Chen
- Department of Rheumatology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, P.R. China
| | - Tingting Zhou
- Department of Public Health, People`s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, P.R. China
| | - Feili Xu
- Clinical Laboratory Center, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, P.R. China
| | - Chao Zhang
- Urumqi OE Biotech Co., Ltd., Urumqi, Xinjiang, P.R. China
| | - Changmin Wang
- Clinical Laboratory Center, People`s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, P.R. China
| | - Zhiwei Li
- Clinical Laboratory Center, People`s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, P.R. China
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Guerrero-Beltrán CE, Mijares-Rojas IA, Salgado-Garza G, Garay-Gutiérrez NF, Carrión-Chavarría B. Peptidic vaccines: The new cure for heart diseases? Pharmacol Res 2020; 164:105372. [PMID: 33316382 DOI: 10.1016/j.phrs.2020.105372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/12/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022]
Abstract
Cardiovascular disease continues to be the most common cause of death worldwide. The global burden is so high that numerous organizations are providing counseling recommendations and annual revisions of current pharmacological and non-pharmacological treatments as well as risk prediction for disease prevention and further progression. Although primary preventive interventions targeting risk factors such as obesity, hypertension, smoking, and sedentarism have led to a global decline in hospitalization rates, the aging population has overwhelmed these efforts on a global scale. This review focuses on peptidic vaccines, with the known and not well-known autoantigens in atheroma formation or acquired cardiac diseases, as novel potential immunotherapy approaches to counteract harmful heart disease continuance. We summarize how cancer immunomodulatory strategies started novel approaches to modulate the innate and adaptive immune responses, and how they can be targeted for therapeutic purposes in the cardiovascular system. Brief descriptions focused on the processes that start as either immunologic or non-immunologic, and the ultimate loss of cardiac muscle cell contractility as the outcome, are discussed. We conclude debating how novel strategies with nanoparticles and nanovaccines open a promising therapeutic option to reduce or prevent cardiovascular diseases.
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Affiliation(s)
- Carlos Enrique Guerrero-Beltrán
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Medicina Cardiovascular y Metabolómica, Monterrey, N.L., Mexico; Tecnologico de Monterrey, Hospital Zambrano Hellion, TecSalud, Centro de Investigación Biomédica, San Pedro Garza García, N.L., Mexico.
| | - Iván Alfredo Mijares-Rojas
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Medicina Cardiovascular y Metabolómica, Monterrey, N.L., Mexico
| | - Gustavo Salgado-Garza
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Medicina Cardiovascular y Metabolómica, Monterrey, N.L., Mexico
| | - Noé Francisco Garay-Gutiérrez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Medicina Cardiovascular y Metabolómica, Monterrey, N.L., Mexico
| | - Belinda Carrión-Chavarría
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Medicina Cardiovascular y Metabolómica, Monterrey, N.L., Mexico
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5
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Kyrklund M, Bildo M, Akhi R, Nissinen AE, Pussinen P, Hörkkö S, Wang C. Humoral immune response to heat shock protein 60 of Aggregatibacter actinomycetemcomitans and cross-reactivity with malondialdehyde acetaldehyde-modified LDL. PLoS One 2020; 15:e0230682. [PMID: 32210456 PMCID: PMC7094845 DOI: 10.1371/journal.pone.0230682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/05/2020] [Indexed: 11/18/2022] Open
Abstract
Atherosclerosis is a chronic inflammatory disease and major cause of mortality worldwide. One of the crucial steps for atherosclerotic plaque development is oxidation of low-density lipoprotein (LDL). Through the oxidation, highly immunogenic epitopes are created and the immune system is activated. Association between atherosclerosis and periodontal diseases is well documented, and one of the main oral pathogens common in periodontitis is Aggregatibacter actinomycetemcomitans (Aa). Heat shock protein 60 (HSP60) is an important virulence factor for Aa bacteria and a strong activator of the immune system. Cross-reactivity of HSP60 and oxidized LDL (OxLDL) antibodies could be a potential mechanism in the progression of atherosclerosis and one possible link between atherosclerosis and periodontitis. Human plasma samples from neonates and mothers were analyzed to determine if antibody titer to Aa-HSP60 protein is already present in newborns. Further objectives were to characterize antibody response in Aa-HSP60 immunized mice and to determine possible antibody cross-reaction with oxidized LDL. We demonstrated that newborns already have IgM antibody levels to Aa-HSP60. We also showed that in mice, Aa-HSP60 immunization provoked IgG and IgM antibody response not only to Aa-HSP60 but also to malondialdehyde acetaldehyde-modified LDL (MAA-LDL). Competition assay revealed that the antibodies were specific to Aa-HSP60 and cross-reacted with MAA-LDL. Our results suggest a possibility of molecular mimicry between Aa-HSP60 and MAA-LDL, making it intriguing to speculate on the role of HSP60 protein in atherosclerosis that manifests at young age.
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Affiliation(s)
- Mikael Kyrklund
- Research Unit of Biomedicine, Medical Microbiology and Immunology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Medical Research Center and Nordlab Oulu, University Hospital and University of Oulu, Oulu, Finland
| | - Mika Bildo
- Research Unit of Biomedicine, Medical Microbiology and Immunology, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Ramin Akhi
- Research Unit of Biomedicine, Medical Microbiology and Immunology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Medical Research Center and Nordlab Oulu, University Hospital and University of Oulu, Oulu, Finland
| | - Antti E. Nissinen
- Research Unit of Biomedicine, Medical Microbiology and Immunology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Medical Research Center and Nordlab Oulu, University Hospital and University of Oulu, Oulu, Finland
| | - Pirkko Pussinen
- Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sohvi Hörkkö
- Research Unit of Biomedicine, Medical Microbiology and Immunology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Medical Research Center and Nordlab Oulu, University Hospital and University of Oulu, Oulu, Finland
| | - Chunguang Wang
- Research Unit of Biomedicine, Medical Microbiology and Immunology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Medical Research Center and Nordlab Oulu, University Hospital and University of Oulu, Oulu, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
- * E-mail:
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6
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In silico analysis of non-synonymous single nucleotide polymorphism in a human KLK-2 gene associated with prostate cancer. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100578] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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7
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Rostamtabar M, Rahmani A, Baee M, Karkhah A, Prajapati VK, Ebrahimpour S, Nouri HR. Development a multi-epitope driven subunit vaccine for immune response reinforcement against Serogroup B of Neisseria meningitidis using comprehensive immunoinformatics approaches. INFECTION GENETICS AND EVOLUTION 2019; 75:103992. [PMID: 31394292 DOI: 10.1016/j.meegid.2019.103992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/22/2019] [Accepted: 08/02/2019] [Indexed: 11/28/2022]
Abstract
Serogroup B of Neisseria meningitidis is the main cause of mortality due to meningococcal meningitis. Despite of many investigations, there is still no effective vaccine to prevent this serious infection. Therefore, this study was conducted to design a multi-epitope based vaccine through immunoinformatics approaches. The T CD4+ and TCD8+ cells along with IFN-γ inducing epitopes were selected from TspA, FHbp, NspA, TbpB, PilQ and NspA antigens form serogroup B of Neisseria meningitidis. Furthermore, to induce strong helper T lymphocytes (HTLs) responses, Pan HLA DR-binding epitope (PADRE) was used. In addition, loop 5 and 7 of the PorB as a TLR2 agonist were added to the vaccine construct. Physico-chemical properties, secondary and tertiary structures of the proposed construct were assessed. Finally, homology modeling, refinement and molecular docking were carried out to evaluated the construct tertiary structure and protein-protein interaction, respectively. By fusing the CTL, HTL and IFN-γ predicted epitopes along with suitable adjuvant and linkers, a multi-epitope vaccine was constructed with a TAT sequence of HIV at the N-terminal. Immunoinformatics analyses confirmed a soluble and non-allergic protein with a molecular weight of 62.5 kDa and high antigenicity. Furthermore, the stability of the multi-epitope construct was established and showed strong potential to generate humoral and cell-mediated immune responses. In addition, through molecular docking and dynamic simulation, the microscopic interaction between the vaccine construct and TLR-2 were verified. In summary, immunoinformatics analysis demonstrated that the constructed multi-epitope vaccine had a strong potential of T and B-cell stimulation and it could possibly be used for prophylactic or therapeutic aims to protect against serogroup B of N. meningitidis.
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Affiliation(s)
- Maryam Rostamtabar
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Abolfazl Rahmani
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Masoud Baee
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran; Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Ahmad Karkhah
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran; Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, India
| | - Soheil Ebrahimpour
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Hamid Reza Nouri
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran; Immunoregulation Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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8
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Mohammad Hasani S, Mohammadi E, Sekhavati MH. Region-Based Epitope Prediction, Docking and Dynamic Studies of OMP31 as a Dominant Antigen in Human and Sheep Brucella. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09847-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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9
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Validi M, Karkhah A, Prajapati VK, Nouri HR. Immuno-informatics based approaches to design a novel multi epitope-based vaccine for immune response reinforcement against Leptospirosis. Mol Immunol 2018; 104:128-138. [PMID: 30448609 DOI: 10.1016/j.molimm.2018.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 09/04/2018] [Accepted: 11/08/2018] [Indexed: 01/03/2023]
Abstract
Leptospirosis is known as a zoonotic disease of global importance originated from infection with the spirochete bacterium Leptospira. Although several leptospirosis vaccines have been tested, the vaccination is relatively unsuccessful in clinical application despite decades of research. Therefore, this study was conducted to construct a novel multi-epitope based vaccine against leptospirosis by using Hap1, LigA, LAg42, SphH and HSP58 antigens. T cell and IFN gamma epitopes were predicted from these antigens. In addition, to induce strong CD4+ helper T lymphocytes (HTLs) responses, Pan HLA DR-binding epitope (PADRE) and helper epitopes selected from Tetanus toxin fragment C (TTFrC) were applied. Moreover, for boosting immune response, Heparin-Binding Hemagglutinin (HBHA), a novel TLR4 agonist was added to the construct as an adjuvant. Finally, selected epitopes were linked together using EAAAK, GPGPG, AAY and HEYGAEALERAG linkers. Based on the predicted epitopes, a multi-epitope vaccine was construct with 490 amino acids. Physico-chemical properties, secondary and tertiary structures, stability, intrinsic protein disorder, solubility, and allergenicity of this vaccine construct were assessed by applying immunoinformatics analyses. A soluble, and non-allergic protein with a molecular weight of 53.476 kDa was obtained. Further analyses validated the stability of the chimeric protein and the predicted epitopes in the chimeric vaccine indicated strong potential to induce B-cell and T-cell mediated immune response. Therefore, immunoinformatics analysis showed that the modeled multi-epitope vaccine can properly stimulate the both T and B cells immune responses and could potentially be used for prophylactic or therapeutic usages.
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Affiliation(s)
- Majid Validi
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Ahmad Karkhah
- Student Research Committee, School of Medicine, Babol University of Medical Sciences, Babol, Iran; Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, India
| | - Hamid Reza Nouri
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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Tourani M, Karkhah A, Najafi A. Development of an epitope-based vaccine inhibiting immune cells rolling and migration against atherosclerosis using in silico approaches. Comput Biol Chem 2017; 70:156-163. [DOI: 10.1016/j.compbiolchem.2017.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/07/2017] [Accepted: 08/23/2017] [Indexed: 12/21/2022]
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11
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Saadi M, Karkhah A, Nouri HR. Development of a multi-epitope peptide vaccine inducing robust T cell responses against brucellosis using immunoinformatics based approaches. INFECTION GENETICS AND EVOLUTION 2017; 51:227-234. [PMID: 28411163 DOI: 10.1016/j.meegid.2017.04.009] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/08/2017] [Accepted: 04/10/2017] [Indexed: 01/18/2023]
Abstract
Current investigations have demonstrated that a multi-epitope peptide vaccine targeting multiple antigens could be considered as an ideal approach for prevention and treatment of brucellosis. According to the latest findings, the most effective immunogenic antigens of brucella to induce immune responses are included Omp31, BP26, BLS, DnaK and L7-L12. Therefore, in the present study, an in silico approach was used to design a novel multi-epitope vaccine to elicit a desirable immune response against brucellosis. First, five novel T-cell epitopes were selected from Omp31, BP26, BLS, DnaK and L7-L12 proteins using different servers. In addition, helper epitopes selected from Tetanus toxin fragment C (TTFrC) were applied to induce CD4+ helper T lymphocytes (HTLs) responses. Selected epitopes were fused together by GPGPG linkers to facilitate the immune processing and epitope presentation. Moreover, cholera toxin B (CTB) was linked to N terminal of vaccine construct as an adjuvant by using EAAAK linker. A multi-epitope vaccine was designed based on predicted epitopes which was 377 amino acid residues in length. Then, the physico-chemical properties, secondary and tertiary structures, stability, intrinsic protein disorder, solubility and allergenicity of this multi-epitope vaccine were assessed using immunoinformatics tools and servers. Based on obtained results, a soluble, and non-allergic protein with 40.59kDa molecular weight was constructed. Expasy ProtParam classified this chimeric protein as a stable protein and also 89.8% residues of constructed vaccine were located in favored regions of the Ramachandran plot. Furthermore, this multi-epitope peptide vaccine was able to strongly induce T cell and B-cell mediated immune responses. In conclusion, immunoinformatics analysis indicated that this multi-epitope peptide vaccine can be effectively expressed and potentially be used for prophylactic or therapeutic usages against brucellosis.
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Affiliation(s)
- Mahdiye Saadi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran; Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Ahmad Karkhah
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran; Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Hamid Reza Nouri
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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12
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Karkhah A, Saadi M, Nouri HR. In silico analyses of heat shock protein 60 and calreticulin to designing a novel vaccine shifting immune response toward T helper 2 in atherosclerosis. Comput Biol Chem 2017; 67:244-254. [PMID: 28189968 DOI: 10.1016/j.compbiolchem.2017.01.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/17/2017] [Accepted: 01/27/2017] [Indexed: 02/07/2023]
Abstract
Recent experiments demonstrated that atherosclerosis is a Th1 dominant autoimmune condition, whereas Th2 cells are rarely detected within the atherosclerotic lesions. Several studies have indicated that Th2 type cytokines could be effective in the reduction and stabilization of atherosclerotic plaque. Therefore, the modulation of the adaptive immune response by shifting immune responses toward Th2 cells by a novel vaccine could represent a promising approach to prevent from progression and thromboembolic events in coronary artery disease. In the present study, an in silico approach was applied to design a novel multi-epitope vaccine to elicit a desirable immune response against atherosclerosis. Six novel IL-4 inducing epitopes were selected from HSP60 and calreticulin proteins. To enhance epitope presentation, IL-4 inducing epitopes were linked together by AAY and HEYGAEALERAG linkers. In addition, helper epitopes selected from Tetanus toxin fragment C (TTFrC) were applied to induce CD4+ helper T lymphocytes (HTLs) responses. Moreover, cholera toxin B (CTB) was employed as an adjuvant. A multi-epitope construct was designed based on predicted epitopes which was 320 residues in length. Then, the physico-chemical properties, secondary and tertiary structures, stability, intrinsic protein disorder, solubility and allergenicity of this chimeric protein were analyzed using bioinformatics tools and servers. Based on bioinformatics analysis, a soluble, and non-allergic protein with 35.405kDa molecular weight was designed. Expasy ProtParam classified this chimeric protein as a stable protein. In addition, predicted epitopes in the chimeric vaccine indicated strong potential to induce B-cell mediated immune response and shift immune responses toward protective Th2 immune response. Various in silico analyses indicate that this vaccine is a qualified candidate for improvement of atherosclerosis by inducing immune responses toward T helper 2.
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Affiliation(s)
- Ahmad Karkhah
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran; Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Mahdiye Saadi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Hamid Reza Nouri
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
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13
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Webster GR, Teh AYH, Ma JKC. Synthetic gene design-The rationale for codon optimization and implications for molecular pharming in plants. Biotechnol Bioeng 2016; 114:492-502. [PMID: 27618314 DOI: 10.1002/bit.26183] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 08/10/2016] [Accepted: 09/05/2016] [Indexed: 12/14/2022]
Abstract
Degeneracy in the genetic code allows multiple codon sequences to encode the same protein. Codon usage bias in genes is the term given to the preferred use of particular synonymous codons. Synonymous codon substitutions had been regarded as "silent" as the primary structure of the protein was not affected; however, it is now accepted that synonymous substitutions can have a significant effect on heterologous protein expression. Codon optimization, the process of altering codons within the gene sequence to improve recombinant protein expression, has become widely practised. Multiple inter-linked factors affecting protein expression need to be taken into consideration when optimizing a gene sequence. Over the years, various computer programmes have been developed to aid in the gene sequence optimization process. However, as the rulebook for altering codon usage to affect protein expression is still not completely understood, it is difficult to predict which strategy, if any, will design the "optimal" gene sequence. In this review, codon usage bias and factors affecting codon selection will be discussed and the evidence for codon optimization impact will be reviewed for recombinant protein expression using plants as a case study. These developments will be relevant to all recombinant expression systems; however, molecular pharming in plants is an area which has consistently encountered difficulties with low levels of recombinant protein expression, and should benefit from an evidence based rational approach to synthetic gene design. Biotechnol. Bioeng. 2017;114: 492-502. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Gina R Webster
- Molecular Immunology Unit, Institute for Infection and Immunity, St. George's University of London, SW17 0RE, London, UK
| | - Audrey Y-H Teh
- Molecular Immunology Unit, Institute for Infection and Immunity, St. George's University of London, SW17 0RE, London, UK
| | - Julian K-C Ma
- Molecular Immunology Unit, Institute for Infection and Immunity, St. George's University of London, SW17 0RE, London, UK
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