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Zhu X, Chu X, Wang H, Liao Z, Xiang H, Zhao W, Yang L, Wu P, Liu X, Chen D, Xie J, Dai W, Li L, Wang J, Zhao H. Investigating neuropathological changes and underlying neurobiological mechanisms in the early stages of primary blast-induced traumatic brain injury: Insights from a rat model. Exp Neurol 2024; 375:114731. [PMID: 38373483 DOI: 10.1016/j.expneurol.2024.114731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 02/21/2024]
Abstract
The utilization of explosives and chemicals has resulted in a rise in blast-induced traumatic brain injury (bTBI) in recent times. However, there is a dearth of diagnostic biomarkers and therapeutic targets for bTBI due to a limited understanding of biological mechanisms, particularly in the early stages. The objective of this study was to examine the early neuropathological characteristics and underlying biological mechanisms of primary bTBI. A total of 83 Sprague Dawley rats were employed, with their heads subjected to a blast shockwave of peak overpressure ranging from 172 to 421 kPa in the GI, GII, and GIII groups within a closed shock tube, while the body was shielded. Neuromotor dysfunctions, morphological changes, and neuropathological alterations were detected through modified neurologic severity scores, brain water content analysis, MRI scans, histological, TUNEL, and caspase-3 immunohistochemical staining. In addition, label-free quantitative (LFQ)-proteomics was utilized to investigate the biological mechanisms associated with the observed neuropathology. Notably, no evident damage was discernible in the GII and GI groups, whereas mild brain injury was observed in the GIII group. Neuropathological features of bTBI were characterized by morphologic changes, including neuronal injury and apoptosis, cerebral edema, and cerebrovascular injury in the shockwave's path. Subsequently, 3153 proteins were identified and quantified in the GIII group, with subsequent enriched neurological responses consistent with pathological findings. Further analysis revealed that signaling pathways such as relaxin signaling, hippo signaling, gap junction, chemokine signaling, and sphingolipid signaling, as well as hub proteins including Prkacb, Adcy5, and various G-protein subunits (Gnai2, Gnai3, Gnao1, Gnb1, Gnb2, Gnb4, and Gnb5), were closely associated with the observed neuropathology. The expression of hub proteins was confirmed via Western blotting. Accordingly, this study proposes signaling pathways and key proteins that exhibit sensitivity to brain injury and are correlated with the early pathologies of bTBI. Furthermore, it highlights the significance of G-protein subunits in bTBI pathophysiology, thereby establishing a theoretical foundation for early diagnosis and treatment strategies for primary bTBI.
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Affiliation(s)
- Xiyan Zhu
- Department of Military Traffic Injury Prevention and Control, Daping Hospital, Army Medical University, Chongqing, China
| | - Xiang Chu
- Cognitive Development and Learning and Memory Disorders Translational Medicine Laboratory, Children's Hospital, Chongqing Medical University, Chongqing, China; Emergency department, Daping Hospital, Army Medical University, Chongqing, China
| | - Hao Wang
- Neurosurgery department, Daping Hospital, Army Medical University, Chongqing, China
| | - Zhikang Liao
- Department of Military Traffic Injury Prevention and Control, Daping Hospital, Army Medical University, Chongqing, China
| | - Hongyi Xiang
- Department of Military Traffic Injury Prevention and Control, Daping Hospital, Army Medical University, Chongqing, China
| | - Wenbing Zhao
- Department of Military Traffic Injury Prevention and Control, Daping Hospital, Army Medical University, Chongqing, China
| | - Li Yang
- Department of Military Traffic Injury Prevention and Control, Daping Hospital, Army Medical University, Chongqing, China
| | - Pengfei Wu
- Department of Military Traffic Injury Prevention and Control, Daping Hospital, Army Medical University, Chongqing, China
| | - Xing Liu
- Department of Military Traffic Injury Prevention and Control, Daping Hospital, Army Medical University, Chongqing, China
| | - Diyou Chen
- Department of Military Traffic Injury Prevention and Control, Daping Hospital, Army Medical University, Chongqing, China
| | - Jingru Xie
- Department of Military Traffic Injury Prevention and Control, Daping Hospital, Army Medical University, Chongqing, China
| | - Wei Dai
- Department of Military Traffic Injury Prevention and Control, Daping Hospital, Army Medical University, Chongqing, China
| | - Lei Li
- Trauma Medical Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Jianmin Wang
- Department of Weapon Bioeffect Assessment, Daping Hospital, Army Medical University, Chongqing, China.
| | - Hui Zhao
- Department of Military Traffic Injury Prevention and Control, Daping Hospital, Army Medical University, Chongqing, China.
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2
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Duran T, Naik S, Sharifi L, DiLuzio WR, Chanda A, Chaudhuri B. Studying the ssDNA loaded adeno-associated virus aggregation using coarse-grained molecular dynamics simulations. Int J Pharm 2024; 655:123985. [PMID: 38484860 DOI: 10.1016/j.ijpharm.2024.123985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
The aggregation of adeno-associated viral (AAV) capsids in an aqueous environment was investigated via coarse-grained molecular dynamics (CG-MD) simulations. The primary driving force and mechanism of the aggregation were investigated with or without single-strand DNA (ssDNA) loaded at various process temperatures. Capsid aggregation appeared to involve multiple residue interactions (i.e., hydrophobic, polar and charged residues) leading to complex protein aggregation. In addition, two aggregation mechanisms (i.e., the fivefold face-to-face contact and the edge-to-edge contact) were identified from this study. The ssDNA with its asymmetric structure could be the reason for destabilizing protein subunits and enhancing the interaction between the charged residues, and further result in the non-reversible face-to-face contact. At higher temperature, the capsid structure was found to be unstable with the significant size expansion of the loaded ssDNA which could be attributed to reduced number of intramolecular hydrogen bonds, the increased conformational deviations of protein subunits and the higher residue fluctuations. The CG-MD model was further validated with previous experimental and simulation data, including the full capsid size measurement and the capsid internal pressure. Thus, a good understanding of AAV capsid aggregation, instability and the role of ssDNA were revealed by applying the developed computational model.
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Affiliation(s)
- Tibo Duran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
| | - Shivangi Naik
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
| | - Leila Sharifi
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
| | - Willow R DiLuzio
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
| | - Arani Chanda
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
| | - Bodhisattwa Chaudhuri
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA; Institute of Material Sciences (IMS), University of Connecticut, Storrs, CT, USA.
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3
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Hollerbach AL, Ibrahim YM, Lin VS, Schultz KJ, Huntley AP, Armentrout PB, Metz TO, Ewing RG. Identification of Unique Fragmentation Patterns of Fentanyl Analog Protomers Using Structures for Lossless Ion Manipulations Ion Mobility-Orbitrap Mass Spectrometry. J Am Soc Mass Spectrom 2024; 35:793-803. [PMID: 38469802 DOI: 10.1021/jasms.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The opioid crisis in the United States is being fueled by the rapid emergence of new fentanyl analogs and precursors that can elude traditional library-based screening methods, which require data from known reference compounds. Since reference compounds are unavailable for new fentanyl analogs, we examined if fentanyls (fentanyl + fentanyl analogs) could be identified in a reference-free manner using a combination of electrospray ionization (ESI), high-resolution ion mobility (IM) spectrometry, high-resolution mass spectrometry (MS), and higher-energy collision-induced dissociation (MS/MS). We analyzed a mixture containing nine fentanyls and W-15 (a structurally similar molecule) and found that the protonated forms of all fentanyls exhibited two baseline-separated IM distributions that produced different MS/MS patterns. Upon fragmentation, both IM distributions of all fentanyls produced two high intensity fragments, resulting from amine site cleavages. The higher mobility distributions of all fentanyls also produced several low intensity fragments, but surprisingly, these same fragments exhibited much greater intensities in the lower mobility distributions. This observation demonstrates that many fragments of fentanyls predominantly originate from one of two different gas-phase structures (suggestive of protomers). Furthermore, increasing the water concentration in the ESI solution increased the intensity of the lower mobility distribution relative to the higher mobility distribution, which further supports that fentanyls exist as two gas-phase protomers. Our observations on the IM and MS/MS properties of fentanyls can be exploited to positively differentiate fentanyls from other compounds without requiring reference libraries and will hopefully assist first responders and law enforcement in combating new and emerging fentanyls.
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Affiliation(s)
- Adam L Hollerbach
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vivian S Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Katherine J Schultz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Adam P Huntley
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Robert G Ewing
- Nuclear, Chemistry & Biology Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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Mao W, Chen S. Assembly mechanisms of the neuronal gap junction channel connexin 36 elucidated by Cryo-EM. Arch Biochem Biophys 2024; 754:109959. [PMID: 38490311 DOI: 10.1016/j.abb.2024.109959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/20/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
Electrical synapses are essential components of neural circuits. Neuronal signal transduction across electrical synapses is primarily mediated by gap junction channels composed of Connexin36 (Cx36), the lack of which causes impaired electrical coupling between certain neurons including cortical interneurons and thalamic reticular nucleus (TRN) neurons. However, the structural basis underlying Cx36 function and assembly remains elusive. Recently, Lee et al. reported cryo-EM structures of Cx36, thus provided first insights of its gating mechanism. Here, we report a consistent cryo-EM structure of Cx36 determined in parallel, and describe unique interactions underpinning its assembly mechanism in complementary to the competing work. In particular, we found non-canonical electrostatic interactions between protomers from opposing hemichannels and a steric complementary site between adjacent protomers within a hemichannel, which together provide a structural explanation for the assembly specificity in homomeric and heteromeric gap junction channels.
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Affiliation(s)
- Wenxuan Mao
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shanshuang Chen
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Zhang D, Czapinska H, Bochtler M, Wlodawer A, Lubkowski J. RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short-chain L-asparaginases. Protein Sci 2024; 33:e4920. [PMID: 38501449 PMCID: PMC10949315 DOI: 10.1002/pro.4920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 03/20/2024]
Abstract
L-Asparaginases (ASNases) catalyze the hydrolysis of L-Asn to L-Asp and ammonia. Members of the ASNase family are used as drugs in the treatment of leukemia, as well as in the food industry. The protomers of bacterial ASNases typically contain 300-400 amino acids (typical class 1 ASNases). In contrast, the chain of ASNase from Rhodospirillum rubrum, reported here and referred to as RrA, consists of only 172 amino acid residues. RrA is homologous to the N-terminal domain of typical bacterial class 1 ASNases and exhibits millimolar affinity for L-Asn. In this study, we demonstrate that RrA belongs to a unique family of cytoplasmic, short-chain ASNases (scASNases). These proteins occupy a distinct region in the sequence space, separate from the regions typically assigned to class 1 ASNases. The scASNases are present in approximately 7% of eubacterial species, spanning diverse bacterial lineages. They seem to be significantly enriched in species that encode for more than one class 1 ASNase. Here, we report biochemical, biophysical, and structural properties of RrA, a member of scASNases family. Crystal structures of the wild-type RrA, both with and without bound L-Asp, as well as structures of several RrA mutants, reveal topologically unique tetramers. Moreover, the active site of one protomer is complemented by two residues (Tyr21 and Asn26) from another protomer. Upon closer inspection, these findings clearly outline scASNases as a stand-alone subfamily of ASNases that can catalyze the hydrolysis of L-Asn to L-Asp despite the lack of the C-terminal domain that is present in all ASNases described structurally to date.
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Affiliation(s)
- Di Zhang
- Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
| | - Honorata Czapinska
- Laboratory of Structural BiologyInternational Institute of Molecular and Cell BiologyWarsawPoland
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Matthias Bochtler
- Laboratory of Structural BiologyInternational Institute of Molecular and Cell BiologyWarsawPoland
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Alexander Wlodawer
- Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
| | - Jacek Lubkowski
- Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
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Kim E, Shin J, Ferrari A, Huang S, An E, Han D, Khan MS, Kenniston TW, Cassaniti I, Baldanti F, Jeong D, Gambotto A. Fourth dose of microneedle array patch of SARS-CoV-2 S1 protein subunit vaccine elicits robust long-lasting humoral responses in mice. Int Immunopharmacol 2024; 129:111569. [PMID: 38340419 DOI: 10.1016/j.intimp.2024.111569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
The COVID-19 pandemic has underscored the pressing need for safe and effective booster vaccines, particularly in considering the emergence of new SARS-CoV-2 variants and addressing vaccine distribution inequalities. Dissolving microneedle array patches (MAP) offer a promising delivery method, enhancing immunogenicity and improving accessibility through the skin's immune potential. In this study, we evaluated a microneedle array patch-based S1 subunit protein COVID-19 vaccine candidate, which comprised a bivalent formulation targeting the Wuhan and Beta variant alongside a monovalent Delta variant spike proteins in a murine model. Notably, the second boost of homologous bivalent MAP-S1(WU + Beta) induced a 15.7-fold increase in IgG endpoint titer, while the third boost of heterologous MAP-S1RS09Delta yielded a more modest 1.6-fold increase. Importantly, this study demonstrated that the administration of four doses of the MAP vaccine induced robust and long-lasting immune responses, persisting for at least 80 weeks. These immune responses encompassed various IgG isotypes and remained statistically significant for one year. Furthermore, neutralizing antibodies against multiple SARS-CoV-2 variants were generated, with comparable responses observed against the Omicron variant. Overall, these findings emphasize the potential of MAP-based vaccines as a promising strategy to combat the evolving landscape of COVID-19 and to deliver a safe and effective booster vaccine worldwide.
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Affiliation(s)
- Eun Kim
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Juyeop Shin
- Medical Business Division, Raphas Co., Ltd., Seoul, Republic of Korea
| | - Alessandro Ferrari
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Pavia, Italy
| | - Shaohua Huang
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Eunjin An
- Medical Business Division, Raphas Co., Ltd., Seoul, Republic of Korea
| | - Donghoon Han
- Medical Business Division, Raphas Co., Ltd., Seoul, Republic of Korea
| | - Muhammad S Khan
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Thomas W Kenniston
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Irene Cassaniti
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Pavia, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Dohyeon Jeong
- Medical Business Division, Raphas Co., Ltd., Seoul, Republic of Korea
| | - Andrea Gambotto
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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7
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Kim M, Le MT, Fan L, Campbell C, Sen S, Capdevila DA, Stemmler TL, Giedroc DP. Characterization of the Zinc Uptake Repressor (Zur) from Acinetobacter baumannii. Biochemistry 2024; 63:660-670. [PMID: 38385972 PMCID: PMC11019503 DOI: 10.1021/acs.biochem.3c00679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Bacterial cells tightly regulate the intracellular concentrations of essential transition metal ions by deploying a panel of metal-regulated transcriptional repressors and activators that bind to operator-promoter regions upstream of regulated genes. Like other zinc uptake regulator (Zur) proteins, Acinetobacter baumannii Zur represses transcription of its regulon when ZnII is replete and binds more weakly to DNA when ZnII is limiting. Previous studies established that Zur proteins are homodimeric and harbor at least two metal sites per protomer or four per dimer. CdII X-ray absorption spectroscopy (XAS) of the Cd2Zn2 AbZur metalloderivative with CdII bound to the allosteric sites reveals a S(N/O)3 first coordination shell. Site-directed mutagenesis suggests that H89 and C100 from the N-terminal DNA binding domain and H107 and E122 from the C-terminal dimerization domain comprise the regulatory metal site. KZn for this allosteric site is 6.0 (±2.2) × 1012 M-1 with a functional "division of labor" among the four metal ligands. N-terminal domain ligands H89 and C100 contribute far more to KZn than H107 and E122, while C100S AbZur uniquely fails to bind to DNA tightly as measured by an in vitro transcription assay. The heterotropic allosteric coupling free energy, ΔGc, is negative, consistent with a higher KZn for the AbZur-DNA complex and defining a bioavailable ZnII set-point of ≈6 × 10-14 M. Small-angle X-ray scattering (SAXS) experiments reveal that only the wild-type Zn homodimer undergoes allosteric switching, while the C100S AbZur fails to switch. These data collectively suggest that switching to a high affinity DNA-binding conformation involves a rotation/translation of one protomer relative to the other in a way that is dependent on the integrity of C100. We place these findings in the context of other Zur proteins and Fur family repressors more broadly.
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Affiliation(s)
- Minyong Kim
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - My Tra Le
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility of the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Courtney Campbell
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201-2417, United States
| | - Sambuddha Sen
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Daiana A Capdevila
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405 BWE Buenos Aires, Argentina
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201-2417, United States
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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Jian H, Chen Z, Du H, Liao T, Sun Y, Ke D, Yu Y. Inhibition of ferroptosis by POLE2 in gastric cancer cells involves the activation of NRF2/GPX4 pathway. J Cell Mol Med 2024; 28:e17983. [PMID: 38070189 PMCID: PMC10805511 DOI: 10.1111/jcmm.17983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/14/2023] [Accepted: 09/26/2023] [Indexed: 01/25/2024] Open
Abstract
Gastric cancer results in great cancer mortality worldwide, and inducing ferroptosis dramatically improves the malignant phenotypes of gastric cancer. DNA polymerase epsilon subunit 2 (POLE2) plays indispensable roles in tumorigenesis; however, its involvement and molecular basis in ferroptosis and gastric cancer are not clear. Human gastric cancer cells were infected with lentiviral vectors to knock down or overexpress POLE2, and cell ferroptosis was detected. To further validate the involvement of nuclear factor erythroid 2-related factor 2 (NRF2) and glutathione peroxidase 4 (GPX4), lentiviral vectors were used. POLE2 expression was elevated in human gastric cancer cells and tissues and closely correlated with clinicopathological features in gastric cancer patients. POLE2 knockdown was induced, while POLE2 overexpression inhibited ferroptosis of human gastric cancer cells, thereby modulating the malignant phenotypes of gastric cancer. Mechanistic studies revealed that POLE2 overexpression elevated NRF2 expression and activity and subsequently activated GPX4, which then prevented lipid peroxidation and ferroptosis in human gastric cancer cells. In contrast, either NRF2 or GPX4 silence significantly prevented POLE2 overexpression-mediated inductions of cell proliferation, migration, invasion and inhibition of ferroptosis. POLE2 overexpression inhibits ferroptosis in human gastric cancer cells through activating NRF2/GPX4 pathway, and inhibiting POLE2 may be a crucial strategy to treat gastric cancer.
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Affiliation(s)
- Hui Jian
- Department of Gastrointestinal SurgeryAffiliated Hospital of Jianghan UniversityWuhanHubeiChina
| | - Zhi‐Qiang Chen
- Department of Gastrointestinal SurgeryAffiliated Hospital of Jianghan UniversityWuhanHubeiChina
| | - Heng Du
- Department of Gastrointestinal SurgeryHuanggang Central Hospital Affiliated to Yangtze UniversityHuanggangHubeiChina
| | - Ting Liao
- Department of GastroenterologyAffiliated Hospital of Jianghan UniversityWuhanHubeiChina
| | - Yi‐Chen Sun
- Department of OncologyAffiliated Hospital of Jianghan UniversityWuhanHubeiChina
| | - Dong Ke
- Department of Gastrointestinal SurgeryRenmin Hospital of Wuhan UniversityWuhanHubeiChina
| | - Yang Yu
- Department of Gastrointestinal SurgeryAffiliated Hospital of Jianghan UniversityWuhanHubeiChina
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Vasta JD, Michaud A, Aaron Crapster J, Robers MB. A Method to Conditionally Measure Target Engagement at Intracellular RAS and RAF Complexes. Methods Mol Biol 2024; 2797:287-297. [PMID: 38570468 DOI: 10.1007/978-1-0716-3822-4_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Dysfunction of the RAS/mitogen-activated protein kinase (MAPK) pathway is a common driver of human cancers. As such, both the master regulator of the pathway, RAS, and its proximal kinase effectors, RAFs, have been of interest as drug targets for decades. Importantly, signaling within the RAS/MAPK pathway is highly coordinated due to the formation of a higher-order complex called the RAS/RAF signalosome, which may minimally contain dimers of both RAS and RAF protomers. In the disease state, RAS and RAF assemble in homo- and/or heterodimeric forms. Traditionally, drug development campaigns for both RAS and RAF have utilized biochemical assays of purified recombinant protein. As these assays do not query the RAS or RAF proteins in their full-length and complexed forms in cells, potency results collected using these assays have often failed to correlate with inhibition of the MAPK pathway. To more accurately quantify engagement at this signaling components, we present a bioluminescence resonance energy transfer (BRET)-based method to conditionally measure target engagement at individual protomers within the RAS/RAF signalosome in live cells.
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Vishwakarma C, Ansari A, Pratap JV. Distinct oligomerization and NADPH binding modes observed between L. donovani and human quinone oxidoreductases. Biochem Biophys Res Commun 2024; 690:149096. [PMID: 37988924 DOI: 10.1016/j.bbrc.2023.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 11/23/2023]
Abstract
Electron-driven process helps the living organism in the generations of energy, biomass production and detoxification of synthetic compounds. Soluble quinone oxidoreductases (QORs) mediate the transfer of an electron from NADPH to various quinone and other compounds, helping in the detoxification of quinones. QORs play a crucial role in cellular metabolism and are thus potential targets for drug development. Here we report the crystal structure of the NADPH-dependent QOR from Leishmania donovani (LdQOR) at 2.05 Å. The enzyme exists as a homo-dimer, with each protomer consisting of two domains, responsible for binding NADPH cofactor and the substrate. Interestingly, the human QOR exists as a tetramer. Comparative analysis of the oligomeric interfaces of LdQOR with HsQOR shows no significant differences in the protomer/dimer assembly. The tetrameric interface of HsQOR is stabilized by salt bridges formed between Arg 169 and Glu 271 which is non-existent in LdQOR, with an Alanine replacing the glutamate. This distinct feature is conserved across other dimeric QORs, indicating the importance of this interaction for tetramer association. Among the homologs, the sequences of the loop region involved in the stabilization and binding of the adenine ring of the NADPH shows significant differences except for an Arginine & glycine residues. In dimer QORs, this Arginine acts as a gate to the co-factor, while the NADPH binding mode in the human homolog is distinct, stabilized by His 200 and Asn 229, which are not conserved in LdQOR. These distinct features have the potential to be utilized for therapeutic interventions.
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Affiliation(s)
- Chandan Vishwakarma
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Ahmadullah Ansari
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - J Venkatesh Pratap
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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11
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Fatehi F, Twarock R. An interaction network approach predicts protein cage architectures in bionanotechnology. Proc Natl Acad Sci U S A 2023; 120:e2303580120. [PMID: 38060565 PMCID: PMC10723117 DOI: 10.1073/pnas.2303580120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/21/2023] [Indexed: 12/17/2023] Open
Abstract
Protein nanoparticles play pivotal roles in many areas of bionanotechnology, including drug delivery, vaccination, and diagnostics. These technologies require control over the distinct particle morphologies that protein nanocontainers can adopt during self-assembly from their constituent protein components. The geometric construction principle of virus-derived protein cages is by now fairly well understood by analogy to viral protein shells in terms of Caspar and Klug's quasi-equivalence principle. However, many artificial, or genetically modified, protein containers exhibit varying degrees of quasi-equivalence in the interactions between identical protein subunits. They can also contain a subset of protein subunits that do not participate in interactions with other assembly units, called capsomers, leading to gaps in the particle surface. We introduce a method that exploits information on the local interactions between the capsomers to infer the geometric construction principle of these nanoparticle architectures. The predictive power of this approach is demonstrated here for a prominent system in nanotechnology, the AaLS pentamer. Our method not only rationalises hitherto discovered cage structures but also predicts geometrically viable options that have not yet been observed. The classification of nanoparticle architecture based on the geometric properties of the interaction network closes a gap in our current understanding of protein container structure and can be widely applied in protein nanotechnology, paving the way to programmable control over particle polymorphism.
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Affiliation(s)
- Farzad Fatehi
- Departments of Mathematics, University of York, YorkYO10 5DD, United Kingdom
| | - Reidun Twarock
- Departments of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
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12
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Bethel NP, Borst AJ, Parmeggiani F, Bick MJ, Brunette TJ, Nguyen H, Kang A, Bera AK, Carter L, Miranda MC, Kibler RD, Lamb M, Li X, Sankaran B, Baker D. Precisely patterned nanofibres made from extendable protein multiplexes. Nat Chem 2023; 15:1664-1671. [PMID: 37667012 PMCID: PMC10695826 DOI: 10.1038/s41557-023-01314-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/04/2023] [Indexed: 09/06/2023]
Abstract
Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C2 to C8 and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.
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Affiliation(s)
- Neville P Bethel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Andrew J Borst
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Fabio Parmeggiani
- School of Chemistry, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
- Bristol Biodesign Institute, University of Bristol, Bristol, UK
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ryan D Kibler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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13
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Förste S, Vonshak O, Daube SS, Bar-Ziv RH, Lipowsky R, Rudorf S. Computational analysis of protein synthesis, diffusion, and binding in compartmental biochips. Microb Cell Fact 2023; 22:244. [PMID: 38037098 PMCID: PMC10688499 DOI: 10.1186/s12934-023-02237-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023] Open
Abstract
Protein complex assembly facilitates the combination of individual protein subunits into functional entities, and thus plays a crucial role in biology and biotechnology. Recently, we developed quasi-twodimensional, silicon-based compartmental biochips that are designed to study and administer the synthesis and assembly of protein complexes. At these biochips, individual protein subunits are synthesized from locally confined high-density DNA brushes and are captured on the chip surface by molecular traps. Here, we investigate single-gene versions of our quasi-twodimensional synthesis systems and introduce the trap-binding efficiency to characterize their performance. We show by mathematical and computational modeling how a finite trap density determines the dynamics of protein-trap binding and identify three distinct regimes of the trap-binding efficiency. We systematically study how protein-trap binding is governed by the system's three key parameters, which are the synthesis rate, the diffusion constant and the trap-binding affinity of the expressed protein. In addition, we describe how spatially differential patterns of traps modulate the protein-trap binding dynamics. In this way, we extend the theoretical knowledge base for synthesis, diffusion, and binding in compartmental systems, which helps to achieve better control of directed molecular self-assembly required for the fabrication of nanomachines for synthetic biology applications or nanotechnological purposes.
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Affiliation(s)
- Stefanie Förste
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Ohad Vonshak
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shirley S Daube
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Roy H Bar-Ziv
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Reinhard Lipowsky
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Sophia Rudorf
- Institute of Cell Biology and Biophysics, Leibniz University Hannover, 30419, Hannover, Germany.
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14
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Ida K, Sato Y, Hikami K, Magnay M, Shaw MH. Signal conversion as tumor micro environment (TME) specifically activated cytokine. Biochem Biophys Res Commun 2023; 683:149077. [PMID: 37890200 DOI: 10.1016/j.bbrc.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023]
Abstract
Targeted cytokine delivery has been gaining popularity in cancer immunotherapy since systemic recombinant cytokine treatment has not been successful due to low response rate and systemic toxicities in the clinical studies. In order to address these issues, we propose a new concept that cytokine signal is specifically activated at tumor-micro-environment (TME) by delivering two protein subunits of heterodimeric cytokine fused with a tumor targeting antibody respectively to TME and by bridging the two subunits into active heterodimeric form.Interleukin-12 (IL-12) is one of the major cytokines which can induce immune activation. IL-12 consists of two protein subunits which are p35 and p40. IL-12 signaling is initiated when it forms as the heterodimeric protein and binds to IL-12 receptor complex. We made fusion proteins of both IL-12p35 and IL-12p40 targeting specific tumor associated antigens (TAAs) and demonstrated the formation of bioactive IL12p70 with TME targeting antibody toward both p35 and p40 to form as the active molecule. We describe our concept validation in an in vitro based functional assay.
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Affiliation(s)
- Koh Ida
- Takeda Pharmaceuticals International Co., Cambridge, MA, USA.
| | - Yosuke Sato
- Takeda Pharmaceuticals International Co., Cambridge, MA, USA
| | - Koki Hikami
- Takeda Pharmaceuticals International Co., Cambridge, MA, USA
| | - Maureen Magnay
- Takeda Pharmaceuticals International Co., Cambridge, MA, USA
| | - Michael H Shaw
- Takeda Pharmaceuticals International Co., Cambridge, MA, USA
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15
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Dalby KN. Raf protomers: Drug binding preferences in living cells. Cell Chem Biol 2023; 30:1329-1331. [PMID: 37977126 PMCID: PMC10954368 DOI: 10.1016/j.chembiol.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023]
Abstract
The precise and selective quantification of drug-target interactions within the context of RAS-RAF heterodimers in live cells offers a powerful tool for drug development and personalized medicine, particularly in cancer research, where the RAS-RAF pathway is pivotal.
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Affiliation(s)
- Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA.
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16
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Nakasone Y, Murakami H, Tokonami S, Oda T, Terazima M. Time-resolved study on signaling pathway of photoactivated adenylate cyclase and its nonlinear optical response. J Biol Chem 2023; 299:105285. [PMID: 37742920 PMCID: PMC10634658 DOI: 10.1016/j.jbc.2023.105285] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/06/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023] Open
Abstract
Photoactivated adenylate cyclases (PACs) are multidomain BLUF proteins that regulate the cellular levels of cAMP in a light-dependent manner. The signaling route and dynamics of PAC from Oscillatoria acuminata (OaPAC), which consists of a light sensor BLUF domain, an adenylate cyclase domain, and a connector helix (α3-helix), were studied by detecting conformational changes in the protein moiety. Although circular dichroism and small-angle X-ray scattering measurements did not show significant changes upon light illumination, the transient grating method successfully detected light-induced changes in the diffusion coefficient (diffusion-sensitive conformational change (DSCC)) of full-length OaPAC and the BLUF domain with the α3-helix. DSCC of full-length OaPAC was observed only when both protomers in a dimer were photoconverted. This light intensity dependence suggests that OaPAC is a cyclase with a nonlinear light intensity response. The enzymatic activity indeed nonlinearly depends on light intensity, that is, OaPAC is activated under strong light conditions. It was also found that both DSCC and enzymatic activity were suppressed by a mutation in the W90 residue, indicating the importance of the highly conserved Trp in many BLUF domains for the function. Based on these findings, a reaction scheme was proposed together with the reaction dynamics.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hiroto Murakami
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shunrou Tokonami
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Takashi Oda
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.
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17
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Gerber M, Suppanz I, Oeljeklaus S, Niemann M, Käser S, Warscheid B, Schneider A, Dewar CE. A Msp1-containing complex removes orphaned proteins in the mitochondrial outer membrane of T. brucei. Life Sci Alliance 2023; 6:e202302004. [PMID: 37586887 PMCID: PMC10432679 DOI: 10.26508/lsa.202302004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
The AAA-ATPase Msp1 extracts mislocalised outer membrane proteins and thus contributes to mitochondrial proteostasis. Using pulldown experiments, we show that trypanosomal Msp1 localises to both glycosomes and the mitochondrial outer membrane, where it forms a complex with four outer membrane proteins. The trypanosome-specific pATOM36 mediates complex assembly of α-helically anchored mitochondrial outer membrane proteins such as protein translocase subunits. Inhibition of their assembly triggers a pathway that results in the proteasomal digestion of unassembled substrates. Using inducible single, double, and triple RNAi cell lines combined with proteomic analyses, we demonstrate that not only Msp1 but also the trypanosomal homolog of the AAA-ATPase VCP are implicated in this quality control pathway. Moreover, in the absence of VCP three out of the four Msp1-interacting mitochondrial proteins are required for efficient proteasomal digestion of pATOM36 substrates, suggesting they act in concert with Msp1. pATOM36 is a functional analog of the yeast mitochondrial import complex complex and possibly of human mitochondrial animal-specific carrier homolog 2, suggesting that similar mitochondrial quality control pathways linked to Msp1 might also exist in yeast and humans.
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Affiliation(s)
- Markus Gerber
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Ida Suppanz
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Silke Oeljeklaus
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Moritz Niemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Sandro Käser
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Warscheid
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
- Institute for Advanced Study (Wissenschaftskolleg) Berlin, Berlin, Germany
| | - Caroline E Dewar
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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18
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Ge X, Qu Q, Wang Z, Zhang S, Chi Y, Shan C, Liu R, Zhao Q. [Research progress in vaccines of SARS-CoV-2]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2023; 39:946-951. [PMID: 37882719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
Since the outbreak of corona virus disease 2019 (COVID-19), viral strains have mutated and evolved. Vaccine research is the most direct and effective way to control COVID-19. According to different production mechanisms, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines included inactivated virus vaccine, live attenuated vaccine, mRNA vaccine, DNA vaccine, viral vector vaccine, virus-like particle vaccine and protein subunit vaccine. Among them, viral protein subunit vaccine has a wide application prospect due to its high safety and effectiveness. Viral nucleocapsid protein has high immunogenicity and low variability which could be a new direction for vaccine production. We summarized the current development of vaccine research by reviewing the current progress, vaccine safety and vaccine immune efficiency. It is hoped that the proposed possible development strategies could provide a reference for epidemic prevention work in future.
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Affiliation(s)
- Xinbin Ge
- School of Clinical Medicine, Jining Medical University, Jining 272007, China
| | - Qigan Qu
- School of Clinical Medicine, Jining Medical University, Jining 272007, China
| | - Zeguang Wang
- School of Clinical Medicine, Jining Medical University, Jining 272007, China
| | - Shungeng Zhang
- School of Clinical Medicine, Jining Medical University, Jining 272007, China
| | - Yan Chi
- School of Clinical Medicine, Jining Medical University, Jining 272007, China
| | - Chunhui Shan
- School of Clinical Medicine, Jining Medical University, Jining 272007, China
| | - Ruihan Liu
- School of Clinical Medicine, Jining Medical University, Jining 272007; Department of Paediatrics, Affiliated Hospital of Jining Medical University, Jining 272029, China. *Corresponding authors, E-mail:
| | - Qing Zhao
- School of Clinical Medicine, Jining Medical University, Jining 272007; Department of Paediatrics, Affiliated Hospital of Jining Medical University, Jining 272029, China. *Corresponding authors, E-mail:
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19
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Leroux J, Kotobi A, Hirsch K, Lau T, Ortiz-Mahecha C, Maksimov D, Meißner R, Oostenrijk B, Rossi M, Schubert K, Timm M, Trinter F, Unger I, Zamudio-Bayer V, Schwob L, Bari S. Mapping the electronic transitions of protonation sites in peptides using soft X-ray action spectroscopy. Phys Chem Chem Phys 2023; 25:25603-25618. [PMID: 37721108 DOI: 10.1039/d3cp02524a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Near-edge X-ray absorption mass spectrometry (NEXAMS) around the nitrogen and oxygen K-edges was employed on gas-phase peptides to probe the electronic transitions related to their protonation sites, namely at basic side chains, the N-terminus and the amide oxygen. The experimental results are supported by replica exchange molecular dynamics and density-functional theory and restricted open-shell configuration with single calculations to attribute the transitions responsible for the experimentally observed resonances. We studied five tailor-made glycine-based pentapeptides, where we identified the signature of the protonation site of N-terminal proline, histidine, lysine and arginine, at 406 eV, corresponding to N 1s → σ*(NHx+) (x = 2 or 3) transitions, depending on the peptides. We compared the spectra of pentaglycine and triglycine to evaluate the sensitivity of NEXAMS to protomers. Separate resonances have been identified to distinguish two protomers in triglycine, the protonation site at the N-terminus at 406 eV and the protonation site at the amide oxygen characterized by a transition at 403.1 eV.
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Affiliation(s)
- Juliette Leroux
- CIMAP, CEA/CNRS/ENSICAEN/Université de Caen Normandie, 14050 Caen, France
- Deutsches Elektronen-Synchrotron DESY, Germany.
| | - Amir Kotobi
- Deutsches Elektronen-Synchrotron DESY, Germany.
- Helmholtz-Zentrum Hereon, Institute of Surface Science, 21502 Geesthacht, Germany
| | - Konstantin Hirsch
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Tobias Lau
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Carlos Ortiz-Mahecha
- Hamburg University of Technology, Institute of Polymers and Composites, 21073 Hamburg, Germany
| | - Dmitrii Maksimov
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Robert Meißner
- Helmholtz-Zentrum Hereon, Institute of Surface Science, 21502 Geesthacht, Germany
- Hamburg University of Technology, Institute of Polymers and Composites, 21073 Hamburg, Germany
| | | | - Mariana Rossi
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | | | - Martin Timm
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Florian Trinter
- Institut für Kernphysik, Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
- Molecular Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Isaak Unger
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
| | - Vicente Zamudio-Bayer
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | | | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Germany.
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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20
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Andjelkovic M, Zinovjev K, Ramos-Guzmán CA, Ruiz- Pernía JJ, Tuñón I. Elucidation of the Active Form and Reaction Mechanism in Human Asparaginase Type III Using Multiscale Simulations. J Chem Inf Model 2023; 63:5676-5688. [PMID: 37635309 PMCID: PMC10852353 DOI: 10.1021/acs.jcim.3c00900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Indexed: 08/29/2023]
Abstract
l-asparaginases catalyze the asparagine hydrolysis to aspartate. These enzymes play an important role in the treatment of acute lymphoblastic leukemia because these cells are unable to produce their own asparagine. Due to the immunogenic response and various side effects of enzymes of bacterial origin, many attempts have been made to replace these enzymes with mammalian enzymes such as human asparaginase type III (hASNaseIII). This study investigates the reaction mechanism of hASNaseIII through molecular dynamics simulations, quantum mechanics/molecular mechanics methods, and free energy calculations. Our simulations reveal that the dimeric form of the enzyme plays a vital role in stabilizing the substrate in the active site, despite the active site residues coming from a single protomer. Protomer-protomer interactions are essential to keep the enzyme in an active conformation. Our study of the reaction mechanism indicates that the self-cleavage process that generates an N-terminal residue (Thr168) is required to activate the enzyme. This residue acts as the nucleophile, attacking the electrophilic carbon of the substrate after a proton transfer from its hydroxyl group to the N-terminal amino group. The reaction mechanism proceeds with the formation of an acyl-enzyme complex and its hydrolysis, which turns out to be the rate-determining step. Our proposal of the enzymatic mechanism sheds light on the role of different active site residues and rationalizes the studies on mutations. The insights provided here about hASNaseIII activity could contribute to the comprehension of the disparities among different ASNases and might even guide the design of new variants with improved properties for acute lymphoblastic leukemia treatment.
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Affiliation(s)
- Milorad Andjelkovic
- Departamento
de Química Física, Universidad
de Valencia, 46100 Burjassot, Spain
| | - Kirill Zinovjev
- Departamento
de Química Física, Universidad
de Valencia, 46100 Burjassot, Spain
| | - Carlos Alberto Ramos-Guzmán
- Departamento
de Química Física, Universidad
de Valencia, 46100 Burjassot, Spain
- Instituto
de Materiales Avanzados, Universidad Jaume
I, 12071 Castelló, Spain
| | | | - Iñaki Tuñón
- Departamento
de Química Física, Universidad
de Valencia, 46100 Burjassot, Spain
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21
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Luo SC, Yeh MC, Lien YH, Yeh HY, Siao HL, Tu IP, Chi P, Ho MC. A RAD51-ADP double filament structure unveils the mechanism of filament dynamics in homologous recombination. Nat Commun 2023; 14:4993. [PMID: 37591853 PMCID: PMC10435448 DOI: 10.1038/s41467-023-40672-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
ATP-dependent RAD51 recombinases play an essential role in eukaryotic homologous recombination by catalyzing a four-step process: 1) formation of a RAD51 single-filament assembly on ssDNA in the presence of ATP, 2) complementary DNA strand-exchange, 3) ATP hydrolysis transforming the RAD51 filament into an ADP-bound disassembly-competent state, and 4) RAD51 disassembly to provide access for DNA repairing enzymes. Of these steps, filament dynamics between the ATP- and ADP-bound states, and the RAD51 disassembly mechanism, are poorly understood due to the lack of near-atomic-resolution information of the ADP-bound RAD51-DNA filament structure. We report the cryo-EM structure of ADP-bound RAD51-DNA filaments at 3.1 Å resolution, revealing a unique RAD51 double-filament that wraps around ssDNA. Structural analysis, supported by ATP-chase and time-resolved cryo-EM experiments, reveals a collapsing mechanism involving two four-protomer movements along ssDNA for mechanical transition between RAD51 single- and double-filament without RAD51 dissociation. This mechanism enables elastic change of RAD51 filament length during structural transitions between ATP- and ADP-states.
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Affiliation(s)
- Shih-Chi Luo
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan
| | - Min-Chi Yeh
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan
| | - Yu-Hsiang Lien
- Institute of Statistical Science, Academia Sinica, 11529, Taipei, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan
| | - Huei-Lun Siao
- Institute of Statistical Science, Academia Sinica, 11529, Taipei, Taiwan
| | - I-Ping Tu
- Institute of Statistical Science, Academia Sinica, 11529, Taipei, Taiwan
| | - Peter Chi
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan.
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22
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Abstract
Tuberculosis (TB), also known as the "White Plague", is caused by Mycobacterium tuberculosis (Mtb). Before the COVID-19 epidemic, TB had the highest mortality rate of any single infectious disease. Vaccination is considered one of the most effective strategies for controlling TB. Despite the limitations of the Bacille Calmette-Guérin (BCG) vaccine in terms of protection against TB among adults, it is currently the only licensed TB vaccine. Recently, with the evolution of bioinformatics and structural biology techniques to screen and optimize protective antigens of Mtb, the tremendous potential of protein subunit vaccines is being exploited. Multistage subunit vaccines obtained by fusing immunodominant antigens from different stages of TB infection are being used both to prevent and to treat TB. Additionally, the development of novel adjuvants is compensating for weaknesses of immunogenicity, which is conducive to the flourishing of subunit vaccines. With advances in the development of animal models, preclinical vaccine protection assessments are becoming increasingly accurate. This review summarizes progress in the research of protein subunit TB vaccines during the past decades to facilitate the further optimization of protein subunit vaccines that may eradicate TB.
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Affiliation(s)
- Ying Zhang
- Shanghai Public Health Clinical Center, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Jin-chuan Xu
- Shanghai Public Health Clinical Center, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Zhi-dong Hu
- Shanghai Public Health Clinical Center, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- TB Center, Shanghai Emerging and Re-emerging Infectious Disease Institute, Fudan University, Shanghai, China
| | - Xiao-yong Fan
- Shanghai Public Health Clinical Center, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- TB Center, Shanghai Emerging and Re-emerging Infectious Disease Institute, Fudan University, Shanghai, China
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Güiza J, Solís F, Valenzuela B, Arancibia D, Zamorano P, González J, Saavedra J, Neely A, Salgado M, Martínez AD, Sáez JC, Vega JL. Unnexin is a protein subunit of a large-pore channel expressed by unicellular organisms. Proc Natl Acad Sci U S A 2023; 120:e2307898120. [PMID: 37487087 PMCID: PMC10400985 DOI: 10.1073/pnas.2307898120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/23/2023] [Indexed: 07/26/2023] Open
Abstract
Cells of vertebrate and invertebrate organisms express proteins specialized in membrane channel-based cell-cell communication that are absent in unicellular organisms. We recently described the prediction of some members of the large-pore channel family in kinetoplastids, consisting of proteins called unnexins, which share several structural features with innexin and pannexin proteins. Here, we demonstrated that the unnexin1 protein (Unx1) is delivered to the cell membrane, displaying a topology consisting of four transmembrane domains with C and N termini on the cytoplasmic side and form large-pore channels that are permeable to small molecules. Low extracellular Ca2+/Mg2+ levels or extracellular alkalinization, but not mechanical stretching, increases channel activity. The Unx1 channel mediates the influx of Ca2+ and does not form intercellular dye coupling between HeLa Unx1 transfected cells. Unx1 channel function was further evidenced by its ability to mediate ionic currents when expressed in Xenopus oocytes. Downregulation of Unx1 mRNA with morpholine contains Trypanosoma cruzi invasion. Phylogenetic analysis revealed the presence of Unx1 homologs in other protozoan parasites, suggesting a conserved function for these channel parasites in other protists. Our data demonstrate that Unx1 forms large-pore membrane channels, which may serve as a diffusional pathway for ions and small molecules that are likely to be metabolic substrates or waste products, and signaling autocrine and paracrine molecules that could be involved in cell invasion. As morpholinos-induced downregulation of Unx1 reduces the infectivity of trypomastigotes, the Unx1 channels might be an attractive target for developing trypanocide drugs.
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Affiliation(s)
- Juan Güiza
- Laboratory of Gap Junction Proteins and Parasitic Diseases (GaPaL), Instituto Antofagasta, Universidad de Antofagasta, Antofagasta1240000, Chile
| | - Francisco Solís
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta1240000, Chile
| | - Bernardita Valenzuela
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta1240000, Chile
| | - Duxan Arancibia
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta1240000, Chile
| | - Pedro Zamorano
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta1240000, Chile
| | - Jorge González
- Departamento de Tecnología Médica, Unidad de Parasitología Molecular, Facultad Ciencias de la Salud, Universidad de Antofagasta, Antofagasta1240000, Chile
| | - Jonathan Saavedra
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso2381850, Chile
| | - Alan Neely
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso2381850, Chile
| | - Magdiel Salgado
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso2381850, Chile
| | - Agustín D. Martínez
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso2381850, Chile
| | - Juan C. Sáez
- Instituto de Neurociencias, Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso2381850, Chile
| | - José L. Vega
- Laboratory of Gap Junction Proteins and Parasitic Diseases (GaPaL), Instituto Antofagasta, Universidad de Antofagasta, Antofagasta1240000, Chile
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta1240000, Chile
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Liao HC, Huang MS, Chiu FF, Chai KM, Liao CL, Wu SC, Chen HW, Liu SJ. Co-delivery of a trimeric spike DNA and protein vaccine with aluminum hydroxide enhanced Th1-dominant humoral and cellular immunity against SARS-CoV-2. J Med Virol 2023; 95:e29040. [PMID: 37635380 DOI: 10.1002/jmv.29040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/18/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023]
Abstract
Protein subunit vaccines have been used as prophylactic vaccines for a long time. The well-established properties of these vaccines make them the first choice for the coronavirus disease 2019 (COVID-19) outbreak. However, it is not easy to develop a protein vaccine that induces cytotoxic T lymphocyte responses and requires a longer time for manufacturing, which limits the usage of this vaccine type. Here, we report the combination of a recombinant spike (S)-trimer protein with a DNA vaccine-encoded S protein as a novel COVID-19 vaccine. The recombinant S protein was formulated with different adjuvants and mixed with the DNA plasmid before injection. We found that the recombinant S protein formulated with the adjuvant aluminum hydroxide and mixed with the DNA plasmid could enhance antigen-specific antibody titers, neutralizing antibody titers. We further evaluated the IgG2a/IgG1 isotype and cytokine profiles of the specific boosted T-cell response, which indicated that the combined vaccine induced a T-helper 1 cell-biased immune response. Immunized hamsters were challenged with severe acute respiratory syndrome coronavirus 2, and the body weight of the hamsters that received the recombinant S protein with aluminum hydroxide and/or the DNA plasmid was not reduced. Alternatively, those that received control or only the DNA plasmid immunization were reduced. Interestingly, after the third day of the viral load in the lungs, the viral challenge could not be detected in hamsters immunized with the recombinant S protein in aluminum hydroxide mixed with DNA (tissue culture infectious dose < 10). The viral load in the lungs was 109 , 106 , and 107 for the phosphate-buffered saline, protein in aluminum hydroxide, and DNA-only immunizations, respectively. These results indicated that antiviral mechanisms neutralizing antibodies play important roles. Furthermore, we found that the combination of protein and DNA vaccination could induce relatively strong CD8+ T-cell responses. In summary, the protein subunit vaccine combined with a DNA vaccine could induce strong CD8+ T-cell responses to increase antiviral immunity for disease control.
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Affiliation(s)
- Hung-Chun Liao
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
- Institute of Biotechnology, College of Life Science and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Min-Syuan Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
- Institute of Biotechnology, College of Life Science and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Fang-Feng Chiu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Kit Man Chai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Ching-Len Liao
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Suh-Chin Wu
- Institute of Biotechnology, College of Life Science and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Hsin-Wei Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shih-Jen Liu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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25
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Gulsevin A, Han B, Porta JC, Mchaourab HS, Meiler J, Kenworthy AK. Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2. Biophys J 2023; 122:2041-2052. [PMID: 36352786 PMCID: PMC10257013 DOI: 10.1016/j.bpj.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/20/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
AlphaFold2 (AF2) has revolutionized the field of protein structural prediction. Here, we test its ability to predict the tertiary and quaternary structure of a previously undescribed scaffold with new folds and unusual architecture, the monotopic membrane protein caveolin-1 (CAV1). CAV1 assembles into a disc-shaped oligomer composed of 11 symmetrically arranged protomers, each assuming an identical new fold, and contains the largest parallel β-barrel known to exist in nature. Remarkably, AF2 predicts both the fold of the protomers and the interfaces between them. It also assembles between seven and 15 copies of CAV1 into disc-shaped complexes. However, the predicted multimers are energetically strained, especially the parallel β-barrel. These findings highlight the ability of AF2 to correctly predict new protein folds and oligomeric assemblies at a granular level while missing some elements of higher-order complexes, thus positing a new direction for the continued development of deep-learning protein structure prediction approaches.
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Affiliation(s)
- Alican Gulsevin
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Bing Han
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia; Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Jason C Porta
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Institute for Drug Discovery, Leipzig University, Leipzig, Germany.
| | - Anne K Kenworthy
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia; Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.
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26
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Munezero D, Aliff H, Salido E, Saravanan T, Sanzhaeva U, Guan T, Ramamurthy V. HSP90α is needed for the survival of rod photoreceptors and regulates the expression of rod PDE6 subunits. J Biol Chem 2023; 299:104809. [PMID: 37172722 PMCID: PMC10250166 DOI: 10.1016/j.jbc.2023.104809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Heat shock protein 90 (HSP90) is an abundant molecular chaperone that regulates the stability of a small set of proteins essential in various cellular pathways. Cytosolic HSP90 has two closely related paralogs: HSP90α and HSP90β. Due to the structural and sequence similarities of cytosolic HSP90 paralogs, identifying the unique functions and substrates in the cell remains challenging. In this article, we assessed the role of HSP90α in the retina using a novel HSP90α murine knockout model. Our findings show that HSP90α is essential for rod photoreceptor function but was dispensable in cone photoreceptors. In the absence of HSP90α, photoreceptors developed normally. We observed rod dysfunction in HSP90α knockout at 2 months with the accumulation of vacuolar structures, apoptotic nuclei, and abnormalities in the outer segments. The decline in rod function was accompanied by progressive degeneration of rod photoreceptors that was complete at 6 months. The deterioration in cone function and health was a "bystander effect" that followed the degeneration of rods. Tandem mass tag proteomics showed that HSP90α regulates the expression levels of <1% of the retinal proteome. More importantly, HSP90α was vital in maintaining rod PDE6 and AIPL1 cochaperone levels in rod photoreceptor cells. Interestingly, cone PDE6 levels were unaffected. The robust expression of HSP90β paralog in cones likely compensates for the loss of HSP90α. Overall, our study demonstrated the critical need for HSP90α chaperone in the maintenance of rod photoreceptors and showed potential substrates regulated by HSP90α in the retina.
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Affiliation(s)
- Daniella Munezero
- Department of Pharmaceutical and Pharmacological Sciences, West Virginia University, Morgantown, West Virginia, USA; Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA
| | - Hunter Aliff
- Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA; Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Ezequiel Salido
- Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA; Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Thamaraiselvi Saravanan
- Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA; Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Urikhan Sanzhaeva
- Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA; Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Tongju Guan
- Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA; Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Visvanathan Ramamurthy
- Department of Pharmaceutical and Pharmacological Sciences, West Virginia University, Morgantown, West Virginia, USA; Ophthalmology and Visual Sciences, West Virginia University, Morgantown, West Virginia, USA; Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA.
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27
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Ramezani A, Sorouri R, Haji Maghsoudi S, Dahmardeh S, Doroud D, Sadat Larijani M, Eybpoosh S, Mostafavi E, Olyaeemanesh A, Salehi-Vaziri M, Bavand A, Zarghani G, Moradi L, Ashrafian F, Bagheri Amiri F, Mashayekhi P, Tahmasebi Z, Biglari A. PastoCovac and PastoCovac Plus as protein subunit COVID-19 vaccines led to great humoral immune responses in BBIP-CorV immunized individuals. Sci Rep 2023; 13:8065. [PMID: 37202438 PMCID: PMC10195798 DOI: 10.1038/s41598-023-35147-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/13/2023] [Indexed: 05/20/2023] Open
Abstract
The optimal booster vaccine schedule against COVID-19 is still being explored. The present study aimed at assessment of the immunogenicity and antibody persistency of inactivated-virus based vaccine, BBIP-CorV and protein-subunit based vaccines, PastoCovac/Plus through heterologous and homologous prime-boost vaccination. Totally, 214 individuals who were previously primed with BBIBP-CorV vaccines were divided into three arms on their choice as heterologous regimens BBIBP-CorV/PastoCovac (n = 68), BBIBP-CorV/PastoCovac Plus (n = 72) and homologous BBIBP-CorV (n = 74). PastoCovac booster recipients achieved the highest rate of anti-Spike IgG titer rise with a fourfold rise in 50% of the group. Anti-RBD IgG and neutralizing antibody mean rise and fold rise were almost similar between the PastoCovac and PastoCovac Plus booster receivers. The antibody durability results indicated that the generated antibodies were persistent until day 180 in all three groups. Nevertheless, a higher rate of antibody titer was seen in the heterologous regimen compared to BBIP-CorV group. Furthermore, no serious adverse event was recorded. The protein subunit-based booster led to a stronger humoral immune response in comparison with the BBIP-CorV booster receivers. Both the protein subunit boosters neutralized SARS-CoV-2 significantly more than BBIP-CorV. Notably, PastoCovac protein subunit-based vaccine could be successfully applied as a booster with convenient immunogenicity and safety profile.
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Affiliation(s)
- Amitis Ramezani
- Clinical Research Department, Pasteur Institute of Iran, No 69, Pasteur Ave., Tehran, Iran
| | - Rahim Sorouri
- IPI Directorate, Pasteur Institute of Iran, Tehran, Iran
| | - Saiedeh Haji Maghsoudi
- Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- Department of Biostatistics and Epidemiology, School of Public Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Sarah Dahmardeh
- Department of Vaccination, Pasteur Institute of Iran, Tehran, Iran
| | - Delaram Doroud
- Quality Control Department, Production and Research Complex, Pasteur Institute of Iran, Tehran, Iran
| | - Mona Sadat Larijani
- Clinical Research Department, Pasteur Institute of Iran, No 69, Pasteur Ave., Tehran, Iran.
| | - Sana Eybpoosh
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Ehsan Mostafavi
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Alireza Olyaeemanesh
- Health Equity Research Centre and National Institute of Health Research, Tehran University of Medical Science, Tehran, Iran
| | | | - Anahita Bavand
- Clinical Research Department, Pasteur Institute of Iran, No 69, Pasteur Ave., Tehran, Iran
| | | | - Ladan Moradi
- Clinical Research Department, Pasteur Institute of Iran, No 69, Pasteur Ave., Tehran, Iran
| | - Fatemeh Ashrafian
- Clinical Research Department, Pasteur Institute of Iran, No 69, Pasteur Ave., Tehran, Iran
| | - Fahimeh Bagheri Amiri
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Parisa Mashayekhi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Zahra Tahmasebi
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Alireza Biglari
- School of Medicine, Tehran University of Medical Sciences, Enghelab Street, P.O. BOX 14155-6559, Tehran, Iran.
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28
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Salvage SC, Jeevaratnam K, Huang CL, Jackson AP. Cardiac sodium channel complexes and arrhythmia: structural and functional roles of the β1 and β3 subunits. J Physiol 2023; 601:923-940. [PMID: 36354758 PMCID: PMC10953345 DOI: 10.1113/jp283085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
In cardiac myocytes, the voltage-gated sodium channel NaV 1.5 opens in response to membrane depolarisation and initiates the action potential. The NaV 1.5 channel is typically associated with regulatory β-subunits that modify gating and trafficking behaviour. These β-subunits contain a single extracellular immunoglobulin (Ig) domain, a single transmembrane α-helix and an intracellular region. Here we focus on the role of the β1 and β3 subunits in regulating NaV 1.5. We catalogue β1 and β3 domain specific mutations that have been associated with inherited cardiac arrhythmia, including Brugada syndrome, long QT syndrome, atrial fibrillation and sudden death. We discuss how new structural insights into these proteins raises new questions about physiological function.
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Affiliation(s)
| | | | - Christopher L.‐H. Huang
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Department of PhysiologyDevelopment and NeuroscienceUniversity of CambridgeCambridgeUK
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29
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Ma B, Niu W, Guo J. Proximity-enhanced protein crosslinking through an alkene-tetrazine reaction. Bioorg Chem 2023; 132:106359. [PMID: 36642019 PMCID: PMC9957846 DOI: 10.1016/j.bioorg.2023.106359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 01/13/2023]
Abstract
The inverse electron demand Diels-Alder (iEDDA) reaction between a tetrazine and a strained alkene has been widely explored as useful bioorthogonal chemistry for selective labeling of biomolecules. In this work, we exploit the slow reaction between a non-conjugated terminal alkene and a tetrazine, and apply this reaction to achieving a proximity-enhanced protein crosslinking. In one protein subunit, a terminal alkene-containing amino acid was site-specifically incorporated in response to an amber nonsense codon. In another protein subunit, a tetrazine moiety was introduced through the attachment to a cysteine residue. Fast protein crosslinking was achieved due to a large increase in effective molarity of the two reactants that were brought to close proximity by the two interacting protein subunits. Such a proximity-enhanced protein crosslinking is useful for the study of protein-protein interactions.
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Affiliation(s)
- Bin Ma
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE 68588, United States.
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30
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Salimian J, Ahmadi A, Amani J, Olad G, Halabian R, Saffaei A, Arabfard M, Nasiri M, Nazarian S, Abolghasemi H, Alishiri G. Safety and immunogenicity of a recombinant receptor-binding domain-based protein subunit vaccine (Noora vaccine™) against COVID-19 in adults: A randomized, double-blind, placebo-controlled, Phase 1 trial. J Med Virol 2023; 95:10.1002/jmv.28097. [PMID: 36029105 PMCID: PMC9539327 DOI: 10.1002/jmv.28097] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/01/2022] [Accepted: 08/25/2022] [Indexed: 11/11/2022]
Abstract
The development of a safe and effective vaccine is essential to protect populations against coronavirus disease 2019 (COVID-19). There are several vaccine candidates under investigation with different mechanisms of action. In the present study, we have evaluated the safety and immunogenicity of a recombinant receptor-binding domain (RBD)-based protein subunit vaccine (Noora vaccine) against COVID-19 in adults. This Phase 1 trial is a randomized, double-blind, placebo-controlled study to evaluate the safety and immunogenicity of the recombinant RBD-based protein subunit vaccine (Noora vaccine) against COVID-19 in healthy adults volunteers. Eligible participants were included in this study after evaluating their health status and considering the exclusion criteria. They were then randomized into three groups and received three doses of vaccine (80 µg, 120 µg, and placebo) on Days 0, 21, and 35. Primary outcomes including solicited, unsolicited, and medically attended adverse events were recorded during this study. Secondary outcomes including the humoral and cellular immunity (including anti-RBD IgG antibody and neutralizing antibody) were measured on Days 0, 21, 28, 35, 42, and 49 by using the ELISA kit and the Virus Neutralization Test (VNT) was performed on day 49. Totally 70 cases were included in this Phase 1 trial and 60 of them completed the study. Safety assessments showed no severe adverse events. Local pain at the vaccine injection site occurred in 80% of the vaccinated volunteers. Induration and redness at the injection site were the other adverse reactions of this vaccine. There was no significant difference between the studied groups regarding adverse reactions. Anti-RBD IgG antibody and neutralizing antibody assessment showed significant seroconversion in comparison to the placebo group (80%, and 100% respectively, p < 0.001). The cellular immunity panel also showed mild to moderate induction of TH1 responses and the VNT showed 78% of seroprotection. The results of this Phase 1 trial showed acceptable safety without serious adverse events and significant seroconversions in the humoral and cellular immunity panel. The dose of 80 µg is an appropriate dose for injection in the next phases of the trial.
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Affiliation(s)
- Jafar Salimian
- Applied Microbiology Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
- Chemical Injuries Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - Gholamreza Olad
- Applied Biotechnology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Raheleh Halabian
- Applied Microbiology Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - Ali Saffaei
- Department of Clinical Pharmacy, School of PharmacyShahid Beheshti University of Medical SciencesTehranIran
- Student Research CommitteeShahid Beheshti University of Medical SciencesTehranIran
- Skull Base Research Center, Loghman Hakim HospitalShahid Beheshti University of Medical SciencesTehranIran
| | - Masoud Arabfard
- Chemical Injuries Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Mojtaba Nasiri
- Clinical Trial CenterTehran University of Medical SciencesTehranIran
| | - Shahram Nazarian
- Department of Biology, Faculty of ScienceImam Hossein UniversityTehranIran
| | - Hassan Abolghasemi
- Applied Microbiology Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
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Adams C, Carbaugh DL, Shu B, Ng TS, Castillo IN, Bhowmik R, Segovia-Chumbez B, Puhl AC, Graham S, Diehl SA, Lazear HM, Lok SM, de Silva AM, Premkumar L. Structure and neutralization mechanism of a human antibody targeting a complex Epitope on Zika virus. PLoS Pathog 2023; 19:e1010814. [PMID: 36626401 PMCID: PMC9870165 DOI: 10.1371/journal.ppat.1010814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/23/2023] [Accepted: 12/05/2022] [Indexed: 01/11/2023] Open
Abstract
We currently have an incomplete understanding of why only a fraction of human antibodies that bind to flaviviruses block infection of cells. Here we define the footprint of a strongly neutralizing human monoclonal antibody (mAb G9E) with Zika virus (ZIKV) by both X-ray crystallography and cryo-electron microscopy. Flavivirus envelope (E) glycoproteins are present as homodimers on the virion surface, and G9E bound to a quaternary structure epitope spanning both E protomers forming a homodimer. As G9E mainly neutralized ZIKV by blocking a step after viral attachment to cells, we tested if the neutralization mechanism of G9E was dependent on the mAb cross-linking E molecules and blocking low-pH triggered conformational changes required for viral membrane fusion. We introduced targeted mutations to the G9E paratope to create recombinant antibodies that bound to the ZIKV envelope without cross-linking E protomers. The G9E paratope mutants that bound to a restricted epitope on one protomer poorly neutralized ZIKV compared to the wild-type mAb, demonstrating that the neutralization mechanism depended on the ability of G9E to cross-link E proteins. In cell-free low pH triggered viral fusion assay, both wild-type G9E, and epitope restricted paratope mutant G9E bound to ZIKV but only the wild-type G9E blocked fusion. We propose that, beyond antibody binding strength, the ability of human antibodies to cross-link E-proteins is a critical determinant of flavivirus neutralization potency.
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Affiliation(s)
- Cameron Adams
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Derek L. Carbaugh
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Bo Shu
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
- Centre for Bio-Imaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Thiam-Seng Ng
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
- Centre for Bio-Imaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Izabella N. Castillo
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Ryan Bhowmik
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Bruno Segovia-Chumbez
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Ana C. Puhl
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Stephen Graham
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Sean A. Diehl
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicine, Burlington, Vermont, United States of America
| | - Helen M. Lazear
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Shee-mei Lok
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
- Centre for Bio-Imaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Aravinda M. de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
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Chmelyuk NS, Oda VV, Gabashvili AN, Abakumov MA. Encapsulins: Structure, Properties, and Biotechnological Applications. Biochemistry Moscow 2023; 88:35-49. [PMID: 37068871 PMCID: PMC9937530 DOI: 10.1134/s0006297923010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
In 1994 a new class of prokaryotic compartments was discovered, collectively called "encapsulins" or "nanocompartments". Encapsulin shell protomer proteins self-assemble to form icosahedral structures of various diameters (24-42 nm). Inside of nanocompartments shells, one or several cargo proteins, diverse in their functions, can be encapsulated. In addition, non-native cargo proteins can be loaded into nanocompartments, and shell surfaces can be modified via various compounds, which makes it possible to create targeted drug delivery systems, labels for optical and MRI imaging, and to use encapsulins as bioreactors. This review describes a number of strategies of encapsulins application in various fields of science, including biomedicine and nanobiotechnologies.
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Affiliation(s)
- Nelly S Chmelyuk
- National University of Science and Technology "MISIS", Moscow, 119049, Russia
- Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, Moscow, 117977, Russia
| | - Vera V Oda
- National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Anna N Gabashvili
- National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Maxim A Abakumov
- National University of Science and Technology "MISIS", Moscow, 119049, Russia.
- Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, Moscow, 117977, Russia
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Han L, An C, Liu D, Wang Z, Bian L, He Q, Liu J, Wang Q, Liu M, Mao Q, Hang T, Wang A, Gao F, Tan D, Liang Z. Development of an ELISA Assay for the Determination of SARS-CoV-2 Protein Subunit Vaccine Antigen Content. Viruses 2022; 15:62. [PMID: 36680102 PMCID: PMC9860593 DOI: 10.3390/v15010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/17/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protein subunit vaccine is one of the mainstream technology platforms for the development of COVID-19 vaccines, and most R&D units use the receptor-binding domain (RBD) or spike (S) protein as the main target antigen. The complexity of vaccine design, sequence, and expression systems makes it urgent to establish common antigen assays to facilitate vaccine development. In this study, we report the development of a double-antibody sandwich enzyme-linked immunosorbent assay (ELISA) to determine the antigen content of SARS-CoV-2 protein subunit vaccines based on the United States Pharmacopeia <1220> and ICH (international conference on harmonization) Q14 and Q2 (R2) requirements. A monoclonal antibody (mAb), 20D8, was identified as the detection antibody based on its high RBD binding activity (EC50 = 8.4 ng/mL), broad-spectrum anti-variant neutralizing activity (EC50: 2.7−9.8 ng/mL for pseudovirus and EC50: 9.6−127 ng/mL for authentic virus), good in vivo protection, and a recognized linear RBD epitope (369−379 aa). A porcine anti-RBD polyclonal antibody was selected as the coating antibody. Assay performance met the requirements of the analytical target profile with an accuracy and precision of ≥90% and adequate specificity. Within the specification range of 70−143%, the method capability index was >0.96; the misjudgment probability was <0.39%. The method successfully detected SARS-CoV-2 protein subunit vaccine antigens (RBD or S protein sequences in Alpha, Beta, Gamma, or Delta variants) obtained from five different manufacturers. Thus, we present a new robust, reliable, and general method for measuring the antigenic content of SARS-CoV-2 protein subunit vaccines. In addition to currently marketed and emergency vaccines, it is suitable for vaccines in development containing antigens derived from pre-Omicron mutant strains.
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Affiliation(s)
- Lu Han
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- College of Pharmacy, China Pharmaceutical University, Nanjing 210000, China
| | - Chaoqiang An
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- Beijing Minhai Biotechnology Co., Ltd., Beijing 102629, China
| | - Dong Liu
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
- Changchun Institute of Biological Products Co., Ltd., Changchun 130062, China
| | - Zejun Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430070, China
| | - Lianlian Bian
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Qian He
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Jianyang Liu
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Qian Wang
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Mingchen Liu
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Qunying Mao
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Taijun Hang
- College of Pharmacy, China Pharmaceutical University, Nanjing 210000, China
| | - Aiping Wang
- College of Life Sciences, Zheng Zhou University, Zhengzhou 450001, China
| | - Fan Gao
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Dejiang Tan
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
| | - Zhenglun Liang
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, Beijing 102600, China
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Khazma T, Golan-Vaishenker Y, Guez-Haddad J, Grossman A, Sain R, Weitman M, Plotnikov A, Zalk R, Yaron A, Hons M, Opatowsky Y. A duplex structure of SARM1 octamers stabilized by a new inhibitor. Cell Mol Life Sci 2022; 80:16. [PMID: 36564647 DOI: 10.1007/s00018-022-04641-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 12/25/2022]
Abstract
In recent years, there has been growing interest in SARM1 as a potential breakthrough drug target for treating various pathologies of axon degeneration. SARM1-mediated axon degeneration relies on its TIR domain NADase activity, but recent structural data suggest that the non-catalytic ARM domain could also serve as a pharmacological site as it has an allosteric inhibitory function. Here, we screened for synthetic small molecules that inhibit SARM1, and tested a selected set of these compounds in a DRG axon degeneration assay. Using cryo-EM, we found that one of the newly discovered inhibitors, a calmidazolium designated TK106, not only stabilizes the previously reported inhibited conformation of the octamer, but also a meta-stable structure: a duplex of octamers (16 protomers), which we have now determined to 4.0 Å resolution. In the duplex, each ARM domain protomer is engaged in lateral interactions with neighboring protomers, and is further stabilized by contralateral contacts with the opposing octamer ring. Mutagenesis of the duplex contact sites leads to a moderate increase in SARM1 activation in cultured cells. Based on our data we propose that the duplex assembly constitutes an additional auto-inhibition mechanism that tightly prevents pre-mature activation and axon degeneration.
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Affiliation(s)
- Tami Khazma
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Julia Guez-Haddad
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Atira Grossman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Radhika Sain
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Michal Weitman
- Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel
| | - Alexander Plotnikov
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ran Zalk
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Avraham Yaron
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Hons
- European Molecular Biology Laboratory, Grenoble, France.
| | - Yarden Opatowsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
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35
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Williams CA, Wong TAS, Ball AH, Lieberman MM, Lehrer AT. Maternal Immunization Using a Protein Subunit Vaccine Mediates Passive Immunity against Zaire ebolavirus in a Murine Model. Viruses 2022; 14:2784. [PMID: 36560788 PMCID: PMC9785068 DOI: 10.3390/v14122784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/10/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
The Ebola virus has caused outbreaks in Central and West Africa, with high rates of morbidity and mortality. Clinical trials of recombinant virally vectored vaccines did not explicitly include pregnant or nursing women, resulting in a gap in knowledge of vaccine-elicited maternal antibody and its potential transfer. The role of maternal antibody in Ebola virus disease and vaccination remains understudied. Here, we demonstrate that a protein subunit vaccine can elicit robust humoral responses in pregnant mice, which are transferred to pups in breastmilk. These findings indicate that an intramuscular protein subunit vaccine may elicit Ebola-specific IgG capable of being transferred across the placenta as well as into the breastmilk. We have previously shown protective efficacy with these vaccines in non-human primates, offering a potential safe and practical alternative to recombinant virally vectored vaccines for pregnant and nursing women in Ebola endemic regions.
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Affiliation(s)
| | | | | | | | - Axel T. Lehrer
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
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36
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Liao Y, Chen Y, Chen B, Liang Z, Hu X, Xing B, Yang J, Zheng Q, Hua Q, Yan C, Lv H. Safety and immunogenicity of heterologous recombinant protein subunit vaccine (ZF2001) booster against COVID-19 at 3-9-month intervals following two-dose inactivated vaccine (CoronaVac). Front Immunol 2022; 13:1017590. [PMID: 36426361 PMCID: PMC9679005 DOI: 10.3389/fimmu.2022.1017590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/17/2022] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND In response to SARS-CoV-2 mutations and waning antibody levels after two-dose inactivated vaccines, we assessed whether a third dose of recombinant protein subunit vaccine (ZF2001) boosts immune responses. METHODS An open-label single-center non-random trial was conducted on people aged 18 years and above at five sites in China. All participants received a two-dose inactivated vaccine (CoronaVac) as their prime doses within 3-9 months of the trial. Primary outcomes were safety and immunogenicity, primarily the geometric mean titers (GMTs) of neutralizing antibodies to live wildtype SARS-CoV-2. RESULTS A total of 480 participants (median age, 51; range 21-84 years) previously vaccinated with two-dose CoronaVac received a third booster dose of ZF2001 3-4, 5-6, or 7-9-months later. The overall incidence of adverse reactions within 30 days after vaccination was 5.83% (28/480). No serious adverse reactions were reported after the third dose of ZF2001. GMTs in the 3-4-, 5-6-, and 7-9-month groups before vaccination were 3.96, 4.60, and 3.78, respectively. On Day 14, GMTs increased to 33.06, 47.51, and 44.12, respectively. After the booster, GMTs showed no significant difference among the three prime-boost interval groups (all P>0.05). Additionally, GMTs in older adults were lower than those in younger adults on Day 14 for the three groups (P=0.0005, P<0.0001, and P<0.0001). CONCLUSION Heterologous boosting with ZF2001 was safe and immunogenic, and prime-boost intervals did not affect the immune response. The immune response was weaker in older than younger adults.
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Affiliation(s)
- Yuting Liao
- State 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, China
| | - Yingping Chen
- Department of Immunization Program, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Bo Chen
- Kaihua Center for Disease Control and Prevention, Quzhou, Zhejiang, China
| | - Zhenzhen Liang
- Department of Immunization Program, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Xiaosong Hu
- Department of Immunization Program, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Bo Xing
- Department of Immunization Program, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Juan Yang
- State 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, China
| | - Qianhui Zheng
- Kaihua Center for Disease Control and Prevention, Quzhou, Zhejiang, China
| | - Qianhui Hua
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Chuanfu Yan
- Kaihua Center for Disease Control and Prevention, Quzhou, Zhejiang, China
| | - Huakun Lv
- Department of Immunization Program, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
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Zhang Y, Yao M, Guo X, Han S, Zhang S, Zhang J, Jiang X, Wang J, Fang M, Wang S, Pang B, Liu X, Kou Z, Jiang X. Humoral immunity and transcriptome differences of COVID-19 inactivated vacciane and protein subunit vaccine as third booster dose in human. Front Immunol 2022; 13:1027180. [PMID: 36341453 PMCID: PMC9634958 DOI: 10.3389/fimmu.2022.1027180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Under the background of the severe human health and world economic burden caused by COVID-19, the attenuation of vaccine protection efficacy, and the prevalence and immune escape of emerging variants of concern (VOCs), the third dose of booster immunization has been put on the agenda. Systems biology approaches can help us gain new perspectives on the characterization of immune responses and the identification of factors underlying vaccine-induced immune efficacy. We analyzed the antibody signature and transcriptional responses of participants vaccinated with COVID-19 inactivated vaccine and protein subunit vaccine as a third booster dose. The results from the antibody indicated that the third booster dose was effective, and that heterologous vaccination with the protein subunit vaccine as a booster dose induced stronger humoral immune responses than the homologous vaccination with inactivated vaccine, and might be more effective against VOCs. In transcriptomic analysis, protein subunit vaccine induced more differentially expressed genes that were significantly associated with many important innate immune pathways. Both the homologous and heterologous boosters could increase the effectiveness against COVID-19, and compared with the inactivated vaccine, the protein subunit vaccine, mediated a stronger humoral immune response and had a more significant correlation with the innate immune function module, which provided certain data support for the third booster immunization strategy.
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Affiliation(s)
- Yuwei Zhang
- Infectious Disease Prevention and Control Section, Shandong Provincial Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Mingxiao Yao
- Infectious Disease Prevention and Control Section, Shandong Provincial Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Xingyu Guo
- School of Public Health and Health Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Shanshan Han
- School of Public Health and Health Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Shu Zhang
- Infectious Disease Prevention and Control Section, Shandong Provincial Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Jinzhong Zhang
- Institute of Immunization and Prevention, Liaocheng Center for Disease Control and Prevention, Liaocheng, Shandong, China
| | - Xiangkun Jiang
- Institute of Immunization and Prevention, Liaocheng Center for Disease Control and Prevention, Liaocheng, Shandong, China
| | - Jianxing Wang
- Infectious Disease Prevention and Control Section, Shandong Provincial Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Ming Fang
- Infectious Disease Prevention and Control Section, Shandong Provincial Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Shuang Wang
- Infectious Disease Prevention and Control Section, Shandong Provincial Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Bo Pang
- Infectious Disease Prevention and Control Section, Shandong Provincial Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Xiaolin Liu
- Infectious Disease Prevention and Control Section, Shandong Provincial Center for Disease Control and Prevention, Jinan, Shandong, China
| | - Zengqiang Kou
- Infectious Disease Prevention and Control Section, Shandong Provincial Center for Disease Control and Prevention, Jinan, Shandong, China
- *Correspondence: Zengqiang Kou, ; Xiaolin Jiang,
| | - Xiaolin Jiang
- School of Public Health and Health Management, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Provincial Center for Disease Control and Prevention, Jinan, China
- *Correspondence: Zengqiang Kou, ; Xiaolin Jiang,
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Wan J, Brož B, Liu Y, Huang SR, Marek A, Tureček F. Resolution of Identity in Gas-Phase Dissociations of Mono- and Diprotonated DNA Trinucleotide Codons by 15N-Labeling and Computational Structure Analysis. J Am Soc Mass Spectrom 2022; 33:1936-1950. [PMID: 36040435 DOI: 10.1021/jasms.2c00194] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dissociations of DNA trinucleotide codons as gas-phase singly and doubly protonated ions were studied by tandem mass spectrometry using 15N-labeling to resolve identity in the nucleobase loss and backbone cleavages. The monocations showed different distributions of nucleobase loss from the 5'-, middle, and 3'-positions depending on the nucleobase, favoring cytosine over guanine, adenine, and thymine in an ensemble-averaged 62:27:11:<1 ratio. The distribution for the loss of the 5'-, middle, and 3'-nucleobase was 49:18:33, favoring the 5'-nucleobase, but also depending on its nature. The formation of sequence w2+ ions was unambiguously established for all codon mono- and dications. Structures of low-Gibbs-energy protomers and conformers of dAAA+, dGGG+, dCCC+, dTTT+, dACA+, and dATC+ were established by Born-Oppenheimer molecular dynamics and density functional theory calculations. Monocations containing guanine favored classical structures protonated at guanine N7. Structures containing adenine and cytosine produced classical nucleobase-protonated isomers as well as zwitterions in which two protonated bases were combined with a phosphate anion. Protonation at thymine was disfavored. Low threshold energies for nucleobase loss allowed extensive proton migration to occur prior to dissociation. Loss of the nucleobase from monocations was assisted by neighboring group participation in nucleophilic addition or proton abstraction, as well as allosteric proton migrations remote from the reaction center. The optimized structures of diprotonated isomers for dAAA2+ and dACA2+ revealed combinations of classical and zwitterionic structures. The threshold and transition-state energies for nucleobase-ion loss from dications were low, resulting in facile dissociations involving cytosine, guanine, and adenine.
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Affiliation(s)
- Jiahao Wan
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Břetislav Brož
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Yue Liu
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Shu R Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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39
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Pu J, Xiao J, Bai X, Chen H, Zheng R, Gu X, Xie Y, He R, Xu J, Jing B, Peng X, Yang G. Prokaryotic Expression of Eimeria magna SAG10 and SAG11 Genes and the Preliminary Evaluation of the Effect of the Recombinant Protein on Immune Protection in Rabbits. Int J Mol Sci 2022; 23:ijms231810942. [PMID: 36142854 PMCID: PMC9506328 DOI: 10.3390/ijms231810942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Eimeria magna is a common coccidia in the intestines of rabbits, causing anorexia, weight loss, diarrhea, and bloody stools. This study cloned and determined the expression levels of four Eimeria surface antigens (EmSAGs) at different developmental stages and showed that EmSAG10 and EmSAG11 are highly expressed at the merozoite stage. Rabbits were immunized with rEmSAG10 and rEmSAG11, and then challenged with E. magna after 2 weeks. Serum-specific antibodies and cytokine levels were detected using ELISA. Immune protection was evaluated based on the rate of the oocysts decrease, the output of oocysts (p < 0.05), the average weight gain, and the feed: meat ratio. Our results showed that rabbits immunized with rEmSAG10 and rEmSAG11 had a higher average weight gain (62.7%, 61.1%), feed; meat ratio (3.8:1, 4.5:1), and the oocysts decrease rate (70.8%, 81.2%) than those in the control group, and also significantly reduced intestinal lesions. The specific IgG level increased one week after the first rEmSAG10 and rEmSAG11 immunization and was maintained until two weeks after the challenge (p < 0.05). The TGF-β, IL-4, and IL-10 levels in the serum increased significantly after the secondary immunization with rEmSAG10 and rEmSAG11, while the IL-2 levels increased significantly after the secondary immunization with rEmSAG11 (both p < 0.05), suggesting that rEmSAG10 can induce a humoral and cellular immunity, while rEmSAG11 can only induce a humoral immunity. Therefore, rEmSAG10 is a candidate antigen for E. magna recombinant subunit vaccines.
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Affiliation(s)
- Jiayan Pu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jie Xiao
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Xin Bai
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Hao Chen
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Ruoyu Zheng
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Bo Jing
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Xuerong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
- Correspondence:
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González-Gamboa I, Caparco AA, McCaskill JM, Steinmetz NF. Bioconjugation Strategies for Tobacco Mild Green Mosaic Virus. Chembiochem 2022; 23:e202200323. [PMID: 35835718 PMCID: PMC9624232 DOI: 10.1002/cbic.202200323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/03/2022] [Indexed: 11/06/2022]
Abstract
Tobacco mild green mosaic virus (TMGMV) is a plant virus closely related to Tobacco mosaic virus (TMV), sharing many of its structural and chemical features. These rod-shaped viruses, comprised of 2130 identical coat protein subunits, have been utilized as nanotechnological platforms for a myriad of applications, ranging from drug delivery to precision agriculture. This versatility for functionalization is due to their chemically active external and internal surfaces. While both viruses are similar, they do exhibit some key differences in their surface chemistry, suggesting the reactive residue distribution on TMGMV should not overlap with TMV. In this work, we focused on the establishment and refinement of chemical bioconjugation strategies to load molecules into or onto TMGMV for targeted delivery. A combination of NHS, EDC, and diazo coupling reactions in combination with click chemistry were used to modify the N-terminus, glutamic/aspartic acid residues, and tyrosines in TMGMV. We report loading with over 600 moieties per TMGMV via diazo-coupling, which is a >3-fold increase compared to previous studies. We also report that cargo can be loaded to the solvent-exposed N-terminus and carboxylates on the exterior/interior surfaces. Mass spectrometry revealed the most reactive sites to be Y12 and Y72, both tyrosine side chains are located on the exterior surface. For the carboxylates, interior E106 (66.53 %) was the most reactive for EDC-propargylamine coupled reactions, with the exterior E145 accounting for >15 % reactivity, overturning previous assumptions that only interior glutamic acid residues are accessible. A deeper understanding of the chemical properties of TMGMV further enables its functionalization and use as a multifunctional nanocarrier platform for applications in medicine and precision farming.
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Affiliation(s)
- Ivonne González-Gamboa
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Adam A Caparco
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Justin M McCaskill
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Department of Radiology, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Institute for Materials Discovery and Design, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Moores Cancer Center, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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Chen CC, Huang YJ, Lai MJ, Lin MH, Lin WC, Lin HY, Lin YC, Huang YT, Lee YF, Tsai MK, Lee CY. Immunogenicity and safety of two-dose SARS-CoV-2 vaccination via different platforms in kidney transplantation recipients. Front Immunol 2022; 13:951576. [PMID: 36189313 PMCID: PMC9523367 DOI: 10.3389/fimmu.2022.951576] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
After kidney transplantation, patients exhibit a poor response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination. However, the efficacy and adverse effects of vaccines based on different platforms in these patients remain unclear. We prospectively analyzed both anti-spike protein antibody and cellular responses 1 month after the first and second doses of SARS-CoV-2 vaccines in 171 kidney transplant patients. Four vaccines, including one viral vector (ChAdOx1 nCov-19, n = 30), two mRNA (mRNA1273, n = 81 and BNT162b2, n = 38), and one protein subunit (MVC-COV1901, n = 22) vaccines were administered. Among the four vaccines, mRNA1273 elicited the strongest humoral response and induced the highest interferon-γ levels in patients with a positive cellular response against the spike protein. Antiproliferative agents were negatively associated with both the antibody and cellular responses. A transient elevation in creatinine levels was noted in approximately half of the patients after the first dose of mRNA1273 or ChadOx1, and only one of them presented with borderline cellular rejection without definite causality to vaccination. In conclusion, mRNA1273 had better immunogenicity than the other vaccines. Further, renal function needs to be carefully monitored after vaccination, and vaccination strategies should be tailored according to the transplant status and vaccine characteristics.
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Affiliation(s)
- Chien-Chia Chen
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Jen Huang
- Department of Pharmacy, National Taiwan University Hospital, Taipei, Taiwan
| | - Mei-Jun Lai
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Min-Huey Lin
- Department of Nursing, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Chou Lin
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Hui-Ying Lin
- Department of Nursing, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Chun Lin
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Tsung Huang
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ya-Fen Lee
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Meng-Kun Tsai
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
- Division of General Surgery, Department of Surgery, National Taiwan University Biomedical Park Hospital, National Taiwan University Hospital Hsinchu Branch, Hsinchu, Taiwan
- *Correspondence: Chih-Yuan Lee, ; Meng-Kun Tsai,
| | - Chih-Yuan Lee
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
- *Correspondence: Chih-Yuan Lee, ; Meng-Kun Tsai,
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Seephetdee C, Bhukhai K, Buasri N, Leelukkanaveera P, Lerdwattanasombat P, Manopwisedjaroen S, Phueakphud N, Kuhaudomlarp S, Olmedillas E, Saphire EO, Thitithanyanont A, Hongeng S, Wongtrakoongate P. A circular mRNA vaccine prototype producing VFLIP-X spike confers a broad neutralization of SARS-CoV-2 variants by mouse sera. Antiviral Res 2022; 204:105370. [PMID: 35772601 PMCID: PMC9235288 DOI: 10.1016/j.antiviral.2022.105370] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022]
Abstract
Next-generation COVID-19 vaccines are critical due to the ongoing evolution of SARS-CoV-2 virus and rapid waning duration of the neutralizing antibody response against current vaccines. The mRNA vaccines mRNA-1273 and BNT162b2 were developed using linear transcripts encoding the prefusion-stabilized trimers (S-2P) of the wildtype spike, which have shown a reduced neutralizing activity against the variants of concern B.1.617.2 and B.1.1.529. Recently, a new version of spike trimer, termed VFLIP (five (V) prolines, Flexibly-Linked, Inter-Protomer disulfide) was developed. Based on the original amino acid sequence of the wildtype spike, VFLIP was genetically engineered by using five proline substitutions, a flexible cleavage site amino acid linker, and an inter-protomer disulfide bond. It has been suggested to possess native-like glycosylation, and greater pre-fusion trimeric stability as opposed to S-2P. Here, we report that the spike protein VFLIP-X, containing six rationally substituted amino acids to reflect emerging variants (K417N, L452R, T478K, E484K, N501Y and D614G), offers a promising candidate for a next-generation SARS-CoV-2 vaccine. Mice immunized by a circular mRNA (circRNA) vaccine prototype producing VFLIP-X had detectable neutralizing antibody titers for up to 7 weeks post-boost against SARS-CoV-2 variants of concern (VOCs) and variants of interest (VOIs). In addition, a balance in TH1 and TH2 responses was achieved by immunization with VFLIP-X. Our results indicate that the VFLIP-X delivered by circRNA induces humoral and cellular immune responses, as well as broad neutralizing activity against SARS-CoV-2 variants.
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Affiliation(s)
- Chotiwat Seephetdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Kanit Bhukhai
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Nattawut Buasri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Puttipatch Leelukkanaveera
- International Program of Bioinnovation, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Pat Lerdwattanasombat
- International Program of Biomedical Science, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | | | - Nut Phueakphud
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Sakonwan Kuhaudomlarp
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand; Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | | | | | - Arunee Thitithanyanont
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.
| | - Patompon Wongtrakoongate
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand; Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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Kouhpayeh H, Ansari H. Adverse events following COVID-19 vaccination: A systematic review and meta-analysis. Int Immunopharmacol 2022; 109:108906. [PMID: 35671640 PMCID: PMC9148928 DOI: 10.1016/j.intimp.2022.108906] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND High speed of COVID-19 vaccination has raised some concerns about the safety of the new vaccines. It is of a great importance to perform a review of the safety and efficacy of the COVID-19 vaccines. METHODS Two International electronic databases (PubMed, ISI) were searched for clinical trials reporting efficacy and safety of COVID-19 vaccines compared to control group. Pooled risk ratio (RR) for total, systemic and local adverse events following immunization was calculated for different vaccine modalities. RESULTS The pooled RRs of total adverse reactions for Inactivated, mRNA, and vector vaccines were 1.46 (95% CI: 1.19-1.78), 2.01 (95% CI: 1.82 - 2.23), and 1.65 (95% CI: 1.31 - 2.32) respectively. The pooled RR for occurrence of systemic adverse reactions following immunization for different vaccine modalities was 1.13 (95% CI: 0.79 - 1.61), 1.53 (95% CI 1.08 - 2.16), 1.58 (95% CI: 1.13 - 1.90), 0.72 (95% CI: 0.34 - 1.55), and 1.62 (95% CI: 1.39 - 1.89) for inactivated vaccine, mRNA, vector, DNA, and protein subunit vaccines respectively. The pooled RR of local adverse event following immunization with inactivated vaccine, mRNA vaccine, vector vaccine, DNA vaccine, and protein subunit vaccine was 2.18 (95% CI: 1.32 - 3.59), 4.96 (95% CI: 4.02 - 6.11), 1.48 (95% CI: 0.88-2.50) 1.04 (95% CI: 0.12-8.75), and 4.09 (95% CI: 2.63-6.35) respectively. CONCLUSION mRNA vaccines are associated with greater risk of adverse events following immunization. However, at the present moment the benefits of all types of vaccines approved by WHO, still outweigh the risks of them and vaccination if available, is highly recommended.
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Affiliation(s)
- Hamidreza Kouhpayeh
- Tropical and Infectious Diseases Department, Zahedan University of Medical Sciences, Zahedan, Iran; Zahedan University of Medical Sciences Research Center, Emam Ali Hospital, Zahedan, Iran.
| | - Hossein Ansari
- Health Promotion Research Center, Department of Epidemiology and Biostatistics, Zahedan University of Medical Sciences, Zahedan, Iran
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Tian X, Zhang Y, He Z, Li S, Yan D, Zhu Z, Wan Y, Wang W. Successive Site Translocating Inoculation Improved T Cell Responses Elicited by a DNA Vaccine Encoding SARS-CoV-2 S Protein. Front Immunol 2022; 13:875236. [PMID: 35514964 PMCID: PMC9062103 DOI: 10.3389/fimmu.2022.875236] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
A variety of methods have been explored to increase delivery efficiencies for DNA vaccine. However, the immunogenicity of DNA vaccines has not been satisfactorily improved. Unlike most of the previous attempts, we provided evidence suggesting that changing the injection site successively (successively site-translocated inoculation, SSTI) could significantly enhance the immunogenicity of DNA vaccines in a previous study. To simplify the strategy and to evaluate its impact on candidate SARS-CoV-2 vaccines, we immunized mice with either a SARS-CoV-2 spike-based DNA vaccine or a spike protein subunit vaccine via three different inoculation strategies. Our data demonstrated that S protein specific antibody responses elicited by the DNA vaccine or the protein subunit vaccine showed no significant difference among different inoculation strategies. Of interest, compared with the conventional site fixed inoculation (SFI), both successive site-translocating inoculation (SSTI) and the simplified translocating inoculation (STI) strategy improved specific T cell responses elicited by the DNA vaccine. More specifically, the SSTI strategy significantly improved both the monofunctional (IFN-γ+IL-2-TNF-α-CD8+) and the multifunctional (IFN-γ+IL-2-TNF-α+CD8+, IFN-γ+IL-2-TNF-α+CD4+, IFN-γ+IL-2+TNF-α+CD4+) T cell responses, while the simplified translocating inoculation (STI) strategy significantly improved the multifunctional CD8+ (IFN-γ+IL-2-TNF-α+CD8+, IFN-γ+IL-2+TNF-α+CD8+) and CD4+ (IFN-γ+IL-2-TNF-α+CD4+, IFN-γ+IL-2+TNF-α+CD4+) T cell responses. The current study confirmed that changing the site of intra muscular injection can significantly improve the immunogenicity of DNA vaccines.
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Affiliation(s)
- Xiangxiang Tian
- Department of Medical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Infectious Disease, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, China
| | - Yifan Zhang
- Department of Medical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Infectious Disease, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, China
| | - Zhangyufan He
- Department of Infectious Disease, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shaoshuai Li
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, China
- Department of Immunology, School of Basic Medical, Jiamusi University, Jiamusi, China
| | - Dongmei Yan
- Department of Immunology, School of Basic Medical, Jiamusi University, Jiamusi, China
| | - Zhaoqin Zhu
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, China
| | - Yanmin Wan
- Department of Infectious Disease, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
- Department of Radiology, Shanghai Public Health Clinical Center, Shanghai, China
| | - Wanhai Wang
- Department of Medical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Abstract
The SARS-CoV-2 virus has been known to gain entry into the host cell through the spike protein that binds to the host ACE2 cell surface protein. However, the role of the putative sugar-binding sites in the spike protein has remained unclear. We provide a comprehensive in silico outlook into the infection initiation wherein the virus first recognizes the sialosides on the cell via its S1A domain of the spike protein as it surfs over the cell surface. This facilitates the subsequent interaction with the cellular glycosaminoglycans through the S1B domain of the spike protein as it binds to the ACE2 receptor. The unique coadaptation to recognize both the host protein and the cell-surface carbohydrate receptors provides an additional coupling mechanism for efficient viral attachment and infection.
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Affiliation(s)
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute
of Science, Bangalore-560012, India
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Espinosa LA, Ramos Y, Andújar I, Torres EO, Cabrera G, Martín A, Roche D, Chinea G, Becquet M, González I, Canaán-Haden C, Nelson E, Rojas G, Pérez-Massón B, Pérez-Martínez D, Boggiano T, Palacio J, Lozada Chang SL, Hernández L, de la Luz Hernández KR, Markku S, Vitikainen M, Valdés-Balbín Y, Santana-Medero D, Rivera DG, Vérez-Bencomo V, Emalfarb M, Tchelet R, Guillén G, Limonta M, Pimentel E, Ayala M, Besada V, González LJ. In-solution buffer-free digestion allows full-sequence coverage and complete characterization of post-translational modifications of the receptor-binding domain of SARS-CoV-2 in a single ESI-MS spectrum. Anal Bioanal Chem 2021; 413:7559-7585. [PMID: 34739558 PMCID: PMC8569510 DOI: 10.1007/s00216-021-03721-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/16/2021] [Accepted: 10/05/2021] [Indexed: 11/04/2022]
Abstract
Subunit vaccines based on the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 provide one of the most promising strategies to fight the COVID-19 pandemic. The detailed characterization of the protein primary structure by mass spectrometry (MS) is mandatory, as described in ICHQ6B guidelines. In this work, several recombinant RBD proteins produced in five expression systems were characterized using a non-conventional protocol known as in-solution buffer-free digestion (BFD). In a single ESI-MS spectrum, BFD allowed very high sequence coverage (≥ 99%) and the detection of highly hydrophilic regions, including very short and hydrophilic peptides (2-8 amino acids), and the His6-tagged C-terminal peptide carrying several post-translational modifications at Cys538 such as cysteinylation, homocysteinylation, glutathionylation, truncated glutathionylation, and cyanylation, among others. The analysis using the conventional digestion protocol allowed lower sequence coverage (80-90%) and did not detect peptides carrying most of the above-mentioned PTMs. The two C-terminal peptides of a dimer [RBD(319-541)-(His)6]2 linked by an intermolecular disulfide bond (Cys538-Cys538) with twelve histidine residues were only detected by BFD. This protocol allows the detection of the four disulfide bonds present in the native RBD, low-abundance scrambling variants, free cysteine residues, O-glycoforms, and incomplete processing of the N-terminal end, if present. Artifacts generated by the in-solution BFD protocol were also characterized. BFD can be easily implemented; it has been applied to the characterization of the active pharmaceutical ingredient of two RBD-based vaccines, and we foresee that it can be also helpful to the characterization of mutated RBDs.
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Affiliation(s)
- Luis Ariel Espinosa
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Yassel Ramos
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Ivan Andújar
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Enso Onill Torres
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Gleysin Cabrera
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Alejandro Martín
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Diamilé Roche
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Glay Chinea
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Mónica Becquet
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Isabel González
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Camila Canaán-Haden
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Elías Nelson
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Gertrudis Rojas
- Center of Molecular Immunology, 216 St., P.O. Box 16040, Havana, Cuba
| | | | | | - Tamy Boggiano
- Center of Molecular Immunology, 216 St., P.O. Box 16040, Havana, Cuba
| | - Julio Palacio
- Center of Molecular Immunology, 216 St., P.O. Box 16040, Havana, Cuba
| | | | - Lourdes Hernández
- Center of Molecular Immunology, 216 St., P.O. Box 16040, Havana, Cuba
| | | | - Saloheimo Markku
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT, Espoo, Finland
| | - Marika Vitikainen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT, Espoo, Finland
| | | | | | - Daniel G Rivera
- Laboratory of Synthetic and Biomolecular Chemistry, Faculty of Chemistry, University of Havana, Zapata & G, 10400, Havana, Cuba
| | | | - Mark Emalfarb
- Dyadic International, Inc, 140 Intercoastal Pointe Drive, Suite #404, Jupiter, FL, 33477, USA
| | - Ronen Tchelet
- Dyadic International, Inc, 140 Intercoastal Pointe Drive, Suite #404, Jupiter, FL, 33477, USA
| | - Gerardo Guillén
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Miladys Limonta
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Eulogio Pimentel
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Marta Ayala
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Vladimir Besada
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Luis Javier González
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba.
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Lim K, Nishide G, Yoshida T, Watanabe‐Nakayama T, Kobayashi A, Hazawa M, Hanayama R, Ando T, Wong RW. Millisecond dynamic of SARS-CoV-2 spike and its interaction with ACE2 receptor and small extracellular vesicles. J Extracell Vesicles 2021; 10:e12170. [PMID: 34874124 PMCID: PMC8650025 DOI: 10.1002/jev2.12170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/21/2021] [Accepted: 11/08/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 spike protein (S) binds to human angiotensin-converting enzyme 2 (hACE2), allowing virus to dock on cell membrane follow by viral entry. Here, we use high-speed atomic force microscopy (HS-AFM) for real-time visualization of S, and its interaction with hACE2 and small extracellular vesicles (sEVs). Results show conformational heterogeneity of S, flexibility of S stalk and receptor-binding domain (RBD), and pH/temperature-induced conformational change of S. S in an S-ACE2 complex appears as an all-RBD up conformation. The complex acquires a distinct topology upon acidification. S and S2 subunit demonstrate different membrane docking mechanisms on sEVs. S-hACE2 interaction facilitates S to dock on sEVs, implying the feasibility of ACE2-expressing sEVs for viral neutralization. In contrary, S2 subunit docks on lipid layer and enters sEV using its fusion peptide, mimicking the viral entry scenario. Altogether, our study provides a platform that is suitable for real-time visualization of various entry inhibitors, neutralizing antibodies, and sEV-based decoy in blocking viral entry. Teaser: Comprehensive observation of SARS-CoV-2 spike and its interaction with receptor ACE2 and sEV-based decoy in real time using HS-AFM.
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Affiliation(s)
- Keesiang Lim
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
| | - Goro Nishide
- Division of Nano Life Science in the Graduate School of Frontier Science InitiativeWISE Program for Nano‐Precision MedicineScience and TechnologyKanazawa UniversityKanazawaIshikawaJapan
| | - Takeshi Yoshida
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
- Department of ImmunologyKanazawa University Graduate School of Medical SciencesKanazawaIshikawaJapan
| | | | - Akiko Kobayashi
- Cell‐Bionomics Research UnitInstitute for Frontier Science Initiative (INFINITI)Kanazawa UniversityKanazawaIshikawaJapan
| | - Masaharu Hazawa
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
- Cell‐Bionomics Research UnitInstitute for Frontier Science Initiative (INFINITI)Kanazawa UniversityKanazawaIshikawaJapan
| | - Rikinari Hanayama
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
- Department of ImmunologyKanazawa University Graduate School of Medical SciencesKanazawaIshikawaJapan
| | - Toshio Ando
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
| | - Richard W. Wong
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
- Cell‐Bionomics Research UnitInstitute for Frontier Science Initiative (INFINITI)Kanazawa UniversityKanazawaIshikawaJapan
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Tsukinoki K, Yamamoto T, Handa K, Iwamiya M, Saruta J, Ino S, Sakurai T. Detection of cross-reactive immunoglobulin A against the severe acute respiratory syndrome-coronavirus-2 spike 1 subunit in saliva. PLoS One 2021; 16:e0249979. [PMID: 34813596 PMCID: PMC8610234 DOI: 10.1371/journal.pone.0249979] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/06/2021] [Indexed: 11/20/2022] Open
Abstract
Abundant secretory immunoglobulin A (SIgA) in the mucus, breast milk, and saliva provides immunity against infection of mucosal surfaces. Pre-pandemic breast milk samples containing SIgA have been reported to cross-react with SARS-CoV-2; however, it remains unknown whether SIgA showing the cross-reaction with SARS-CoV-2 exists in saliva. We aimed to clarify whether SIgA in saliva cross-reacts with SARS-CoV-2 spike 1 subunit in individuals who have not been infected with this virus. The study involved 137 (men, n = 101; women, n = 36; mean age, 38.7; age range, 24-65 years) dentists and doctors from Kanagawa Dental University Hospital. Saliva and blood samples were analyzed by polymerase chain reaction (PCR) and immunochromatography for IgG and IgM, respectively. We then identified patients with saliva samples that were confirmed to be PCR-negative and IgM-negative for SARS-CoV-2. The cross-reactivity of IgA-positive saliva samples with SARS-CoV-2 was determined by enzyme-linked immunosorbent assay using a biotin-labeled spike recombinant protein (S1-mFc) covering the receptor-binding domain of SARS-CoV-2. The proportion of SARS-CoV-2 cross-reactive IgA-positive individuals was 46.7%, which correlated negatively with age (r = -0.218, p = 0.01). The proportion of IgA-positive individuals aged ≥50 years was significantly lower than that of patients aged ≤49 years (p = 0.008). SIgA was purified from the saliva of patients, which could partially suppress the binding of SARS-CoV-2 spike protein to the angiotensin converting enzyme-2 receptor. This study demonstrates the presence of SARS-CoV-2 cross-reactive SIgA in the saliva of individuals who had never been infected with the virus, suggesting that SIgA may help prevent SARS-CoV-2 infection.
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Affiliation(s)
- Keiichi Tsukinoki
- Department of Environmental Pathology, Graduate School of Dentistry, Kanagawa Dental University, Yokosuka, Kanagawa, Japan
| | - Tatsuo Yamamoto
- Department of Dental Sociology, Graduate School of Dentistry, Kanagawa Dental University, Yokosuka, Kanagawa, Japan
| | - Keisuke Handa
- Department of Oral Biochemistry, Graduate School of Dentistry, Kanagawa Dental University, Yokosuka, Kanagawa, Japan
| | - Mariko Iwamiya
- Department of Clinical Laboratory, Kanagawa Dental University Hospital, Yokosuka, Kanagawa, Japan
| | - Juri Saruta
- Department of Environmental Pathology, Graduate School of Dentistry, Kanagawa Dental University, Yokosuka, Kanagawa, Japan
| | - Satoshi Ino
- Department of Minimal Intervention Prosthodontics, Graduate School of Dentistry, Kanagawa Dental University, Yokohama, Kanagawa, Japan
| | - Takashi Sakurai
- Department of Maxillofacial Radiology, Graduate School of Dentistry, Kanagawa Dental University, Yokosuka, Kanagawa, Japan
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49
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Lam JH, Khan AK, Cornell TA, Chia TW, Dress RJ, Yeow WWW, Mohd-Ismail NK, Venkataraman S, Ng KT, Tan YJ, Anderson DE, Ginhoux F, Nallani M. Polymersomes as Stable Nanocarriers for a Highly Immunogenic and Durable SARS-CoV-2 Spike Protein Subunit Vaccine. ACS Nano 2021; 15:15754-15770. [PMID: 34618423 PMCID: PMC8525042 DOI: 10.1021/acsnano.1c01243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/30/2021] [Indexed: 05/05/2023]
Abstract
Multiple successful vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed to address the ongoing coronavirus disease 2019 (Covid-19) pandemic. In the present work, we describe a subunit vaccine based on the SARS-CoV-2 spike protein coadministered with CpG adjuvant. To enhance the immunogenicity of our formulation, both antigen and adjuvant were encapsulated with our proprietary artificial cell membrane (ACM) polymersome technology. Structurally, ACM polymersomes are self-assembling nanoscale vesicles made up of an amphiphilic block copolymer comprising poly(butadiene)-b-poly(ethylene glycol) and a cationic lipid, 1,2-dioleoyl-3-trimethylammonium-propane. Functionally, ACM polymersomes serve as delivery vehicles that are efficiently taken up by dendritic cells (DC1 and DC2), which are key initiators of the adaptive immune response. Two doses of our formulation elicit robust neutralizing antibody titers in C57BL/6 mice that persist at least 40 days. Furthermore, we confirm the presence of functional memory CD4+ and CD8+ T cells that produce T helper type 1 cytokines. This study is an important step toward the development of an efficacious vaccine in humans.
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Affiliation(s)
| | - Amit K. Khan
- ACM
Biolabs Pte Ltd, Singapore 638075, Singapore
| | | | | | - Regine J. Dress
- Singapore Immunology
Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | | | - Nur Khairiah Mohd-Ismail
- Infectious
Diseases Translational Research Program, Department of Microbiology
and Immunology, Yong Loo Lin School of Medicine, National University
Health System, National University of Singapore, Singapore 117545, Singapore
| | | | - Kim Tien Ng
- Infectious
Diseases Translational Research Program, Department of Microbiology
and Immunology, Yong Loo Lin School of Medicine, National University
Health System, National University of Singapore, Singapore 117545, Singapore
| | - Yee-Joo Tan
- Infectious
Diseases Translational Research Program, Department of Microbiology
and Immunology, Yong Loo Lin School of Medicine, National University
Health System, National University of Singapore, Singapore 117545, Singapore
- Institute
of Molecular and Cell Biology, Agency for Science, Technology
and Research, Singapore 138673, Singapore
| | - Danielle E. Anderson
- Program
in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore 169857, Singapore
| | - Florent Ginhoux
- Singapore Immunology
Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
- SingHealth
Translational Immunology and Inflammation Centre, Singapore 169856, Singapore
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50
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Fort J, Nicolàs-Aragó A, Palacín M. The Ectodomains of rBAT and 4F2hc Are Fake or Orphan α-Glucosidases. Molecules 2021; 26:6231. [PMID: 34684812 PMCID: PMC8537225 DOI: 10.3390/molecules26206231] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/22/2022] Open
Abstract
It is known that 4F2hc and rBAT are the heavy subunits of the heteromeric amino acid transporters (HATs). These heavy subunits are N-glycosylated proteins, with an N-terminal domain, one transmembrane domain and a bulky extracellular domain (ectodomain) that belongs to the α-amylase family. The heavy subunits are covalently linked to a light subunit from the SLC7 family, which is responsible for the amino acid transport activity, forming a heterodimer. The functions of 4F2hc and rBAT are related mainly to the stability and trafficking of the HATs in the plasma membrane of vertebrates, where they exert the transport activity. Moreover, 4F2hc is a modulator of integrin signaling, has a role in cell fusion and it is overexpressed in some types of cancers. On the other hand, some mutations in rBAT are found to cause the malfunctioning of the b0,+ transport system, leading to cystinuria. The ectodomains of 4F2hc and rBAT share both sequence and structure homology with α-amylase family members. Very recently, cryo-EM has revealed the structure of several HATs, including the ectodomains of rBAT and 4F2hc. Here, we analyze available data on the ectodomains of rBAT and 4Fhc and their relationship with the α-amylase family. The physiological relevance of this relationship remains largely unknown.
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Affiliation(s)
- Joana Fort
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (M.P.)
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Adrià Nicolàs-Aragó
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (M.P.)
| | - Manuel Palacín
- Laboratory of Amino Acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; (A.N.-A.); (M.P.)
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
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