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Aleem MT, Munir F, Shakoor A, Gao F. mRNA vaccines against infectious diseases and future direction. Int Immunopharmacol 2024; 135:112320. [PMID: 38788451 DOI: 10.1016/j.intimp.2024.112320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/28/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
Vaccines are used for the control of infectious diseases of animals. Over other types of vaccinations like live attenuated or killed vaccines, mRNA-based vaccines have significant advantages. As only a small portion of the pathogen's genetic material is employed and the dose rate of mRNA-based vaccines is low, there is the least possibility that the pathogen will reverse itself. A carrier or vehicle that shields mRNA-based vaccines from the host's cellular RNases is necessary for their delivery. mRNA vaccines have been shown to be effective and to induce both a cell-mediated immune response and a humoral immune response in clinical trials against various infectious diseases (viral and parasitic) affecting the animals, including rabies, foot and mouth disease, toxoplasmosis, Zikavirus, leishmaniasis, and COVID-19. The current review aims to highlight the use of mRNA-based vaccines both in viral and parasitic diseases of animals.
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Affiliation(s)
- Muhammad Tahir Aleem
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China; Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Clevaland State University, Clevaland, OH 44115, USA.
| | - Furqan Munir
- Department of Parasitology, Faculty of Veterinary Science, University of Agriculture, Faisalabad 38040, Pakistan
| | - Amna Shakoor
- Department of Anatomy, Faculty of Veterinary Science, University of Agriculture, Faisalabad 38040, Pakistan
| | - Fenfei Gao
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China.
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Bukhari SNH, Elshiekh E, Abbas M. Physicochemical properties-based hybrid machine learning technique for the prediction of SARS-CoV-2 T-cell epitopes as vaccine targets. PeerJ Comput Sci 2024; 10:e1980. [PMID: 38686005 PMCID: PMC11057572 DOI: 10.7717/peerj-cs.1980] [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: 01/19/2024] [Accepted: 03/15/2024] [Indexed: 05/02/2024]
Abstract
Majority of the existing SARS-CoV-2 vaccines work by presenting the whole pathogen in the attenuated form to immune system to invoke an immune response. On the other hand, the concept of a peptide based vaccine (PBV) is based on the identification and chemical synthesis of only immunodominant peptides known as T-cell epitopes (TCEs) to induce a specific immune response against a particular pathogen. However PBVs have received less attention despite holding huge untapped potential for boosting vaccine safety and immunogenicity. To identify these TCEs for designing PBV, wet-lab experiments are difficult, expensive, and time-consuming. Machine learning (ML) techniques can accurately predict TCEs, saving time and cost for speedy vaccine development. This work proposes novel hybrid ML techniques based on the physicochemical properties of peptides to predict SARS-CoV-2 TCEs. The proposed hybrid ML technique was evaluated using various ML model evaluation metrics and demonstrated promising results. The hybrid technique of decision tree classifier with chi-squared feature weighting technique and forward search optimal feature searching algorithm has been identified as the best model with an accuracy of 98.19%. Furthermore, K-fold cross-validation (KFCV) was performed to ensure that the model is reliable and the results indicate that the hybrid random forest model performs consistently well in terms of accuracy with respect to other hybrid approaches. The predicted TCEs are highly likely to serve as promising vaccine targets, subject to evaluations both in-vivo and in-vitro. This development could potentially save countless lives globally, prevent future epidemic-scale outbreaks, and reduce the risk of mutation escape.
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Affiliation(s)
- Syed Nisar Hussain Bukhari
- National Institute of Electronics and Information Technology (NIELIT), Srinagar, Jammu and Kashmir, India
| | - E. Elshiekh
- Department of Radiological Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha, Saudi Arabia
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Ghafoor D, Zeb A, Ali SS, Ali M, Akbar F, Ud Din Z, Ur Rehman S, Suleman M, Khan W. Immunoinformatic based designing of potential immunogenic novel mRNA and peptide-based prophylactic vaccines against H5N1 and H7N9 avian influenza viruses. J Biomol Struct Dyn 2024; 42:3641-3658. [PMID: 37222664 DOI: 10.1080/07391102.2023.2214228] [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: 10/31/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
Influenza viruses are the most common cause of serious respiratory illnesses worldwide and are responsible for a significant number of annual fatalities. Therefore, it is crucial to look for new immunogenic sites that might trigger an effective immune response. In the present study, bioinformatics tools were used to design mRNA and multiepitope-based vaccines against H5N1 and H7N9 subtypes of avian influenza viruses. Several Immunoinformatic tools were employed to extrapolate T and B lymphocyte epitopes of HA and NA proteins of both subtypes. The molecular docking approach was used to dock the selected HTL and CTL epitopes with the corresponding MHC molecules. Eight (8) CTL, four (4) HTL, and Six (6) linear B cell epitopes were chosen for the structural arrangement of mRNA and of peptide-based prophylactic vaccine designs. Different physicochemical characteristics of the selected epitopes fitted with suitable linkers were analyzed. High antigenic, non-toxic, and non-allergenic features of the designed vaccines were noted at a neutral physiological pH. Codon optimization tool was used to check the GC content and CAI value of constructed MEVC-Flu vaccine, which were recorded to be 50.42% and 0.97 respectively. the GC content and CAI value verify the stable expression of vaccine in pET28a + vector. In-silico immunological simulation the MEVC-Flu vaccine construct revealed a high level of immune responses. The molecular dynamics simulation and docking results confirmed the stable interaction of TLR-8 and MEVC-Flu vaccine. Based on these parameters, vaccine constructs can be regarded as an optimistic choice against H5N1 and H7N9 strains of the influenza virus. Further experimental testing of these prophylactic vaccine designs against pathogenic avian influenza strains may clarify their safety and efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dawood Ghafoor
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Wuhan, Hubei, China
| | - Adnan Zeb
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fazal Akbar
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Zia Ud Din
- Center for Advanced Studies in Vaccinology and Biotechnology, University of Balochistan Quetta, Quetta, Pakistan
| | - Shoaib Ur Rehman
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Wajid Khan
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
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Ugwu CC, Hair-Bejo M, Nurulfiza MI, Omar AR, Ideris A. Attenuation and molecular characterization of fowl adenovirus 8b propagated in a bioreactor and its immunogenicity, efficacy, and virus shedding in broiler chickens. Vet World 2024; 17:744-755. [PMID: 38798289 PMCID: PMC11111708 DOI: 10.14202/vetworld.2024.744-755] [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: 10/22/2023] [Accepted: 03/05/2024] [Indexed: 05/29/2024] Open
Abstract
Background and Aim Live-attenuated vaccines are the most successful type of vaccine and could be useful in controlling fowl adenovirus (FAdV) 8b infection. This study aimed to attenuate, molecularly characterize, and determine the immunogenicity, efficacy, and challenge virus shedding in broiler chickens. Materials and Methods The FAdV 8b isolate (UPM08136) was passaged onto chicken embryo liver (CEL) cells until attenuation. We sequenced and analyzed the hexon and fiber genes of the passage isolates. The attenuated bioreactor-passage isolate was inoculated into 1-day-old broiler chickens with (attenuated and inactivated) and without booster groups and challenged. Body weight (BW), liver weight (LW), liver: body weight ratio (LBR), FAdV antibody titers, T-lymphocyte subpopulation in the liver, spleen, and thymus, and challenge virus load and shedding were measured. Results Typical cytopathic effects with novel genetic changes on CEL cells were observed. The uninoculated control-challenged (UCC) group had significantly lower BW and higher LW and LBR than the inoculated groups. A significantly higher FAdV antibody titer was observed in the challenged non-booster and attenuated booster groups than in the UCC group. T cells in the spleen and thymus of the liver of inoculated chickens were higher than uninoculated control group levels at all-time points and at different times. A significantly higher FAdV challenge virus load was observed in the liver and shedding in the cloaca of UCC chickens than in non-booster chickens. Conclusion The FAdV 8b isolate was successfully attenuated, safe, and immunogenic. It reduces virus shedding and is effective and recommended as a vaccine against FAdV infection in broiler chickens.
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Affiliation(s)
- Chidozie C. Ugwu
- Department of Veterinary Pathology and Microbiology Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Animal Science and Technology, Federal University of Technology, Owerri 460114, Imo State, Nigeria
| | - Mohd Hair-Bejo
- Department of Veterinary Pathology and Microbiology Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Mat I. Nurulfiza
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Abdul R. Omar
- Department of Veterinary Pathology and Microbiology Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Aini Ideris
- Department of Veterinary Pathology and Microbiology Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
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Mu S, Chen L, Dong H, Li S, Zhang Y, Yin S, Tian Y, Ding Y, Sun S, Shang S, Guo H. Enhanced antigen-specific CD8 T cells contribute to early protection against FMDV through swine DC vaccination. J Virol 2024; 98:e0200223. [PMID: 38289108 PMCID: PMC10878267 DOI: 10.1128/jvi.02002-23] [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: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024] Open
Abstract
Foot-and-mouth disease virus (FMDV) remains a challenge for cloven-hooved animals. The currently licensed FMDV vaccines induce neutralizing antibody (NAb)-mediated protection but show defects in the early protection. Dendritic cell (DC) vaccines have shown great potency in inducing rapid T-cell immunity in humans and mice. Whether DC vaccination could enhance early protection against FMDV has not been elaborately explored in domestic pigs. In this study, we employed DC vaccination as an experimental approach to study the roles of cellular immunity in the early protection against FMDV in pigs. Autologous DCs were differentiated from the periphery blood mononuclear cells of each pig, pulsed with inactivated FMDV (iFMDV-DC) and treated with LPS, and then injected into the original pigs. The cellular immune responses and protective efficacy elicited by the iFMDV-DC were examined by multicolor flow cytometry and tested by FMDV challenge. The results showed that autologous iFMDV-DC immunization induced predominantly FMDV-specific IFN-γ-producing CD4+ T cells and cytotoxic CD8+ T cells (CTLs), high NAb titers, compared to the inactivated FMDV vaccine, and accelerated the development of memory CD4 and CD8 T cells, which was concomitantly associated with early protection against FMDV virulent strain in pigs. Such early protection was associated with the rapid proliferation of secondary T-cell response after challenge and significantly contributed by secondary CD8 effector memory T cells. These results demonstrated that rapid induction of cellular immunity through DC immunization is important for improving early protection against FMDV. Enhancing cytotoxic CD8+ T cells may facilitate the development of more effective FMDV vaccines.IMPORTANCEAlthough the currently licensed FMDV vaccines provide NAb-mediated protection, they have defects in early immune protection, especially in pigs. In this study, we demonstrated that autologous swine DC immunization augmented the cellular immune response and induced an early protective response against FMDV in pigs. This approach induced predominantly FMDV-specific IFN-γ-producing CD4+ T cells and cytotoxic CD8+ T cells, high NAb titers, and rapid development of memory CD4 and CD8 T cells. Importantly, the early protection conferred by this DC immunization is more associated with secondary CD8+ T response rather than NAbs. Our findings highlighted the importance of enhancing cytotoxic CD8+ T cells in early protection to FMDV in addition to Th1 response and identifying a strategy or adjuvant comparable to the DC vaccine might be a future direction for improving the current FMDV vaccines.
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Affiliation(s)
- Suyu Mu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Lingbo Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hu Dong
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shuai Li
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Yun Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shuanghui Yin
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yunfei Tian
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Yaozhong Ding
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shiqi Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shaobin Shang
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China
| | - Huichen Guo
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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Ugwu CC, Hair-Bejo M, Nurulfiza MI, Omar AR, Ideris A. Efficacy, immunogenicity, and virus shedding in broiler chickens inoculated with live attenuated fowl adenovirus serotype 8b propagated a bioreactor. Open Vet J 2024; 14:617-629. [PMID: 38549580 PMCID: PMC10970115 DOI: 10.5455/ovj.2024.v14.i2.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/15/2024] [Indexed: 04/02/2024] Open
Abstract
Background Fowl adenovirus (FAdV) 8b causes huge economic losses in the poultry industry worldwide. Attenuated FAdV 8b could be useful in preventing FAdV infections globally and scale-up obstacles could be solved by bioreactor technology. Aim This study was carried out to attenuate the FAdV 8b isolate, propagate it in a bioreactor, molecularly characterize the passage isolates, and determine the immunogenicity, efficacy, and shedding of the virus of chickens. Methods FAdV serotype 8b (UPM11142) isolate was passaged on chicken embryo liver (CEL) cells until attenuation and propagated in a bioreactor (UPM11142P20B1). Hexon and fiber genes of the isolates were sequenced and analyzed. UPM11142P20B1 was administered to 116-day-old broiler chickens divided into four groups, A (control), B (non-booster), C (booster with UPM11142P20B1), and D (booster with inactivated UPM11142P5B1). Eight chickens from each group were challenged. Body weight (BW) and liver weight (LW), liver: BW ratio (LBR), FAdV antibody titer, T lymphocyte sub-populations in the liver, spleen and thymus; and challenge virus load in the liver and shedding in cloaca were measured at weekly intervals. Results The isolate caused typical cytopathic effects on CEL cells typical of FAdV. Novel molecular changes in the genes occurred which could be markers for FAdV 8b attenuation. BW, LW, and LBR were similar among groups throughout the trial but the uninoculated control-challenged group (UCC) had significantly higher LBR than the inoculated and challenged groups at 35 dpi. Non-booster group had higher FAdV antibodies at all time points than the uninoculated control group (UCG); and the challenged booster groups had higher titer at 35 dpi than UCC. T lymphocytes increased at different time-points in the liver of inoculated chickens, and in the spleen and thymus as well, and was higher in the organs of inoculated challenged groups than the UCC. There was a significantly higher challenge virus load in the liver and cloaca of UCC chickens than in the non-booster chickens. Conclusion UPM11142P20B1 was safe, efficacious, significantly reduced shedding, and is recommended as a candidate vaccine in the prevention and control of FAdV 8b infections in broiler chickens.
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Affiliation(s)
- Chidozie C. Ugwu
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Animal Science and Technology, Federal University of Technology, Owerri, Imo State, Nigeria
| | - Mohd Hair-Bejo
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mat I. Nurulfiza
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Abdul R. Omar
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Aini Ideris
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569310. [PMID: 38077000 PMCID: PMC10705405 DOI: 10.1101/2023.11.29.569310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The precise prediction of Major Histocompatibility Complex (MHC)-peptide complex structures is pivotal for understanding cellular immune responses and advancing vaccine design. In this study, we enhanced AlphaFold's capabilities by fine-tuning it with a specialized dataset comprised by exclusively high-resolution MHC-peptide crystal structures. This tailored approach aimed to address the generalist nature of AlphaFold's original training, which, while broad-ranging, lacked the granularity necessary for the high-precision demands of MHC-peptide interaction prediction. A comparative analysis was conducted against the homology-modeling-based method Pandora [13], as well as the AlphaFold multimer model [8]. Our results demonstrate that our fine-tuned model outperforms both in terms of RMSD (median value is 0.65 Å) but also provides enhanced predicted lDDT scores, offering a more reliable assessment of the predicted structures. These advances have substantial implications for computational immunology, potentially accelerating the development of novel therapeutics and vaccines by providing a more precise computational lens through which to view MHC-peptide interactions.
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Affiliation(s)
- Ernest Glukhov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Dmytro Kalitin
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Darya Stepanenko
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Yimin Zhu
- Department of Computer Science, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Thu Nguyen
- Department of Computer Science, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - George Jones
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, 02215, MA, USA
| | - Ken A. Dill
- Department of Chemistry, Stony Brook University, Stony Brook, 11794, NY, USA
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Dzmitry Padhorny
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, 11794, NY, USA
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Sarfraz A, Wara TU, Sheheryar, Chen K, Ansari SH, Zaman A, Nishan U, Iqbal A, Ullah R, Ali EA, Shah M, Ojha SC. Structural informatics approach for designing an epitope-based vaccine against the brain-eating Naegleria fowleri. Front Immunol 2023; 14:1284621. [PMID: 37965306 PMCID: PMC10642955 DOI: 10.3389/fimmu.2023.1284621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Primary Amoebic Meningoencephalitis (PAM), a severe lethal brain disease, is caused by a parasite, Naegleria fowleri, also known as the "brain-eating amoeba". The chances of a patient's recovery after being affected by this parasite are very low. Only 5% of people are known to survive this life-threatening infection. Despite the fact that N. fowleri causes a severe, fatal infection, there is no proper treatment available to prevent or cure it. In this context, it is necessary to formulate a potential vaccine that could be able to combat N. fowleri infection. The current study aimed at developing a multi-epitope subunit vaccine against N. fowleri by utilizing immunoinformatics techniques and reverse vaccinology approaches. The T- and B-cell epitopes were predicted by various tools. In order to choose epitopes with the ability to trigger both T- and B-cell-mediated immune responses, the epitopes were put through a screening pipeline including toxicity, antigenicity, cytokine-inductivity, and allergenicity analysis. Three vaccine constructs were designed from the generated epitopes linked with linkers and adjuvants. The modeled vaccines were docked with the immune receptors, where vaccine-1 showed the highest binding affinity. Binding affinity and stability of the docked complex were confirmed through normal mode analysis and molecular dynamic simulations. Immune simulations developed the immune profile, and in silico cloning affirmed the expression probability of the vaccine construct in Escherichia coli (E. coli) strain K12. This study demonstrates an innovative preventative strategy for the brain-eating amoeba by developing a potential vaccine through immunoinformatics and reverse vaccinology approaches. This study has great preventive potential for Primary Amoebic Meningoencephalitis, and further research is required to assess the efficacy of the designed vaccine.
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Affiliation(s)
- Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Tehreem Ul Wara
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Sheheryar
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Ke Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | | | - Aqal Zaman
- Department of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Anwar Iqbal
- Department of Chemical Sciences, University of Lakki Marwat, Khyber Pakhtunkhwa, Pakistan
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Essam A. Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Wellington D, Yin Z, Yu Z, Heilig R, Davis S, Fischer R, Felce SL, Antoun E, Hublitz P, Beveridge R, Dong D, Liu G, Yao X, Peng Y, Kessler BM, Dong T. SARS-CoV-2 mutations affect antigen processing by the proteasome to alter CD8 + T cell responses. Heliyon 2023; 9:e20076. [PMID: 37842619 PMCID: PMC10570596 DOI: 10.1016/j.heliyon.2023.e20076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 08/22/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Mutations within viral epitopes can result in escape from T cells, but the contribution of mutations in flanking regions of epitopes in SARS-CoV-2 has not been investigated. Focusing on two SARS-CoV-2 nucleoprotein CD8+ epitopes, we investigated the contribution of these flanking mutations to proteasomal processing and T cell activation. We found decreased NP9-17-B*27:05 CD8+ T cell responses to the NP-Q7K mutation, likely due to a lack of efficient epitope production by the proteasome, suggesting immune escape caused by this mutation. In contrast, NP-P6L and NP-D103 N/Y mutations flanking the NP9-17-B*27:05 and NP105-113-B*07:02 epitopes, respectively, increased CD8+ T cell responses associated with enhanced epitope production by the proteasome. Our results provide evidence that SARS-CoV-2 mutations outside the epitope could have a significant impact on proteasomal processing, either contributing to T cell escape or enhancement that may be exploited for future vaccine design.
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Affiliation(s)
- Dannielle Wellington
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Zixi Yin
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Zhanru Yu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Raphael Heilig
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Simon Davis
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Roman Fischer
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Elie Antoun
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Philip Hublitz
- Genome Engineering Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Ryan Beveridge
- Virus Screening Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Danning Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Guihai Liu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Xuan Yao
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Yanchun Peng
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Benedikt M. Kessler
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
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10
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Pu T, Peddle A, Zhu J, Tejpar S, Verbandt S. Neoantigen identification: Technological advances and challenges. Methods Cell Biol 2023; 183:265-302. [PMID: 38548414 DOI: 10.1016/bs.mcb.2023.06.005] [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] [Indexed: 04/02/2024]
Abstract
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.
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Affiliation(s)
- Ting Pu
- Digestive Oncology Unit, KULeuven, Leuven, Belgium
| | | | - Jingjing Zhu
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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11
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Khalid K, Poh CL. The development of DNA vaccines against SARS-CoV-2. Adv Med Sci 2023; 68:213-226. [PMID: 37364379 PMCID: PMC10290423 DOI: 10.1016/j.advms.2023.05.003] [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: 01/20/2023] [Revised: 04/07/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND The COVID-19 pandemic exerted significant impacts on public health and global economy. Research efforts to develop vaccines at warp speed against SARS-CoV-2 led to novel mRNA, viral vectored, and inactivated vaccines being administered. The current COVID-19 vaccines incorporate the full S protein of the SARS-CoV-2 Wuhan strain but rapidly emerging variants of concern (VOCs) have led to significant reductions in protective efficacies. There is an urgent need to develop next-generation vaccines which could effectively prevent COVID-19. METHODS PubMed and Google Scholar were systematically reviewed for peer-reviewed papers up to January 2023. RESULTS A promising solution to the problem of emerging variants is a DNA vaccine platform since it can be easily modified. Besides expressing whole protein antigens, DNA vaccines can also be constructed to include specific nucleotide genes encoding highly conserved and immunogenic epitopes from the S protein as well as from other structural/non-structural proteins to develop effective vaccines against VOCs. DNA vaccines are associated with low transfection efficiencies which could be enhanced by chemical, genetic, and molecular adjuvants as well as delivery systems. CONCLUSIONS The DNA vaccine platform offers a promising solution to the design of effective vaccines. The challenge of limited immunogenicity in humans might be solved through the use of genetic modifications such as the addition of nuclear localization signal (NLS) peptide gene, strong promoters, MARs, introns, TLR agonists, CD40L, and the development of appropriate delivery systems utilizing nanoparticles to increase uptake by APCs in enhancing the induction of potent immune responses.
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Affiliation(s)
- Kanwal Khalid
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia.
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12
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Matos AS, Invenção MDCV, Moura IAD, Freitas ACD, Batista MVDA. Immunoinformatics applications in the development of therapeutic vaccines against human papillomavirus-related infections and cervical cancer. Rev Med Virol 2023; 33:e2463. [PMID: 37291746 DOI: 10.1002/rmv.2463] [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: 03/15/2023] [Revised: 05/09/2023] [Accepted: 05/27/2023] [Indexed: 06/10/2023]
Abstract
The human papillomavirus (HPV) represents the most prevalent sexually transmitted infectious agent worldwide. HPV penetrates the epithelium through microlesions and establishes an infectious focus that can lead to the development of cervical cancer. Prophylactic HPV vaccines are available, but do not affect already-established infections. Using in silico prediction tools is a promising strategy for identifying and selecting vaccine candidate T cell epitopes. An advantage of this strategy is that epitopes can be selected according to the degree of conservation within a group of antigenic proteins. This makes achieving comprehensive genotypic coverage possible with a small set of epitopes. Therefore, this paper revises the general characteristics of HPV biology and the current knowledge on developing therapeutic peptide vaccines against HPV-related infections and cervical cancer.
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Affiliation(s)
- Alexandre Santos Matos
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, Sao Cristovao, Brazil
| | - Maria da Conceição Viana Invenção
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Ingrid Andrêssa de Moura
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Antonio Carlos de Freitas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Marcus Vinicius de Aragão Batista
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, Sao Cristovao, Brazil
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13
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Federico L, Tvedt THA, Gainullin M, Osen JR, Chaban V, Lund KP, Tietze L, Tran TT, Lund-Johansen F, Kared H, Lind A, Vaage JT, Stratford R, Tennøe S, Malone B, Clancy T, Myhre AEL, Gedde-Dahl T, Munthe LA. Robust spike-specific CD4 + and CD8 + T cell responses in SARS-CoV-2 vaccinated hematopoietic cell transplantation recipients: a prospective, cohort study. Front Immunol 2023; 14:1210899. [PMID: 37503339 PMCID: PMC10369799 DOI: 10.3389/fimmu.2023.1210899] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/13/2023] [Indexed: 07/29/2023] Open
Abstract
Poor overall survival of hematopoietic stem cell transplantation (HSCT) recipients who developed COVID-19 underlies the importance of SARS-CoV-2 vaccination. Previous studies of vaccine efficacy have reported weak humoral responses but conflicting results on T cell immunity. Here, we have examined the relationship between humoral and T cell response in 48 HSCT recipients who received two doses of Moderna's mRNA-1273 or Pfizer/BioNTech's BNT162b2 vaccines. Nearly all HSCT patients had robust T cell immunity regardless of protective humoral responses, with 18/48 (37%, IQR 8.679-5601 BAU/mL) displaying protective IgG anti-receptor binding domain (RBD) levels (>2000 BAU/mL). Flow cytometry analysis of activation induced markers (AIMs) revealed that 90% and 74% of HSCT patients showed reactivity towards immunodominant spike peptides in CD8+ and CD4+ T cells, respectively. The response rate increased to 90% for CD4+ T cells as well when we challenged the cells with a complete set of overlapping peptides spanning the entire spike protein. T cell response was detectable as early as 3 months after transplant, but only CD4+ T cell reactivity correlated with IgG anti-RBD level and time after transplantation. Boosting increased seroconversion rate, while only one patient developed COVID-19 requiring hospitalization. Our data suggest that HSCT recipients with poor serological responses were protected from severe COVID-19 by vaccine-induced T cell responses.
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Affiliation(s)
- Lorenzo Federico
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Murat Gainullin
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Julie Røkke Osen
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Viktoriia Chaban
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Katrine Persgård Lund
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lisa Tietze
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- ImmunoLingo Convergence Center, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Trung The Tran
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- ImmunoLingo Convergence Center, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Fridtjof Lund-Johansen
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- ImmunoLingo Convergence Center, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Hassen Kared
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Andreas Lind
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - John Torgils Vaage
- ImmunoLingo Convergence Center, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | | | | | - Anders Eivind Leren Myhre
- Department of Haematology, Oslo University Hospital, Oslo, Norway
- ImmunoLingo Convergence Center, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Ludvig André Munthe
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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14
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Palmowski J, Kohnhorst S, Bauer P, Puta C, Haunhorst S, Gebhardt K, Reichel T, Keller C, Huber M, Raifer H, Krüger K. T-cell-derived TNF-α and a cluster of immunological parameters from plasma allow a separation between SARS-CoV-2 convalescent versus vaccinated elite athletes. Front Physiol 2023; 14:1203983. [PMID: 37427401 PMCID: PMC10324374 DOI: 10.3389/fphys.2023.1203983] [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: 04/11/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Guidelines for medical clearing after SARS-CoV-2 infection in elite athletes do not include T-cell immunity aspects despite its relevance in the course of COVID-19 disease. Therefore, we aimed to analyze T-cell-related cytokines before and after in-vitro activation of CD4+ T-cells. We sampled professional indoor sports athletes at medical clearing after SARS-CoV-2 infection obtaining clinical, fitness data, and serological data including CD4+ T-cell cytokines. All data were analyzed by principal component analysis and 2 × 2 repeated measures ANOVA. CD4+ T-cells were sampled for cell culture activation with anti-CD3/anti-CD28 tetramers. At medical clearing, CD4+ T-cells from convalescent athletes secreted increased levels of TNF-α 72 h after in-vitro activation compared to vaccinated athletes. IL-18 levels in plasma were elevated and a cluster of parameters differentiated convalescent from vaccinated athletes by 13 parameters at the timepoint of medical clearing. All clinical data indicate infection is resolved, while increased TNF-α may reflect altered proportions of peripheral T-cells as a hangover of infection.
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Affiliation(s)
- Jana Palmowski
- Department of Exercise Physiology and Sports Therapy, Institute of Sports Science, Justus Liebig University Giessen, Giessen, Germany
| | - Sarah Kohnhorst
- Center for Tumor and Immunology, Institute for Systems Immunology, Marburg, Germany
| | - Pascal Bauer
- Department of Cardiology and Angiology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Christian Puta
- Department of Sports Medicine and Health Promotion, Friedrich Schiller University Jena, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany
- Center for Interdisciplinary Prevention of Diseases Related to Professional Activities, Jena, Germany
| | - Simon Haunhorst
- Department of Sports Medicine and Health Promotion, Friedrich Schiller University Jena, Jena, Germany
| | - Kristina Gebhardt
- Department of Exercise Physiology and Sports Therapy, Institute of Sports Science, Justus Liebig University Giessen, Giessen, Germany
| | - Thomas Reichel
- Department of Exercise Physiology and Sports Therapy, Institute of Sports Science, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Keller
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Magdalena Huber
- Center for Tumor and Immunology, Institute for Systems Immunology, Marburg, Germany
| | - Hartmann Raifer
- Center for Tumor and Immunology, Institute for Systems Immunology, Marburg, Germany
| | - Karsten Krüger
- Department of Exercise Physiology and Sports Therapy, Institute of Sports Science, Justus Liebig University Giessen, Giessen, Germany
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15
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Nanda R, Gupta P, Giri AK, Patel S, Shah S, Mohapatra E. Serological Evaluation of Antibody Titers After Vaccination Against COVID-19 in 18-44-Year-Old Individuals at a Tertiary Care Center. Cureus 2023; 15:e40543. [PMID: 37465786 PMCID: PMC10350605 DOI: 10.7759/cureus.40543] [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] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Background The evaluation of the effectiveness of the vaccines (ChAdOx1-nCOV; Covishield and BBV-152; Covaxin) against coronavirus disease 2019 (COVID-19) is necessary to assess their efficacy. Because most antibodies that neutralize the coronavirus are directed against the receptor binding domain within the spike protein of the virus, these antibodies serve as markers for viral neutralizers and, in turn, for vaccine response. The present study aimed to evaluate the anti-neutralizing antibody (receptor binding domain (RBD)) and immunoglobulin G2 (IgG2) titers following the completion of the vaccination schedule (both vaccines) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Methodology In this longitudinal prospective study, conducted in a tertiary care center, 30 sequentially (two doses) vaccinated study participants between the ages of 18 and 44 years were sampled for estimation of anti-RBD antibody titer and IgG2. All statistical analysis was done using SPSS version 20 (IBM Corp., Armonk, NY, USA). P-values less than 0.05 were considered significant. Results There was a statistically significant increase in the neutralizing antibody titer after one month of the second dose (z = -4.597, p < 0.001), while a significant decrease was seen in the IgG2 levels (z = -3.075, p = 0.002). The results showed a significant neutralizing effect of the vaccines being used, with Covishield being more effective than Covaxin. The levels of neutralizing antibodies were independent of all demographic variables such as age, sex, and body mass index. Conclusions This study evaluating the efficacy of the two vaccines, namely, Covishield and Covaxin, is the first of its kind in the state of Chhattisgarh. The results of this study are similar to previous studies conducted in India and outside India, concluding that Covishield is a more effective vaccine.
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Affiliation(s)
- Rachita Nanda
- Biochemistry, All India Institute of Medical Sciences, Raipur, Raipur, IND
| | - Prishni Gupta
- Biochemistry, All India Institute of Medical Sciences, Raipur, Raipur, IND
| | - Anjan Kumar Giri
- Community and Family Medicine, All India Institute of Medical Sciences, Raipur, Raipur, IND
| | - Suprava Patel
- Biochemistry, All India Institute of Medical Sciences, Raipur, Raipur, IND
| | - Seema Shah
- Biochemistry, All India Institute of Medical Sciences, Raipur, Raipur, IND
| | - Eli Mohapatra
- Biochemistry, All India Institute of Medical Sciences, Raipur, Raipur, IND
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16
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Chang CC, Algaissi A, Lai CC, Chang CK, Lin JS, Wang YS, Chang BH, Chang YC, Chen WT, Fan YQ, Peng BH, Chao CY, Tzeng SR, Liang PH, Sung WC, Hu AYC, Chang SC, Chang MF. Subunit vaccines with a saponin-based adjuvant boost humoral and cellular immunity to MERS coronavirus. Vaccine 2023; 41:3337-3346. [PMID: 37085450 PMCID: PMC10083212 DOI: 10.1016/j.vaccine.2023.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) outbreaks have constituted a public health issue with drastic mortality higher than 34%, necessitating the development of an effective vaccine. During MERS-CoV infection, the trimeric spike protein on the viral envelope is primarily responsible for attachment to host cellular receptor, dipeptidyl peptidase 4 (DPP4). With the goal of generating a protein-based prophylactic, we designed a subunit vaccine comprising the recombinant S1 protein with a trimerization motif (S1-Fd) and examined its immunogenicity and protective immune responses in combination with various adjuvants. We found that sera from immunized wild-type and human DPP4 transgenic mice contained S1-specific antibodies that can neutralize MERS-CoV infection in susceptible cells. Vaccination with S1-Fd protein in combination with a saponin-based QS-21 adjuvant provided long-term humoral as well as cellular immunity in mice. Our findings highlight the significance of the trimeric S1 protein in the development of MERS-CoV vaccines and offer a suitable adjuvant, QS-21, to induce robust and prolonged memory T cell response.
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Affiliation(s)
- Chi-Chieh Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Abdullah Algaissi
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555, USA; Center for Biodefense and Emerging Disease, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chia-Chun Lai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan; College of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chun-Kai Chang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100025, Taiwan
| | - Jr-Shiuan Lin
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yi-Shiang Wang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Bo-Hau Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yu-Chiuan Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Wei-Ting Chen
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Yong-Qing Fan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Bi-Hung Peng
- Department of Neurosciences, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chih-Yu Chao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Shiou-Ru Tzeng
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Pi-Hui Liang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100025, Taiwan
| | - Wang-Chou Sung
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Alan Yung-Chih Hu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Shin C Chang
- Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Ming-Fu Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.
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17
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Tavukcuoglu E, Yanik H, Parveen M, Uluturk S, Durusu-Tanriover M, Inkaya AC, Akova M, Unal S, Esendagli G. Human memory T cell dynamics after aluminum-adjuvanted inactivated whole-virion SARS-CoV-2 vaccination. Sci Rep 2023; 13:4610. [PMID: 36944716 PMCID: PMC10028771 DOI: 10.1038/s41598-023-31347-8] [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: 11/22/2022] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
This study evaluates the functional capacity of CD4+ and CD8+ terminally-differentiated effector (TEMRA), central memory (TCM), and effector memory (TEM) cells obtained from the volunteers vaccinated with an aluminum-adjuvanted inactivated whole-virion SARS-CoV-2 vaccine (CoronaVac). The volunteers were followed for T cell immune responses following the termination of a randomized phase III clinical trial. Seven days and four months after the second dose of the vaccine, the memory T cell subsets were collected and stimulated by autologous monocyte-derived dendritic cells (mDCs) loaded with SARS-CoV-2 spike glycoprotein S1. Compared to the placebo group, memory T cells from the vaccinated individuals significantly proliferated in response to S1-loaded mDCs. CD4+ and CD8+ memory T cell proliferation was detected in 86% and 78% of the vaccinated individuals, respectively. More than 73% (after a short-term) and 62% (after an intermediate-term) of the vaccinated individuals harbored TCM and/or TEM cells that responded to S1-loaded mDCs by secreting IFN-γ. The expression of CD25, CD38, 4-1BB, PD-1, and CD107a indicated a modulation in the memory T cell subsets. Especially on day 120, PD-1 was upregulated on CD4+ TEMRA and TCM, and on CD8+ TEM and TCM cells; accordingly, proliferation and IFN-γ secretion capacities tended to decline after 4 months. In conclusion, the combination of inactivated whole-virion particles with aluminum adjuvants possesses capacities to induce functional T cell responses.
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Affiliation(s)
- Ece Tavukcuoglu
- Department of Basic Oncology, Hacettepe University Cancer Institute, 06100, Sihhiye, Ankara, Turkey
| | - Hamdullah Yanik
- Department of Basic Oncology, Hacettepe University Cancer Institute, 06100, Sihhiye, Ankara, Turkey
| | - Mubaida Parveen
- Department of Basic Oncology, Hacettepe University Cancer Institute, 06100, Sihhiye, Ankara, Turkey
| | - Sila Uluturk
- Department of Basic Oncology, Hacettepe University Cancer Institute, 06100, Sihhiye, Ankara, Turkey
| | - Mine Durusu-Tanriover
- Department of Internal Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Ahmet Cagkan Inkaya
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Murat Akova
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Serhat Unal
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Gunes Esendagli
- Department of Basic Oncology, Hacettepe University Cancer Institute, 06100, Sihhiye, Ankara, Turkey.
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18
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Anandhan G, Narkhede YB, Mohan M, Paramasivam P. Immunoinformatics aided approach for predicting potent cytotoxic T cell epitopes of respiratory syncytial virus. J Biomol Struct Dyn 2023; 41:12093-12105. [PMID: 36935101 DOI: 10.1080/07391102.2023.2191136] [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: 10/18/2022] [Accepted: 12/27/2022] [Indexed: 03/21/2023]
Abstract
Respiratory syncytial virus (RSV) is an infectious viral pathogen that causing serious respiratory infection in adults and neonates. The only approved therapies for RSV are the monoclonal antibodies palivizumab and its derivative motavizumab. Both treatments are expensive and require a hospital setting for administration. A vaccine represents a safe, effective and cheaper alternative for preventing RSV infection. In silico prediction methods have proven to be valuable in speeding up the process of vaccine design. In this study, reverse vaccinology methods were used to predict the cytotoxic T lymphocytes (CTL) epitopes from the entire proteome of RSV strain A. From amongst 3402 predicted binders to 12 high frequency alleles from the Immune Epitope Database (IEDB), 567 had positive processing scores while 327 epitopes were predicted to be immunogenic. A thorough examination of the 327 epitopes for possible antigenicity, allergenicity and toxicity resulted in 95 epitopes with desirable properties. A BLASTp analysis revealed 94 unique and non-homologous epitopes that were subjected to molecular docking across the 12 high frequency alleles. The final dataset of 70 epitopes contained 13 experimentally proven and 57 unique epitopes from a total of 11 RSV proteins. From our findings on selected T-cell-specific RSV antigen epitopes, notably the four epitopes confirmed to exhibit stable binding by molecular dynamics. The prediction pipeline used in this study represents an effective way to screen the immunogenic epitopes from other pathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gayathri Anandhan
- Department of Nanoscience and Technology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | | | - Manikandan Mohan
- College of Pharmacy, University of Georgia, Athens, USA
- Vaxigen International Research Center, Coimbatore, Tamil Nadu, India
| | - Premasudha Paramasivam
- Department of Nanoscience and Technology, Bharathiar University, Coimbatore, Tamil Nadu, India
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19
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Ishibashi Y, Sung CYW, Grati M, Chien W. Immune responses in the mammalian inner ear and their implications for AAV-mediated inner ear gene therapy. Hear Res 2023; 432:108735. [PMID: 36965335 DOI: 10.1016/j.heares.2023.108735] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/17/2023] [Accepted: 03/04/2023] [Indexed: 03/13/2023]
Abstract
Adeno-associated virus (AAV)-mediated inner ear gene therapy is a promising treatment option for hearing loss and dizziness. Several studies have shown that AAV-mediated inner ear gene therapy can be applied to various mouse models of hereditary hearing loss to improve their auditory function. Despite the increase in AAV-based animal and clinical studies aiming to rescue auditory and vestibular functions, little is currently known about the host immune responses to AAV in the mammalian inner ear. It has been reported that the host immune response plays an important role in the safety and efficacy of viral-mediated gene therapy. Therefore, in order for AAV-mediated gene therapy to be successfully and safely translated into patients with hearing loss and dizziness, a better understanding of the host immune responses to AAV in the inner ear is critical. In this review, we summarize the current knowledge on host immune responses to AAV-mediated gene therapy in the mammalian inner ear and other organ systems. We also outline the areas of research that are critical for ensuring the safety and efficacy of AAV-mediated inner ear gene therapy in future clinical and translational studies.
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Affiliation(s)
- Yasuko Ishibashi
- Inner Ear Gene Therapy Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, 35A 1F220, 35A Covent Dr., Bethesda, MD 20892, USA; Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, USA
| | - Cathy Yea Won Sung
- Laboratory of Hearing Biology and Therapeutics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, USA
| | - Mhamed Grati
- Inner Ear Gene Therapy Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, 35A 1F220, 35A Covent Dr., Bethesda, MD 20892, USA
| | - Wade Chien
- Inner Ear Gene Therapy Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, 35A 1F220, 35A Covent Dr., Bethesda, MD 20892, USA; Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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20
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Development of Next Generation Vaccines against SARS-CoV-2 and Variants of Concern. Viruses 2023; 15:v15030624. [PMID: 36992333 PMCID: PMC10057551 DOI: 10.3390/v15030624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
SARS-CoV-2 has caused the COVID-19 pandemic, with over 673 million infections and 6.85 million deaths globally. Novel mRNA and viral-vectored vaccines were developed and licensed for global immunizations under emergency approval. They have demonstrated good safety and high protective efficacy against the SARS-CoV-2 Wuhan strain. However, the emergence of highly infectious and transmissible variants of concern (VOCs) such as Omicron was associated with considerable reductions in the protective efficacy of the current vaccines. The development of next-generation vaccines that could confer broad protection against both the SARS-CoV-2 Wuhan strain and VOCs is urgently needed. A bivalent mRNA vaccine encoding the Spike proteins of both the SARS-CoV-2 Wuhan strain and the Omicron variant has been constructed and approved by the US FDA. However, mRNA vaccines are associated with instability and require an extremely low temperature (−80 °C) for storage and transportation. They also require complex synthesis and multiple chromatographic purifications. Peptide-based next-generation vaccines could be developed by relying on in silico predictions to identify peptides specifying highly conserved B, CD4+ and CD8+ T cell epitopes to elicit broad and long-lasting immune protection. These epitopes were validated in animal models and in early phase clinical trials to demonstrate immunogenicity and safety. Next-generation peptide vaccine formulations could be developed to incorporate only naked peptides, but they are costly to synthesize and production would generate extensive chemical waste. Continual production of recombinant peptides specifying immunogenic B and T cell epitopes could be achieved in hosts such as E. coli or yeast. However, recombinant protein/peptide vaccines require purification before administration. The DNA vaccine might serve as the most effective next-generation vaccine for low-income countries, since it does not require an extremely low temperature for storage or need extensive chromatographic purification. The construction of recombinant plasmids carrying genes specifying highly conserved B and T cell epitopes meant that vaccine candidates representing highly conserved antigenic regions could be rapidly developed. Poor immunogenicity of DNA vaccines could be overcome by the incorporation of chemical or molecular adjuvants and the development of nanoparticles for effective delivery.
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21
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Lin F, Lin X, Fu B, Xiong Y, Zaky MY, Wu H. Functional studies of HLA and its role in SARS-CoV-2: Stimulating T cell response and vaccine development. Life Sci 2023; 315:121374. [PMID: 36621539 PMCID: PMC9815883 DOI: 10.1016/j.lfs.2023.121374] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
In the biological immune process, the major histocompatibility complex (MHC) plays an indispensable role in the expression of HLA molecules in the human body when viral infection activates the T-cell response to remove the virus. Since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 2019, how to address and prevent SARS-CoV-2 has become a common problem facing all mankind. The T-cell immune response activated by MHC peptides is a way to construct a defense line and reduce the transmission and harm of the virus. Presentation of SARS-CoV-2 antigen is associated with different types of HLA phenotypes, and different HLA phenotypes induce different immune responses. The prediction of SARS-CoV-2 mutation information and the design of vaccines based on HLAs can effectively activate autoimmunity and cope with virus mutations, which can provide some references for the prevention and treatment of SARS-CoV-2.
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Affiliation(s)
- Feng Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Xiaoyuan Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Mohamed Y Zaky
- Molecular Physiology Division, Zoology Department, Faculty of Science, Beni-Suef University, P.O. Box 62521, Beni-Suef, Egypt; Department of Oncology and Department of Biomedical and Clinical Science, Faculty of Medicine, Linköping University, Sweden
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
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22
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Singh S, Rao A, Kumar K, Mishra A, Prajapati VK. Translational vaccinomics and structural filtration algorithm to device multiepitope vaccine for catastrophic monkeypox virus. Comput Biol Med 2023; 153:106497. [PMID: 36599210 PMCID: PMC9800352 DOI: 10.1016/j.compbiomed.2022.106497] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/17/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023]
Abstract
Recent outbreak of monkeypox disease commenced in April 2022, and on May 7, the first confirmed case was reported. The world health organization then designated monkeypox disease as a public health emergency of international outrage on July 23, after it spread to 70 non-endemic nations in less than 15 days. This catastrophic viral infection encourages the development of antiviral therapeutics due to the lack of specific treatments with negligible adverse effects. This analysis developed a highly immunogenic multiepitope subunit vaccine against the monkeypox virus using an in silico translational vaccinomics technique. Highly antigenic B cell and T cell (HTL and CTL) epitopes were predicted and conjugated with the help of unique linkers. An adjuvant (β-defensin) and a pan-HLA DR sequence were attached at the vaccine construct's N-terminal to invoke a robust immunological response. Additionally, physiochemical, allergic, toxic, and antigenic properties were anticipated. Interactions between the vaccine candidate and the TLR3 demonstrated that the vaccine candidate triggers a robust immunological response. Finally, the stability is confirmed by the molecular dynamics study. In contrast, the modified vaccine candidate's ability to produce a protective immune response were verified by an immune dynamics simulation study conducted via C-ImmSim server. This study validates the generation of B cell, Th cell, and Tc cell populations as well as the production of IFN-γ.
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Affiliation(s)
- Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Abhishek Rao
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Ketan Kumar
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, 305817, Rajasthan, India; Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bhatinda, Punjab, India.
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23
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Øverbø J, Aziz A, Zaman K, Clemens J, Halle Julin C, Qadri F, Stene-Johansen K, Biswas R, Islam S, Rahman Bhuiyan T, Haque W, Sandbu S, Elahee ME, Ali M, Dembinski JL, Dudman S. Immunogenicity and safety of a two-dose regimen with hepatitis E virus vaccine in healthy adults in rural Bangladesh: A randomized, double-blind, controlled, phase 2/pilot trial. Vaccine 2023; 41:1059-1066. [PMID: 36599736 DOI: 10.1016/j.vaccine.2022.12.064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023]
Abstract
BACKGROUND Hepatitis E virus (HEV) is a major cause of acute viral hepatitis worldwide and it contributes to considerable maternal and neonatal mortality and morbidity in many low-income countries like Bangladesh. A three-dose regimen of a vaccine against HEV (HEV 239) has shown promising results in China. The effects and safety of this vaccine in other populations and with different dosing regimens remains uncertain. OBJECTIVES Investigate the immune response and safety of a two-dose regimen with the HEV 239 vaccine among healthy adults. Examine the feasibility of conducting a larger HEV 239 vaccine trial in rural Bangladesh. METHODS One-hundred healthy men and non-pregnant women 16-39 years old were randomized in a 1:1 ratio to receive two doses of either the study (HEV) or control (Hepatitis B virus, HBV) vaccine (at 0, 1 month). Blood samples were collected at day 0, day 60 and 2 years after vaccination. The primary endpoints were the proportion and severity of adverse events up to 2 months after dose one and the longitudinal shift in anti-HEV IgG levels from day 0 to day 60 and 2 years after vaccination. RESULTS Adverse events to HEV 239 were comparable to the control vaccine, mild in severity and resolved within one to nine days. All participants in the study group seroconverted and achieved high levels of HEV IgG antibodies that remained positive for two years in all but one. A T-cell response was detected one month after HEV 239 vaccination. CONCLUSION Our results show that two doses of the HEV 239 vaccine produces broad and likely functional immune responses against HEV that remain for at least two years. The safety profile was acceptable and a phase four study of HEV 239 in rural Bangladesh is feasible. CLINICALTRIALS gov Identifier: NCT02759991.
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Affiliation(s)
- Joakim Øverbø
- Norwegian Institute of Public Health, Oslo, Norway; University of Oslo, Oslo, Norway.
| | - Asma Aziz
- University of Oslo, Oslo, Norway; International Centre for Diarrheal Diseases Research (icddr,b), Dhaka, Bangladesh; International Vaccine Institute, Seoul, Republic of Korea
| | - K Zaman
- International Centre for Diarrheal Diseases Research (icddr,b), Dhaka, Bangladesh
| | - John Clemens
- International Centre for Diarrheal Diseases Research (icddr,b), Dhaka, Bangladesh; International Vaccine Institute, Seoul, Republic of Korea; UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | | | - Firdausi Qadri
- International Centre for Diarrheal Diseases Research (icddr,b), Dhaka, Bangladesh
| | | | - Rajib Biswas
- International Centre for Diarrheal Diseases Research (icddr,b), Dhaka, Bangladesh
| | - Shaumik Islam
- International Centre for Diarrheal Diseases Research (icddr,b), Dhaka, Bangladesh
| | | | - Warda Haque
- International Centre for Diarrheal Diseases Research (icddr,b), Dhaka, Bangladesh
| | - Synne Sandbu
- Norwegian Institute of Public Health, Oslo, Norway
| | - Manzoor E Elahee
- International Centre for Diarrheal Diseases Research (icddr,b), Dhaka, Bangladesh
| | | | | | - Susanne Dudman
- University of Oslo, Oslo, Norway; Oslo University Hospital, Oslo, Norway
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24
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Mestiri S, Merhi M, Inchakalody VP, Taib N, Smatti MK, Ahmad F, Raza A, Ali FH, Hydrose S, Fernandes Q, Ansari AW, Sahir F, Al-Zaidan L, Jalis M, Ghoul M, Allahverdi N, Al Homsi MU, Uddin S, Jeremijenko AM, Nimir M, Abu-Raddad LJ, Abid FB, Zaqout A, Alfheid SR, Saqr HMH, Omrani AS, Hssain AA, Al Maslamani M, Yassine HM, Dermime S. Persistence of spike-specific immune responses in BNT162b2-vaccinated donors and generation of rapid ex-vivo T cells expansion protocol for adoptive immunotherapy: A pilot study. Front Immunol 2023; 14:1061255. [PMID: 36817441 PMCID: PMC9933868 DOI: 10.3389/fimmu.2023.1061255] [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: 10/04/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction The BNT162b2 mRNA-based vaccine has shown high efficacy in preventing COVID-19 infection but there are limited data on the types and persistence of the humoral and T cell responses to such a vaccine. Methods Here, we dissect the vaccine-induced humoral and cellular responses in a cohort of six healthy recipients of two doses of this vaccine. Results and discussion Overall, there was heterogeneity in the spike-specific humoral and cellular responses among vaccinated individuals. Interestingly, we demonstrated that anti-spike antibody levels detected by a novel simple automated assay (Jess) were strongly correlated (r=0.863, P<0.0001) with neutralizing activity; thus, providing a potential surrogate for neutralizing cell-based assays. The spike-specific T cell response was measured with a newly modified T-spot assay in which the high-homology peptide-sequences cross-reactive with other coronaviruses were removed. This response was induced in 4/6 participants after the first dose, and all six participants after the second dose, and remained detectable in 4/6 participants five months post-vaccination. We have also shown for the first time, that BNT162b2 vaccine enhanced T cell responses also against known human common viruses. In addition, we demonstrated the efficacy of a rapid ex-vivo T cell expansion protocol for spike-specific T cell expansion to be potentially used for adoptive-cell therapy in severe COVID-19, immunocompromised individuals, and other high-risk groups. There was a 9 to 13.7-fold increase in the number of expanded T cells with a significant increase of anti-spike specific response showing higher frequencies of both activation and cytotoxic markers. Interestingly, effector memory T cells were dominant in all four participants' CD8+ expanded memory T cells; CD4+ T cells were dominated by effector memory in 2/4 participants and by central memory in the remaining two participants. Moreover, we found that high frequencies of CD4+ terminally differentiated memory T cells were associated with a greater reduction of spike-specific activated CD4+ T cells. Finally, we showed that participants who had a CD4+ central memory T cell dominance expressed a high CD69 activation marker in the CD4+ activated T cells.
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Affiliation(s)
- Sarra Mestiri
- Translational Cancer Research Facility, National Center for Cancer Care and Research/ Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Maysaloun Merhi
- Translational Cancer Research Facility, National Center for Cancer Care and Research/ Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Varghese P Inchakalody
- Translational Cancer Research Facility, National Center for Cancer Care and Research/ Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- Translational Cancer Research Facility, National Center for Cancer Care and Research/ Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Maria K Smatti
- Qatar University Biomedical Research Center, Qatar University, Doha, Qatar
| | - Fareed Ahmad
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar.,Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Afsheen Raza
- Translational Cancer Research Facility, National Center for Cancer Care and Research/ Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Fatma H Ali
- Qatar University Biomedical Research Center, Qatar University, Doha, Qatar
| | - Shereena Hydrose
- Translational Cancer Research Facility, National Center for Cancer Care and Research/ Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Queenie Fernandes
- Translational Cancer Research Facility, National Center for Cancer Care and Research/ Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,College of Medicine, Qatar University, Doha, Qatar
| | - Abdul W Ansari
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar.,Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Fairooz Sahir
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Lobna Al-Zaidan
- Translational Cancer Research Facility, National Center for Cancer Care and Research/ Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Munir Jalis
- Translational Cancer Research Facility, National Center for Cancer Care and Research/ Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Mokhtar Ghoul
- Translational Cancer Research Facility, National Center for Cancer Care and Research/ Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Niloofar Allahverdi
- Translational Cancer Research Facility, National Center for Cancer Care and Research/ Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Mohammed U Al Homsi
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar.,Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | | | - Mai Nimir
- Communicable Disease Center, Hamad Medical Corporation, Doha, Qatar
| | - Laith J Abu-Raddad
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation-Education City, Doha, Qatar.,World Health Organization Collaborating Centre for Disease Epidemiology Analytics on HIV/AIDS, Sexually Transmitted Infections, and Viral Hepatitis, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation-Education City, Doha, Qatar.,Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Fatma Ben Abid
- Communicable Disease Center, Hamad Medical Corporation, Doha, Qatar
| | - Ahmed Zaqout
- Communicable Disease Center, Hamad Medical Corporation, Doha, Qatar
| | - Sameer R Alfheid
- Communicable Disease Center, Hamad Medical Corporation, Doha, Qatar
| | | | - Ali S Omrani
- College of Medicine, Qatar University, Doha, Qatar.,Communicable Disease Center, Hamad Medical Corporation, Doha, Qatar
| | - Ali Ait Hssain
- Medical Intensive Care Unit, Hamad Medical Corporation, Doha, Qatar
| | | | - Hadi M Yassine
- Qatar University Biomedical Research Center, Qatar University, Doha, Qatar
| | - Said Dermime
- Translational Cancer Research Facility, National Center for Cancer Care and Research/ Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.,National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
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25
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Albaqami FF, Altharawi A, Althurwi HN, Alharthy KM, Qasim M, Muhseen ZT, Tahir ul Qamar M. Computational Modeling and Evaluation of Potential mRNA and Peptide-Based Vaccine against Marburg Virus (MARV) to Provide Immune Protection against Hemorrhagic Fever. BIOMED RESEARCH INTERNATIONAL 2023; 2023:5560605. [PMID: 37101690 PMCID: PMC10125739 DOI: 10.1155/2023/5560605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/22/2023] [Accepted: 02/21/2023] [Indexed: 04/28/2023]
Abstract
A hemorrhagic fever caused by the Marburg virus (MARV) belongs to the Filoviridae family and has been classified as a risk group 4 pathogen. To this day, there are no approved effective vaccinations or medications available to prevent or treat MARV infections. Reverse vaccinology-based approach was formulated to prioritize B and T cell epitopes utilizing a numerous immunoinformatics tools. Potential epitopes were systematically screened based on various parameters needed for an ideal vaccine such as allergenicity, solubility, and toxicity. The most suitable epitopes capable of inducing immune response were shortlisted. Epitopes with population coverage of 100% and fulfilling set parameters were selected for docking with human leukocyte antigen molecules, and binding affinity of each peptide was analyzed. Finally, 4 CTL and HTL each while 6 B cell 16-mers were used for designing multiepitope subunit (MSV) and mRNA vaccine joined via suitable linkers. Immune simulations were used to validate the constructed vaccine's capacity to induce a robust immune response whereas molecular dynamics simulations were used to confirm epitope-HLA complex stability. Based on these parameter's studies, both the vaccines constructed in this study offer a promising choice against MARV but require further experimental verification. This study provides a rationale point to begin with the development of an efficient vaccine against Marburg virus; however, the findings need further experimental validation to confirm the computational finding of this study.
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Affiliation(s)
- Faisal F. Albaqami
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Ali Altharawi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Hassan N. Althurwi
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Khalid M. Alharthy
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Ziyad Tariq Muhseen
- Department of Pharmacy, Al-Mustaqbal University College, Hillah, Babylon 51001, Iraq
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
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26
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Arab F, Mollazadeh S, Ghayourbabaei F, Moghbeli M, Saburi E. The role of HLA genotypes in understanding the pathogenesis of severe COVID-19. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023; 24:14. [PMID: 36718139 PMCID: PMC9878497 DOI: 10.1186/s43042-023-00392-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has caused human tragedy through the global spread of the viral pathogen SARS-CoV-2. Although the underlying factors for the severity of COVID-19 in different people are still unknown, several gene variants can be used as predictors of disease severity, particularly variations in viral receptor genes such as angiotensin-converting enzyme 2 (ACE2) or major histocompatibility complex (MHC) genes. The reaction of the immune system, as the most important defense strategy in the case of viruses, plays a decisive role. The innate immune system is important both as a primary line of defense and as a trigger of the acquired immune response. The HLA-mediated acquired immune response is linked to the acquired immune system. In various diseases, it has been shown that genetic alterations in components of the immune system can play a crucial role in how the body responds to pathogens, especially viruses. One of the most important host genetic factors is the human leukocyte antigen (HLA) profile, which includes HLA classes I and II and may be symbolic of the diversity of immune response and genetic predisposition in disease progression. COVID-19 will have direct contact with the acquired immune system as an intracellular pathogen after exposure to the proteasome and its components through class I HLA. Therefore, it is assumed that in different genotypes of the HLA-I class, an undesirable supply causes an insufficient activation of the immune system. Insufficient binding of antigen delivered by class I HLA to host lymphocytes results in uncertain identification and insufficient activation of the acquired immune system. The absence of secretion of immune cytokines such as interferons, which play an important role in controlling viral infection in the early stages, is a complication of this event. Understanding the allelic diversity of HLA in people infected with coronavirus compared with uninfected people of one race not only allows identification of people with HLA susceptible to COVID-19 but also provides better insight into the behavior of the virus, which helps to take effective preventive and curative measures earlier.
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Affiliation(s)
- Fatemeh Arab
- grid.411583.a0000 0001 2198 6209Medical Genetics and Molecular Medicine Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Mollazadeh
- grid.464653.60000 0004 0459 3173Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Farnaz Ghayourbabaei
- grid.411301.60000 0001 0666 1211Department of Biology, Faculty of Sciences, University of Ferdowsi, Mashhad, Iran
| | - Meysam Moghbeli
- grid.411583.a0000 0001 2198 6209Medical Genetics and Molecular Medicine Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Saburi
- grid.411583.a0000 0001 2198 6209Medical Genetics and Molecular Medicine Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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27
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Mohammadi Y, Nezafat N, Negahdaripour M, Eskandari S, Zamani M. In silico design and evaluation of a novel mRNA vaccine against BK virus: a reverse vaccinology approach. Immunol Res 2022; 71:422-441. [PMID: 36580228 PMCID: PMC9797904 DOI: 10.1007/s12026-022-09351-3] [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: 05/25/2022] [Accepted: 12/02/2022] [Indexed: 12/30/2022]
Abstract
Human polyomavirus type 1, or BK virus (BKV), is a ubiquitous pathogen belonging to the polyomaviridae family mostly known for causing BKV-associated nephropathy (BKVN) and allograft rejection in kidney transplant recipients (KTRs) following the immunosuppression regimens recommended in these patients. Reduction of the immunosuppression level and anti-viral agents are the usual approaches for BKV clearance, which have not met a desired outcome yet. There are also debating matters such as the effect of this pathogen on emerging various comorbidities and the related malignancies in the human population. In this study, a reverse vaccinology approach was implemented to design a mRNA vaccine against BKV by identifying the most antigenic proteins of this pathogen. Potential immunogenic T and B lymphocyte epitopes were predicted through various immunoinformatic tools. The final epitopes were selected according to antigenicity, toxicity, allergenicity, and cytokine inducibility scores. According to the obtained results, the designed vaccine was antigenic, neutral at the physiological pH, non-toxic, and non-allergenic with a world population coverage of 93.77%. Since the mRNA codon optimization ensures the efficient expression of the vaccine in a host cell, evaluation of different parameters showed our designed mRNA vaccine has a stable structure. Moreover, it had strong interactions with toll-like receptor 4 (TLR4) according to the molecular dynamic simulation studies. The in silico immune simulation analyses revealed an overall increase in the immune responses following repeated exposure to the designed vaccine. Based on our findings, the vaccine candidate is ready to be tested as a promising novel mRNA therapeutic vaccine against BKV.
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Affiliation(s)
- Yasaman Mohammadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Navid Nezafat
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran.
| | - Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran.
| | - Sedigheh Eskandari
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Science, Shiraz, Iran
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28
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Zhong L, Krummenacher C, Zhang W, Hong J, Feng Q, Chen Y, Zhao Q, Zeng MS, Zeng YX, Xu M, Zhang X. Urgency and necessity of Epstein-Barr virus prophylactic vaccines. NPJ Vaccines 2022; 7:159. [PMID: 36494369 PMCID: PMC9734748 DOI: 10.1038/s41541-022-00587-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV), a γ-herpesvirus, is the first identified oncogenic virus, which establishes permanent infection in humans. EBV causes infectious mononucleosis and is also tightly linked to many malignant diseases. Various vaccine formulations underwent testing in different animals or in humans. However, none of them was able to prevent EBV infection and no vaccine has been approved to date. Current efforts focus on antigen selection, combination, and design to improve the efficacy of vaccines. EBV glycoproteins such as gH/gL, gp42, and gB show excellent immunogenicity in preclinical studies compared to the previously favored gp350 antigen. Combinations of multiple EBV proteins in various vaccine designs become more attractive approaches considering the complex life cycle and complicated infection mechanisms of EBV. Besides, rationally designed vaccines such as virus-like particles (VLPs) and protein scaffold-based vaccines elicited more potent immune responses than soluble antigens. In addition, humanized mice, rabbits, as well as nonhuman primates that can be infected by EBV significantly aid vaccine development. Innovative vaccine design approaches, including polymer-based nanoparticles, the development of effective adjuvants, and antibody-guided vaccine design, will further enhance the immunogenicity of vaccine candidates. In this review, we will summarize (i) the disease burden caused by EBV and the necessity of developing an EBV vaccine; (ii) previous EBV vaccine studies and available animal models; (iii) future trends of EBV vaccines, including activation of cellular immune responses, novel immunogen design, heterologous prime-boost approach, induction of mucosal immunity, application of nanoparticle delivery system, and modern adjuvant development.
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Affiliation(s)
- Ling Zhong
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong PR China
| | - Claude Krummenacher
- grid.262671.60000 0000 8828 4546Department of Biological and Biomedical Sciences, Rowan University, Glassboro, NJ USA
| | - Wanlin Zhang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong PR China
| | - Junping Hong
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian PR China
| | - Qisheng Feng
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong PR China
| | - Yixin Chen
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian PR China
| | - Qinjian Zhao
- grid.203458.80000 0000 8653 0555College of Pharmacy, Chongqing Medical University, Chongqing, PR China
| | - Mu-Sheng Zeng
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong PR China
| | - Yi-Xin Zeng
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong PR China
| | - Miao Xu
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong PR China
| | - Xiao Zhang
- grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong PR China ,grid.203458.80000 0000 8653 0555College of Pharmacy, Chongqing Medical University, Chongqing, PR China
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Zhang Y, Gabere M, Tylor MA, Simoes CC, Dumbauld C, Barro O, Tesfay MZ, Graham AL, Ferdous KU, Savenka AV, Chamcheu JC, Washam CL, Alkam D, Gies A, Byrum SD, Conti M, Post SR, Kelly T, Borad MJ, Cannon MJ, Basnakian A, Nagalo BM. Repurposing live attenuated trivalent MMR vaccine as cost-effective cancer immunotherapy. Front Oncol 2022; 12:1042250. [DOI: 10.3389/fonc.2022.1042250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
It has long been known that oncolytic viruses wield their therapeutic capability by priming an inflammatory state within the tumor and activating the tumor immune microenvironment, resulting in a multifaceted antitumor immune response. Vaccine-derived viruses, such as measles and mumps, have demonstrated promising potential for treating human cancer in animal models and clinical trials. However, the extensive cost of manufacturing current oncolytic viral products makes them far out of reach for most patients. Here by analyzing the impact of intratumoral (IT) administrations of the trivalent live attenuated measles, mumps, and rubella viruses (MMR) vaccine, we unveil the cellular and molecular basis of MMR-induced anti-cancer activity. Strikingly, we found that IT delivery of low doses of MMR correlates with tumor control and improved survival in murine hepatocellular cancer and colorectal cancer models via increased tumor infiltration of CD8+ granzyme B+ T-cells and decreased macrophages. Moreover, our data indicate that MMR activates key cellular effectors of the host’s innate and adaptive antitumor immunity, culminating in an immunologically coordinated cancer cell death. These findings warrant further work on the potential for MMR to be repurposed as safe and cost-effective cancer immunotherapy to impact cancer patients globally.
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Ugwu CC, Hair-Bejo M, Nurulfiza MI, Omar AR, Ideris A. Efficacy, humoral, and cell-mediated immune response of inactivated fowl adenovirus 8b propagated in chicken embryo liver cells using bioreactor in broiler chickens. Vet World 2022; 15:2681-2692. [PMID: 36590109 PMCID: PMC9798058 DOI: 10.14202/vetworld.2022.2681-2692] [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: 08/16/2022] [Accepted: 10/19/2022] [Indexed: 11/28/2022] Open
Abstract
Background and Aim Fowl adenovirus (FAdV) 8b causes inclusion body hepatitis, resulting in major economic losses globally among chickens. The objectives were to inactivate FAdV 8b isolate propagated in chicken embryo liver (CEL) cells using a stirred tank bioreactor (UPM08136P5B1) and determine the humoral and cell-mediated immune response, efficacy, and virus shedding in broiler chickens. Materials and Methods The FAdV 8b isolate UPM08136P5B1 was inactivated using binary ethyleneimine, adjuvanted with Montanide 71VG, inoculated into day-old broiler chickens in a booster group (BG) and non-booster group (NBG), and challenged with a pathogenic FAdV 8b strain. Clinical signs, gross lesions, body weight (BW), liver: body weight ratio, FAdV antibody titer using enzyme-linked immunosorbent assay, and histopathological changes were recorded. The CD3+, CD4+, and CD8+ T-lymphocyte profiles of the liver, spleen, and thymus using flow cytometry, and viral load in liver and cloacal shedding using quantitative polymerase chain reaction were evaluated. Results Chickens in the challenged control group (CCG) exhibited mild clinical signs, gross lesions, and histopathological changes, which were absent in the inoculated groups, and had lower BW and higher liver BW ratio than chickens in the unchallenged control group (UCG); BG and NBG on 35- and 42-days post-inoculation (DPI). Chickens in NBG and BG had higher antibodies than UCG on 7, 21, 35, and 42 DPI. The challenged BG and NBG produced higher antibodies than the CCG on 35 DPI. T-lymphocytes were higher among the inoculated groups than UCG in the liver, spleen, and thymus. Inoculated challenged groups recorded higher CD3+, CD4+, and CD8+ T-lymphocytes on 35 and 42 DPI than CCG. The challenged control group had a significantly higher viral load in the liver than challenged that in BG on 35 DPI and BG and NBG on 42 DPI. The challenged control group had significantly higher challenge FAdV shedding than challenged inoculated groups on 35 and NBG on 42 DPI. Conclusion UPM08136P5B1 was successfully inactivated and mixed with Montanide 71VG. The inactivated vaccine candidate that induced humoral and cellular immunity was effective, reduced FAdV load in the liver, and shedding in the cloaca, and could be useful against FAdV 8b infections in chickens.
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Affiliation(s)
- Chidozie Clifford Ugwu
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia,Department of Animal Science and Technology, Federal University of Technology, Owerri 460114, Imo State, Nigeria
| | - Mohd Hair-Bejo
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia,Laboratory of Vaccines and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia,Corresponding author: Mohd Hair-Bejo, e-mail: Co-authors: CCU: , MIN: , ARO: , AI:
| | - Mat Isa Nurulfiza
- Laboratory of Vaccines and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Abdul Rahman Omar
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia,Laboratory of Vaccines and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Aini Ideris
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia,Laboratory of Vaccines and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
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31
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Althurwi HN, Alharthy KM, Albaqami FF, Altharawi A, Javed MR, Muhseen ZT, Tahir ul Qamar M. mRNA-Based Vaccine Designing against Epstein-Barr Virus to Induce an Immune Response Using Immunoinformatic and Molecular Modelling Approaches. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13054. [PMID: 36293632 PMCID: PMC9602923 DOI: 10.3390/ijerph192013054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Epstein-Barr Virus (EBV) is a human pathogen that has a morbidity rate of 90% in adults worldwide. Infectious mononucleosis is caused by EBV replication in B cells and epithelial cells of the host. EBV has also been related to autoimmune illnesses, including multiple sclerosis and cancers like nasopharyngeal carcinomas and Burkitt's lymphoma. Currently, no effective medications or vaccinations are available to treat or prevent EBV infection. Thus, the current study focuses on a bioinformatics approach to design an mRNA-based multi-epitope (MEV) vaccine to prevent EBV infections. For this purpose, we selected six antigenic proteins from the EBV proteome based on their role in pathogenicity to predict, extract, and analyze T and B cell epitopes using immunoinformatics tools. The epitopes were directed through filtering parameters including allergenicity, toxicity, antigenicity, solubility, and immunogenicity assessment, and finally, the most potent epitopes able to induce T and B cell immune response were selected. In silico molecular docking of prioritized T cell peptides with respective Human Leukocytes Antigens molecules, were carried out to evaluate the individual peptide's binding affinity. Six CTL, four HTL, and ten linear B cell epitopes fulfilled the set parameters and were selected for MEV-based mRNA vaccine. The prioritized epitopes were joined using suitable linkers to improve epitope presentation. The immune simulation results affirmed the designed vaccine's capacity to elicit a proper immune response. The MEV-based mRNA vaccine constructed in this study offers a promising choice for a potent vaccine against EBV.
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Affiliation(s)
- Hassan N. Althurwi
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Khalid M. Alharthy
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Faisal F. Albaqami
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Ali Altharawi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Ziyad Tariq Muhseen
- Department of Pharmacy, Al-Mustaqbal University College, Hillah 51001, Babylon, Iraq
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
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32
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Current Vaccine Platforms in Enhancing T-Cell Response. Vaccines (Basel) 2022; 10:vaccines10081367. [PMID: 36016254 PMCID: PMC9413345 DOI: 10.3390/vaccines10081367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/28/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
The induction of T cell-mediated immunity is crucial in vaccine development. The most effective vaccine is likely to employ both cellular and humoral immune responses. The efficacy of a vaccine depends on T cells activated by antigen-presenting cells. T cells also play a critical role in the duration and cross-reactivity of vaccines. Moreover, pre-existing T-cell immunity is associated with a decreased severity of infectious diseases. Many technical and delivery platforms have been designed to induce T cell-mediated vaccine immunity. The immunogenicity of vaccines is enhanced by controlling the kinetics and targeted delivery. Viral vectors are attractive tools that enable the intracellular expression of foreign antigens and induce robust immunity. However, it is necessary to select an appropriate viral vector considering the existing anti-vector immunity that impairs vaccine efficacy. mRNA vaccines have the advantage of rapid and low-cost manufacturing and have been approved for clinical use as COVID-19 vaccines for the first time. mRNA modification and nanomaterial encapsulation can help address mRNA instability and translation efficacy. This review summarizes the T cell responses of vaccines against various infectious diseases based on vaccine technologies and delivery platforms and discusses the future directions of these cutting-edge platforms.
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33
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Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
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Higuchi A, Sung TC, Wang T, Ling QD, Kumar SS, Hsu ST, Umezawa A. Material Design for Next-Generation mRNA Vaccines Using Lipid Nanoparticles. POLYM REV 2022. [DOI: 10.1080/15583724.2022.2106490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Akon Higuchi
- School of Biomedical Engineering, The Eye Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Chemical and Materials Engineering, National Central University, Jhongli, Taiwan
- R&D Center for Membrane Technology, Chung Yuan Christian University, Chungli, Taiwan
- Department of Reproduction, National Center for Child Health and Development, Okura, Tokyo, Japan
| | - Tzu-Cheng Sung
- School of Biomedical Engineering, The Eye Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ting Wang
- School of Biomedical Engineering, The Eye Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qing-Dong Ling
- Cathay Medical Research Institute, Cathay General Hospital, Taipei, Taiwan
| | - S. Suresh Kumar
- Department of Biotechnology, Bharath Institute of Higher Education and Research, Chennai, India
| | - Shih-Tien Hsu
- Department of Internal Medicine, Taiwan Landseed Hospital, Pingjen City, Taiwan Taoyuan
| | - Akihiro Umezawa
- Department of Reproduction, National Center for Child Health and Development, Okura, Tokyo, Japan
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35
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Role of Histone Deacetylases in T-Cell Development and Function. Int J Mol Sci 2022; 23:ijms23147828. [PMID: 35887172 PMCID: PMC9320103 DOI: 10.3390/ijms23147828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 01/27/2023] Open
Abstract
Histone deacetylases (HDACs) are a group of enzymes called “epigenetic erasers”. They remove the acetyl group from histones changing the condensation state of chromatin, leading to epigenetic modification of gene expression and various downstream effects. Eighteen HDACs have been identified and grouped into four classes. The role of HDACs in T-cells has been extensively studied, and it has been proven that many of them are important players in T-cell development and function. In this review, we present the current state of knowledge on the role of HDACs in the early stages of T-cell development but also in the functioning of mature lymphocytes on the periphery, including activation, cytokine production, and metabolism regulation.
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36
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Jenner AL, Smalley M, Goldman D, Goins WF, Cobbs CS, Puchalski RB, Chiocca EA, Lawler S, Macklin P, Goldman A, Craig M. Agent-based computational modeling of glioblastoma predicts that stromal density is central to oncolytic virus efficacy. iScience 2022; 25:104395. [PMID: 35637733 PMCID: PMC9142563 DOI: 10.1016/j.isci.2022.104395] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/18/2022] [Accepted: 04/08/2022] [Indexed: 11/26/2022] Open
Abstract
Oncolytic viruses (OVs) are emerging cancer immunotherapy. Despite notable successes in the treatment of some tumors, OV therapy for central nervous system cancers has failed to show efficacy. We used an ex vivo tumor model developed from human glioblastoma tissue to evaluate the infiltration of herpes simplex OV rQNestin (oHSV-1) into glioblastoma tumors. We next leveraged our data to develop a computational, model of glioblastoma dynamics that accounts for cellular interactions within the tumor. Using our computational model, we found that low stromal density was highly predictive of oHSV-1 therapeutic success, suggesting that the efficacy of oHSV-1 in glioblastoma may be determined by stromal-to-tumor cell regional density. We validated these findings in heterogenous patient samples from brain metastatic adenocarcinoma. Our integrated modeling strategy can be applied to suggest mechanisms of therapeutic responses for central nervous system cancers and to facilitate the successful translation of OVs into the clinic.
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Affiliation(s)
- Adrianne L. Jenner
- Department of Mathematics and Statistics, Université de Montréal, Montréal, QC, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, QC, Canada
| | - Munisha Smalley
- Division of Engineering in Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - William F. Goins
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Charles S. Cobbs
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | - Ralph B. Puchalski
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | - E. Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sean Lawler
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul Macklin
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Aaron Goldman
- Division of Engineering in Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Morgan Craig
- Department of Mathematics and Statistics, Université de Montréal, Montréal, QC, Canada
- Sainte-Justine University Hospital Research Centre, Montréal, QC, Canada
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37
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Wang L, Rajavel M, Wu CW, Zhang C, Poindexter M, Fulgar C, Mar T, Singh J, Dhillon JK, Zhang J, Yuan Y, Abarca R, Li W, Pinkerton KE. Effects of life-stage and passive tobacco smoke exposure on pulmonary innate immunity and influenza infection in mice. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2022; 85:439-456. [PMID: 35139765 PMCID: PMC8976777 DOI: 10.1080/15287394.2022.2032518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Limited data are available on the effects of perinatal environmental tobacco smoke (ETS) exposure for early childhood influenza infection. The aim of the present study was to examine whether perinatal versus adult ETS exposure might provoke more severe systemic and pulmonary innate immune responses in mice inoculated with influenza A/Puerto Rico/8/34 virus (IAV) compared to phosphate-buffered saline (PBS). BALB/c mice were exposed to filtered air (FA) or ETS for 6 weeks during the perinatal or adult period of life. Immediately following the final exposure, mice were intranasally inoculated with IAV or PBS. Significant inflammatory effects were observed in bronchoalveolar lavage fluid of neonates inoculated with IAV (FA+IAV or ETS+IAV) compared to PBS (ETS+PBS or FA+PBS), and in the lung parenchyma of neonates administered ETS+IAV versus FA+IAV. Type I and III interferons were also elevated in the spleens of neonates, but not adults with ETS+IAV versus FA+IAV exposure. Both IAV-inoculated neonate groups exhibited significantly more CD4 T cells and increasing numbers of CD8 and CD25 T cells in lungs relative to their adult counterparts. Taken together, these results suggest perinatal ETS exposure induces an exaggerated innate immune response, which may overwhelm protective anti-inflammatory defenses against IAV, and enhances severity of infection at early life stages (e.g., in infants and young children).
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Affiliation(s)
- Lei Wang
- Center for Health and the Environment, University of California, Davis, CA, USA
| | - Maya Rajavel
- Center for Health and the Environment, University of California, Davis, CA, USA
| | - Ching-Wen Wu
- Center for Health and the Environment, University of California, Davis, CA, USA
| | - Chuanzhen Zhang
- Center for Health and the Environment, University of California, Davis, CA, USA
- Department of Gastroenterology, the First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, China
| | - Morgan Poindexter
- Center for Health and the Environment, University of California, Davis, CA, USA
| | - Ciara Fulgar
- Center for Health and the Environment, University of California, Davis, CA, USA
| | - Tiffany Mar
- Center for Health and the Environment, University of California, Davis, CA, USA
| | - Jasmine Singh
- Center for Health and the Environment, University of California, Davis, CA, USA
| | - Jaspreet K. Dhillon
- Center for Health and the Environment, University of California, Davis, CA, USA
| | - Jingjing Zhang
- Center for Health and the Environment, University of California, Davis, CA, USA
- Western China School of Public Health Department of Occupational and Environmental Health Sichuan University, Chengdu, China
| | - Yinyu Yuan
- Center for Health and the Environment, University of California, Davis, CA, USA
| | - Radek Abarca
- Center for Health and the Environment, University of California, Davis, CA, USA
| | - Wei Li
- School of Control Science and Engineering, Shandong University, Jinan, Shandong 250014, China
| | - Kent E. Pinkerton
- Center for Health and the Environment, University of California, Davis, CA, USA
- Department of Pediatrics, University of California, Davis, CA, USA
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38
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Marzella DF, Parizi FM, van Tilborg D, Renaud N, Sybrandi D, Buzatu R, Rademaker DT, 't Hoen PAC, Xue LC. PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes. Front Immunol 2022; 13:878762. [PMID: 35619705 PMCID: PMC9127323 DOI: 10.3389/fimmu.2022.878762] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Deeper understanding of T-cell-mediated adaptive immune responses is important for the design of cancer immunotherapies and antiviral vaccines against pandemic outbreaks. T-cells are activated when they recognize foreign peptides that are presented on the cell surface by Major Histocompatibility Complexes (MHC), forming peptide:MHC (pMHC) complexes. 3D structures of pMHC complexes provide fundamental insight into T-cell recognition mechanism and aids immunotherapy design. High MHC and peptide diversities necessitate efficient computational modelling to enable whole proteome structural analysis. We developed PANDORA, a generic modelling pipeline for pMHC class I and II (pMHC-I and pMHC-II), and present its performance on pMHC-I here. Given a query, PANDORA searches for structural templates in its extensive database and then applies anchor restraints to the modelling process. This restrained energy minimization ensures one of the fastest pMHC modelling pipelines so far. On a set of 835 pMHC-I complexes over 78 MHC types, PANDORA generated models with a median RMSD of 0.70 Å and achieved a 93% success rate in top 10 models. PANDORA performs competitively with three pMHC-I modelling state-of-the-art approaches and outperforms AlphaFold2 in terms of accuracy while being superior to it in speed. PANDORA is a modularized and user-configurable python package with easy installation. We envision PANDORA to fuel deep learning algorithms with large-scale high-quality 3D models to tackle long-standing immunology challenges.
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Affiliation(s)
- Dario F Marzella
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Farzaneh M Parizi
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Derek van Tilborg
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands.,Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Nicolas Renaud
- Natural Sciences and Engineering section, Netherlands eScience Center, Amsterdam, Netherlands
| | - Daan Sybrandi
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, Netherlands
| | - Rafaella Buzatu
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Daniel T Rademaker
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Peter A C 't Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Li C Xue
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
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39
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The STING Ligand and Delivery System Synergistically Enhance the Immunogenicity of an Intranasal Spike SARS-CoV-2 Vaccine Candidate. Biomedicines 2022; 10:biomedicines10051142. [PMID: 35625879 PMCID: PMC9138454 DOI: 10.3390/biomedicines10051142] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/23/2022] Open
Abstract
The respiratory organ serves as a primary target site for SARS-CoV-2. Thus, the vaccine-stimulating immune response of the respiratory tract is significant in controlling SARS-CoV-2 transmission and disease development. In this study, mucoadhesive nanoparticles were used to deliver SARS-CoV-2 spike proteins (S-NPs) into the nasal tracts of mice. The responses in the respiratory organ and the systemic responses were monitored. The administration of S-NPs along with cGAMP conferred a robust stimulation of antibody responses in the respiratory tract, as demonstrated by an increase of IgA and IgG antibodies toward the spike proteins in bronchoalveolar lavages (BALs) and the lungs. Interestingly, the elicited antibodies were able to neutralize both the wild-type and Delta variant strains of SARS-CoV-2. Significantly, the intranasal immunization also stimulated systemic responses. This is evidenced by the increased production of circulating IgG and IgA, which were able to neutralize and bind specifically to the SARS-CoV-2 virion and spike protein. Additionally, this intranasal administration potently activated a splenic T cell response and the production of Th-1 cytokines, suggesting that this vaccine may well activate a cellular response in the respiratory tract. The results demonstrate that STING agonist strongly acts as an adjuvant to the immunogenicity of S-NPs. This platform may be an ideal vaccine against SARS-CoV-2.
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40
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Abas AH, Marfuah S, Idroes R, Kusumawaty D, Fatimawali, Park MN, Siyadatpanah A, Alhumaydhi FA, Mahmud S, Tallei TE, Emran TB, Kim B. Can the SARS-CoV-2 Omicron Variant Confer Natural Immunity against COVID-19? Molecules 2022; 27:2221. [PMID: 35408618 PMCID: PMC9000495 DOI: 10.3390/molecules27072221] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is still ongoing, with no signs of abatement in sight. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of this pandemic and has claimed over 5 million lives, is still mutating, resulting in numerous variants. One of the newest variants is Omicron, which shows an increase in its transmissibility, but also reportedly reduces hospitalization rates and shows milder symptoms, such as in those who have been vaccinated. As a result, many believe that Omicron provides a natural vaccination, which is the first step toward ending the COVID-19 pandemic. Based on published research and scientific evidence, we review and discuss how the end of this pandemic is predicted to occur as a result of Omicron variants being surpassed in the community. In light of the findings of our research, we believe that it is most likely true that the Omicron variant is a natural way of vaccinating the masses and slowing the spread of this deadly pandemic. While the mutation that causes the Omicron variant is encouraging, subsequent mutations do not guarantee that the disease it causes will be less severe. As the virus continues to evolve, humans must constantly adapt by increasing their immunity through vaccination.
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Affiliation(s)
- Abdul Hawil Abas
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (A.H.A.); (S.M.)
| | - Siti Marfuah
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (A.H.A.); (S.M.)
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, Aceh, Indonesia;
| | - Diah Kusumawaty
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung 40154, West Java, Indonesia;
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia;
| | - Moon Nyeo Park
- College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Korea;
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand 97178-53577, Iran;
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia;
| | - Shafi Mahmud
- Department of Genome Science, John Curtin School of Medical Research, Australian National University, Canberra, ACT 0200, Australia;
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (A.H.A.); (S.M.)
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Bonglee Kim
- College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Korea;
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41
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Le T, Sun C, Chang J, Zhang G, Yin X. mRNA Vaccine Development for Emerging Animal and Zoonotic Diseases. Viruses 2022; 14:401. [PMID: 35215994 PMCID: PMC8877136 DOI: 10.3390/v14020401] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
In the prevention and treatment of infectious diseases, mRNA vaccines hold great promise because of their low risk of insertional mutagenesis, high potency, accelerated development cycles, and potential for low-cost manufacture. In past years, several mRNA vaccines have entered clinical trials and have shown promise for offering solutions to combat emerging and re-emerging infectious diseases such as rabies, Zika, and influenza. Recently, the successful application of mRNA vaccines against COVID-19 has further validated the platform and opened the floodgates to mRNA vaccine's potential in infectious disease prevention, especially in the veterinary field. In this review, we describe our current understanding of the mRNA vaccines and the technologies used for mRNA vaccine development. We also provide an overview of mRNA vaccines developed for animal infectious diseases and discuss directions and challenges for the future applications of this promising vaccine platform in the veterinary field.
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Affiliation(s)
- Ting Le
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (T.L.); (C.S.)
| | - Chao Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (T.L.); (C.S.)
| | - Jitao Chang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (T.L.); (C.S.)
| | - Guijie Zhang
- Departments of Animal Science, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Xin Yin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (T.L.); (C.S.)
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42
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Kafai NM, Diamond MS, Fox JM. Distinct Cellular Tropism and Immune Responses to Alphavirus Infection. Annu Rev Immunol 2022; 40:615-649. [PMID: 35134315 DOI: 10.1146/annurev-immunol-101220-014952] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alphaviruses are emerging and reemerging viruses that cause disease syndromes ranging from incapacitating arthritis to potentially fatal encephalitis. While infection by arthritogenic and encephalitic alphaviruses results in distinct clinical manifestations, both virus groups induce robust innate and adaptive immune responses. However, differences in cellular tropism, type I interferon induction, immune cell recruitment, and B and T cell responses result in differential disease progression and outcome. In this review, we discuss aspects of immune responses that contribute to protective or pathogenic outcomes after alphavirus infection. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Natasha M Kafai
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA; , .,Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael S Diamond
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA; , .,Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, USA.,Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA.,Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Julie M Fox
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA;
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43
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Immunoinformatics-based characterization of immunogenic CD8 T-cell epitopes for a broad-spectrum cell-mediated immunity against high-risk human papillomavirus infection. Microb Pathog 2022; 165:105462. [DOI: 10.1016/j.micpath.2022.105462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/24/2022]
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44
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Bukhari SNH, Jain A, Haq E, Mehbodniya A, Webber J. Machine Learning Techniques for the Prediction of B-Cell and T-Cell Epitopes as Potential Vaccine Targets with a Specific Focus on SARS-CoV-2 Pathogen: A Review. Pathogens 2022; 11:pathogens11020146. [PMID: 35215090 PMCID: PMC8879824 DOI: 10.3390/pathogens11020146] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 02/01/2023] Open
Abstract
The only part of an antigen (a protein molecule found on the surface of a pathogen) that is composed of epitopes specific to T and B cells is recognized by the human immune system (HIS). Identification of epitopes is considered critical for designing an epitope-based peptide vaccine (EBPV). Although there are a number of vaccine types, EBPVs have received less attention thus far. It is important to mention that EBPVs have a great deal of untapped potential for boosting vaccination safety—they are less expensive and take a short time to produce. Thus, in order to quickly contain global pandemics such as the ongoing outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), as well as epidemics and endemics, EBPVs are considered promising vaccine types. The high mutation rate of SARS-CoV-2 has posed a great challenge to public health worldwide because either the composition of existing vaccines has to be changed or a new vaccine has to be developed to protect against its different variants. In such scenarios, time being the critical factor, EBPVs can be a promising alternative. To design an effective and viable EBPV against different strains of a pathogen, it is important to identify the putative T- and B-cell epitopes. Using the wet-lab experimental approach to identify these epitopes is time-consuming and costly because the experimental screening of a vast number of potential epitope candidates is required. Fortunately, various available machine learning (ML)-based prediction methods have reduced the burden related to the epitope mapping process by decreasing the potential epitope candidate list for experimental trials. Moreover, these methods are also cost-effective, scalable, and fast. This paper presents a systematic review of various state-of-the-art and relevant ML-based methods and tools for predicting T- and B-cell epitopes. Special emphasis is placed on highlighting and analyzing various models for predicting epitopes of SARS-CoV-2, the causative agent of COVID-19. Based on the various methods and tools discussed, future research directions for epitope prediction are presented.
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Affiliation(s)
- Syed Nisar Hussain Bukhari
- University Institute of Computing, Chandigarh University, NH-95, Chandigarh-Ludhiana Highway, Mohali 140413, India;
- Correspondence:
| | - Amit Jain
- University Institute of Computing, Chandigarh University, NH-95, Chandigarh-Ludhiana Highway, Mohali 140413, India;
| | - Ehtishamul Haq
- Department of Biotechnology, University of Kashmir, Srinagar 190006, India;
| | - Abolfazl Mehbodniya
- Department of Electronics and Communication Engineering, Kuwait College of Science and Technology, Kuwait City 20185145, Kuwait;
| | - Julian Webber
- Graduate School of Engineering Science, Osaka University, Osaka 560-8531, Japan;
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45
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Khalili-Tanha G, Khazaei M, Soleimanpour S, Ferns GA, Avan A. The chance of COVID-19 infection after vaccination. Infect Disord Drug Targets 2022; 22:e050122199980. [PMID: 34986778 DOI: 10.2174/1871526522666220105113829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/15/2021] [Accepted: 11/01/2021] [Indexed: 11/22/2022]
Abstract
The outbreak of COVID-19 that began in Wuhan, China, has constituted a new emerging epidemic that has spread around the world. There are some reports on illustrated the patients getting reinfected after recovering from COVID-19. Here we provide an overview of the biphasic cycle of COVID-19, genetic diversity, immune response and chance of reinfection after recovering from COVID-19. The new generation of COVID-19 is highly contagious and pathogenic infection can lead to acute respiratory distress syndrome. Whilst most patients suffer from a mild form of the disease, there is a rising concern that patients who recover from COVID-19 may be at risk of reinfection. The proportion of the infected population, is increasing worldwide; meanwhile, the rate and concern of reinfection by the recovered population are still high. Moreover, there are a few evidence on the chance of COVID-19 infection even after vaccination, which is around one per cent or less. Although the hypothesis of zero reinfections after vaccination has not been clinically proven, further studies should be performed on the recovered class in clusters to study the progression of the exposed with the re-exposed subpopulations to estimate the possibilities of reinfection and, thereby, advocate the use of these antibodies for vaccine creation.
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Affiliation(s)
- Ghazaleh Khalili-Tanha
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saman Soleimanpour
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK
| | - Amir Avan
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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46
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Alefishat E, Jelinek HF, Mousa M, Tay GK, Alsafar HS. Immune response to SARS-CoV-2 Variants: A focus on severity, susceptibility, and preexisting immunity. J Infect Public Health 2022; 15:277-288. [PMID: 35074728 PMCID: PMC8757655 DOI: 10.1016/j.jiph.2022.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/16/2021] [Accepted: 01/09/2022] [Indexed: 01/08/2023] Open
Abstract
The heterogeneous phenotypes among patients with coronavirus disease 2019 (COVID-19) has drawn worldwide attention, especially those with severe symptoms without comorbid conditions. Immune responses to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative virus of COVID-19, occur mainly by the innate immune response via the interferon (IFN)-mediated pathways, and the adaptive immunity via the T lymphocyte and the antibody mediated pathways. The ability of the original Wuhan SARS-CoV-2 strain, and possibly more so with new emerging variants, to antagonize IFN-mediated antiviral responses can be behind the higher early viral load, higher transmissibility, and milder symptoms compared to SARS-CoV and are part of the continued clinical evolution of COVID-19. Since it first emerged, several variants of SARS-CoV-2 have been circulating worldwide. Variants that have the potential to elude natural or vaccine-mediated immunity are variants of concern. This review focuses on the main host factors that may explain the immune responses to SARS-CoV-2 and its variants in the context of susceptibility, severity, and preexisting immunity.
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Affiliation(s)
- Eman Alefishat
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Biopharmaceutics and Clinical Pharmacy, Faculty of Pharmacy, The University of Jordan, Amman, Jordan
| | - Herbert F Jelinek
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Center of Heath Engineering Innovation, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Nuffield Department of Women's and Reproduction Health, Oxford University, Oxford, United Kingdom
| | - Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Discipline of Psychiatry, Medical School, the University of Western Australia, Perth WA, Australia; School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba S Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates.
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47
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Das R, Fernandez JG. Biomaterials for Mimicking and Modelling Tumor Microenvironment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1379:139-170. [DOI: 10.1007/978-3-031-04039-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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48
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T-Cell Response against Varicella Zoster Virus in Patients with Multiple Sclerosis during Relapse and Remission. Int J Mol Sci 2021; 23:ijms23010298. [PMID: 35008726 PMCID: PMC8745673 DOI: 10.3390/ijms23010298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/31/2021] [Accepted: 11/23/2021] [Indexed: 11/25/2022] Open
Abstract
An association between varicella zoster virus (VZV) and multiple sclerosis (MS) has been reported in Mexican populations. The aim of this study was to compare the response of T cells from MS patients, during relapse and remission, to in vitro stimulation with VZV, adenovirus (AV) and Epstein–Barr virus (EBV). Proliferation and cytokine secretion of T cells from 29 relapsing-remitting MS patients and 38 healthy controls (HC) were analyzed by flow cytometry after stimulating with VZV, AV or EBV. IgG and IgM levels against VZV and EBV were quantified using Enzyme-Linked Immunosorbent Assay. Relapsing MS patients showed a higher percentage of responding CD4+ and CD8+ T cells against VZV compared to AV. In HC and remitting MS patients, proliferation of CD4+ T cells was higher when stimulated with VZV as compared to EBV. Moreover, T cells isolated from remitting patients secreted predominantly Th1 cytokines when cell cultures were stimulated with VZV. Finally, high concentration of anti-VZV IgG was found in sera from patients and controls. The results support previous studies of an VZV-MS association in the particular population studied and provide additional information about the possible role of this virus in the pathogenesis of MS.
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49
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Analysis of TCR Repertoire by High-Throughput Sequencing Indicates the Feature of T Cell Immune Response after SARS-CoV-2 Infection. Cells 2021; 11:cells11010068. [PMID: 35011632 PMCID: PMC8750083 DOI: 10.3390/cells11010068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/13/2021] [Accepted: 12/24/2021] [Indexed: 01/10/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a global infectious disease caused by the SARS-CoV-2 coronavirus. T cells play an essential role in the body’s fighting against the virus invasion, and the T cell receptor (TCR) is crucial in T cell-mediated virus recognition and clearance. However, little has been known about the features of T cell response in convalescent COVID-19 patients. In this study, using 5′RACE technology and PacBio sequencing, we analyzed the TCR repertoire of COVID-19 patients after recovery for 2 weeks and 6 months compared with the healthy donors. The TCR clustering and CDR3 annotation were exploited to discover groups of patient-specific TCR clonotypes with potential SARS-CoV-2 antigen specificities. We first identified CD4+ and CD8+ T cell clones with certain clonal expansion after infection, and then observed the preferential recombination usage of V(D) J gene segments in CD4+ and CD8+ T cells of COVID-19 patients with different convalescent stages. More important, the TRBV6-5-TRBD2-TRBJ2-7 combination with high frequency was shared between CD4+ T and CD8+ T cells of different COVID-19 patients. Finally, we found the dominant characteristic motifs of the CDR3 sequence between recovered COVID-19 and healthy control. Our study provides novel insights on TCR in COVID-19 with different convalescent phases, contributing to our understanding of the immune response induced by SARS-CoV-2.
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50
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Kischkel B, Boniche-Alfaro C, Menezes IDG, Rossi SA, Angeli CB, de Almeida SR, Palmisano G, Lopes-Bezerra L, Nosanchuk JD, Taborda CP. Immunoproteomic and Immunopeptidomic Analyses of Histoplasma capsulatum Reveal Promiscuous and Conserved Epitopes Among Fungi With Vaccine Potential. Front Immunol 2021; 12:764501. [PMID: 34880863 PMCID: PMC8645968 DOI: 10.3389/fimmu.2021.764501] [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: 08/25/2021] [Accepted: 10/29/2021] [Indexed: 12/27/2022] Open
Abstract
As there are more than 6 million human deaths due to mycoses each year, there is an urgent need to develop fungal vaccines. Moreover, given the similarities among pathogenic fungi, it may be possible to create a multi-fungi vaccine. In this study, we combined immunoproteomic and immunopeptidomic methods, for which we have adapted a technique based on co-immunoprecipitation (Co-IP) that made it possible to map Histoplasma capsulatum epitopes for the first time in a natural context using murine dendritic cells (DCs) and macrophages (Mφ). Although polysaccharide epitopes exist, this research focused on mapping protein epitopes as these are more immunogenic. We used different algorithms to screen proteins and peptides identified by two-dimensional electrophoresis (2-D) and Co-IP. Seventeen proteins were revealed by 2-D gels, and 45 and 24 peptides from distinct proteins were presented by DCs and Mφ, respectively. We then determined which epitopes were restricted to MHC-I and II from humans and mice and showed high promiscuity, but lacked identity with human proteins. The 4 most promising peptides were synthesized, and the peptides with and without incorporation into glucan particles induced CD4+ and CD8+ T cell proliferation and produced a Th1 and Th17 response marked by the secretion of high levels of IFN-γ, IL-17 and IL-2. These epitopes were from heat shock protein 60, enolase, and the ATP-dependent molecular chaperone HSC82, and they each have a high degree of identity with proteins expressed by other medically important pathogenic fungi. Thus, the epitopes described in this study have the potential for use in the development of vaccines that could result in cross-protection among fungal species.
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Affiliation(s)
- Brenda Kischkel
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Camila Boniche-Alfaro
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Isabela de Godoy Menezes
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Suelen Andreia Rossi
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil.,Department of Dermatology, Tropical Medicine Institute, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Claudia Blanes Angeli
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Sandro Rogério de Almeida
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Leila Lopes-Bezerra
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Joshua D Nosanchuk
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, New York, NY, United States.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, United States
| | - Carlos Pelleschi Taborda
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil.,Department of Dermatology, Tropical Medicine Institute, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
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