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Wang CR, McFarlane LO, Pukala TL. Exploring snake venoms beyond the primary sequence: From proteoforms to protein-protein interactions. Toxicon 2024; 247:107841. [PMID: 38950738 DOI: 10.1016/j.toxicon.2024.107841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Snakebite envenomation has been a long-standing global issue that is difficult to treat, largely owing to the flawed nature of current immunoglobulin-based antivenom therapy and the complexity of snake venoms as sophisticated mixtures of bioactive proteins and peptides. Comprehensive characterisation of venom compositions is essential to better understanding snake venom toxicity and inform effective and rationally designed antivenoms. Additionally, a greater understanding of snake venom composition will likely unearth novel biologically active proteins and peptides that have promising therapeutic or biotechnological applications. While a bottom-up proteomic workflow has been the main approach for cataloguing snake venom compositions at the toxin family level, it is unable to capture snake venom heterogeneity in the form of protein isoforms and higher-order protein interactions that are important in driving venom toxicity but remain underexplored. This review aims to highlight the importance of understanding snake venom heterogeneity beyond the primary sequence, in the form of post-translational modifications that give rise to different proteoforms and the myriad of higher-order protein complexes in snake venoms. We focus on current top-down proteomic workflows to identify snake venom proteoforms and further discuss alternative or novel separation, instrumentation, and data processing strategies that may improve proteoform identification. The current higher-order structural characterisation techniques implemented for snake venom proteins are also discussed; we emphasise the need for complementary and higher resolution structural bioanalytical techniques such as mass spectrometry-based approaches, X-ray crystallography and cryogenic electron microscopy, to elucidate poorly characterised tertiary and quaternary protein structures. We envisage that the expansion of the snake venom characterisation "toolbox" with top-down proteomics and high-resolution protein structure determination techniques will be pivotal in advancing structural understanding of snake venoms towards the development of improved therapeutic and biotechnology applications.
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Affiliation(s)
- C Ruth Wang
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Lewis O McFarlane
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia.
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2
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Cernosek T, Dalphin M, Jain N, Richter N, Beard S, Wang J, Osborne J, Stone T, Mellal M, Behrens S, Wunderli P. Analytical Quality by Design as applied to the development of a SEC-HPLC platform procedure for the determination of monoclonal antibody purity without mobile phase additives. J Pharm Biomed Anal 2024; 246:116220. [PMID: 38795426 DOI: 10.1016/j.jpba.2024.116220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/02/2024] [Accepted: 05/12/2024] [Indexed: 05/28/2024]
Abstract
This work presents the application of AQbD principles to the development of a size exclusion chromatography (SEC) HPLC procedure for the determination of monoclonal antibody (mAb) product purity using state-of-the-art column technology available via the Waters™ XBridge Premier Protein SEC column. Analytical Quality by Design (AQbD) emphasizes a systematic, risk-based lifecycle approach to analytical procedure development based on sound statistical methodologies. It has recently become increasingly recommended by regulatory agencies as a response to the need for greater efficiency, improved reliability, and increased robustness among modern analytical procedures in the pharmaceutical industry. Use of an Analytical Target Profile (ATP) and formal risk assessments informed the application of Design of Experiments (DoE) to optimize this analytical procedure, as well as assess its robustness and ruggedness. Importantly, our ruggedness results demonstrated the transferability of this procedure between two laboratories within the Catalent Biologics Global Network. Application of this analytical procedure as a platform approach for evaluating mAb purity is expected to support expedited, first-in-human timelines of mAb molecules by enabling great quantitative performance with simple mobile phase buffer compositions. Taken together, this case study demonstrates the utility of adopting AQbD principles in analytical procedure development.
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Affiliation(s)
- Terezie Cernosek
- Catalent Biologics, Madison, WI, USA; Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA.
| | | | | | | | | | | | | | - Todd Stone
- Catalent Biologics, Bloomington, IN, USA
| | | | - Sue Behrens
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
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3
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Tang Y, Liu L, Zhou Q, Wang D, Guo H, Liu N, Yan X, Wang Z, He B, Hu L, Jiang G. Rapid determination of toxic and essential metal binding proteins in biological samples by size exclusion chromatography-inductively coupled plasma tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1243:124235. [PMID: 38996753 DOI: 10.1016/j.jchromb.2024.124235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024]
Abstract
Metalloproteins binding with trace elements play a crucial role in biological processes and on the contrary, those binding with exogenous heavy metals have adverse effects. However, the methods for rapid, high sensitivity and simultaneous analysis of these metalloproteins are still lacking. In this study, a fast method for simultaneously determination of both essential and toxic metal-containing proteins was developed by coupling size exclusion chromatography (SEC) with inductively coupled plasma tandem mass spectrometry (ICP-MS/MS). After optimization of the separation and detection conditions, seven metalloproteins with different molecular weight (from 16.0 to 443.0 kDa) were successfully separated within 10 min and the proteins containing iron (Fe), copper (Cu), zinc (Zn), iodine (I) and lead (Pb) elements could be simultaneously detected with the use of oxygen as the collision gas in ICP-MS/MS. Accordingly, the linear relationship between log molecular weight and retention time was established to estimate the molecular weight of unknown proteins. Thus, the trace metal and toxic metal containing proteins could be detected in a single run with high sensitivity (detection limits in the range of 0.0020-2.5 μg/mL) and good repeatability (relative standard deviations lower than 4.5 %). This method was then successfully used to analyze metal (e.g., Pb, Zn, Cu and Fe) binding proteins in the blood of Pb-intoxicated patients, and the results showed a negative correlation between the contents of zinc and lead binding proteins, which was identified to contain hemoglobin subunit. In summary, this work provided a rapid and sensitive tool for screening metal containing proteins in large number of biological samples.
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Affiliation(s)
- Yinyin Tang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lihong Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Qinfei Zhou
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dingyi Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hua Guo
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Nian Liu
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xueting Yan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhenhua Wang
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Bin He
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Ligang Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China.
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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4
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Kane BJ, Okuda‐Shimazaki J, Andrews MM, Kerrigan JA, Murphy KV, Sode K. Discovery of periplasmic solute binding proteins with specificity for ketone bodies: β-hydroxybutyrate binding proteins. Protein Sci 2024; 33:e5025. [PMID: 38864689 PMCID: PMC11167705 DOI: 10.1002/pro.5025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 06/13/2024]
Abstract
Polyhydroxyalkanoates are a class of biodegradable, thermoplastic polymers which represent a major carbon source for various bacteria. Proteins which mediate the translocation of polyhydroxyalkanoate breakdown products, such as β-hydroxybutyrate (BHB)-a ketone body which in humans serves as an important biomarker, have not been well characterized. In our investigation to screen a solute-binding protein (SBP) which can act as a suitable recognition element for BHB, we uncovered insights at the intersection of bacterial metabolism and diagnostics. Herein, we identify SBPs associated with putative ATP-binding cassette transporters that specifically recognize BHB, with the potential to serve as recognition elements for continuous quantification of this analyte. Through bioinformatic analysis, we identified candidate SBPs from known metabolizers of polyhydroxybutyrate-including proteins from Cupriavidus necator, Ensifer meliloti, Paucimonas lemoignei, and Thermus thermophilus. After recombinant expression in Escherichia coli, we demonstrated with intrinsic tryptophan fluorescence spectroscopy that four candidate proteins interacted with BHB, ranging from nanomolar to micromolar affinity. Tt.2, an intrinsically thermostable protein from Thermus thermophilus, was observed to have the tightest binding and specificity for BHB, which was confirmed by isothermal calorimetry. Structural analyses facilitated by AlphaFold2, along with molecular docking and dynamics simulations, were used to hypothesize key residues in the binding pocket and to model the conformational dynamics of substrate unbinding. Overall, this study provides strong evidence identifying the cognate ligands of SBPs which we hypothesize to be involved in prokaryotic cellular translocation of polyhydroxyalkanoate breakdown products, while highlighting these proteins' promising biotechnological application.
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Affiliation(s)
- Bryant J. Kane
- Joint Department of Biomedical EngineeringThe University of North Carolina at Chapel Hill and North Carolina State UniversityChapel HillNorth CarolinaUSA
| | - Junko Okuda‐Shimazaki
- Department of Biotechnology and Life Science, Graduate School of EngineeringTokyo University of Agriculture and TechnologyTokyoJapan
| | - Madelyn M. Andrews
- Joint Department of Biomedical EngineeringThe University of North Carolina at Chapel Hill and North Carolina State UniversityChapel HillNorth CarolinaUSA
| | - Joseph A. Kerrigan
- Joint Department of Biomedical EngineeringThe University of North Carolina at Chapel Hill and North Carolina State UniversityChapel HillNorth CarolinaUSA
| | - Kyle V. Murphy
- Joint Department of Biomedical EngineeringThe University of North Carolina at Chapel Hill and North Carolina State UniversityChapel HillNorth CarolinaUSA
| | - Koji Sode
- Joint Department of Biomedical EngineeringThe University of North Carolina at Chapel Hill and North Carolina State UniversityChapel HillNorth CarolinaUSA
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5
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Khodadadi S, Rabiei H, Sardari S, Mahboudi H, Bayatzadeh MA, Vazifeh Shiran N, Sardabi M, Akbari Eidgahi MR, Madanchi H, Mohammadpour N. Purification, and characterization of a new pro-coagulant protein from Iranian Echis carinatus venom. Biochem Biophys Rep 2024; 38:101701. [PMID: 38601750 PMCID: PMC11004499 DOI: 10.1016/j.bbrep.2024.101701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
This work aimed to purify the proteins that cause blood coagulation in the venom of the Iranian Echis carinatus snake species in a comprehensive manner. Gel filtration chromatography (GFC), Ion exchange chromatography (IEC), and Size Exclusion High-Performance Liquid Chromatography (SEC-HPLC) were utilized in the purification of the coagulation factors. The prothrombin clotting time (PRCT) and SDS-PAGE electrophoresis were performed to confirm the coagulative fractions. The fraction with the shortest coagulation time was selected. The components of this designated fraction were identified through matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF) following thorough purification. Circular dichroism (CD) was employed to determine the second structure of the coagulation factor. The crude venom (CV) was analyzed and had a total protein concentration of 97%. Furthermore, the PRCT of the crude venom solution at a concentration of 1 mg/ml was determined to be 24.19 ± 1.05 s. The dosage administered was found to be a factor in the venom's capacity to induce hemolysis. According to CD analysis, the protein under investigation had a helical structure of 16.7%, a beta structure of 41%, and a turn structure of 9.8%. CHNS proved that the purified coagulant protein had a Carbon content of 77.82%, 5.66% Hydrogen, 3.19% Nitrogen, and 0.49% Sulphur. In the present investigation, a particular type of snake venom metalloproteinase (SVMP) has undergone the process of purification and characterization and has been designated as EC-124. This purified fraction shows significant efficacy as a procoagulant. Our findings have shown that this compound has a function similar to factor X and most likely it can cause blood coagulation by activating factor II (FII).
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Affiliation(s)
- Sayeneh Khodadadi
- Department of Medical Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Hadi Rabiei
- Venomous Animal and Antivenom Production Department, Razi Vaccine and Serum Research Institute, Iran
| | - Soroush Sardari
- Drug Design and Bioinformatics Unit, Medical, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, 13198, Tehran, Iran
| | - Hosein Mahboudi
- Department of Medical Laboratory Sciences, Faculty of Para-Medicine, Alborz University of Medical Sciences, Alborz, Iran
| | - Mohammad Ali Bayatzadeh
- Venomous Animal and Antivenom Production Department, Razi Vaccine and Serum Research Institute, Iran
| | - Nader Vazifeh Shiran
- Department of Hematology, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Sardabi
- Faculty of Biological Sciences, Khwarizmi University, Alborz, Iran
| | | | - Hamid Madanchi
- Department of Medical Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Drug Design and Bioinformatics Unit, Medical, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, 13198, Tehran, Iran
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Nasser Mohammadpour
- Venomous Animal and Antivenom Production Department, Razi Vaccine and Serum Research Institute, Iran
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6
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Kermani AA. Applications of fluorescent protein tagging in structural studies of membrane proteins. FEBS J 2024; 291:2719-2732. [PMID: 37470714 DOI: 10.1111/febs.16910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/16/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Generating active, pure, and monodisperse protein remains a major bottleneck for structural studies using X-ray crystallography and cryo-electron microscopy (cryo-EM). The current methodology heavily relies on overexpressing the recombinant protein fused with a histidine tag in conventional expression systems and evaluating the quality and stability of purified protein using size exclusion chromatography (SEC). This requires a large amount of protein and can be highly laborious and time consuming. Therefore, this approach is not suitable for high-throughput screening and low-expressing macromolecules, particularly eukaryotic membrane proteins. Using fluorescent proteins fused to the target protein (applicable to both soluble and membrane proteins) enables rapid and efficient screening of expression level and monodispersity of tens of unpurified constructs using fluorescence-based size exclusion chromatography (FSEC). Moreover, FSEC proves valuable for screening multiple detergents to identify the most stabilizing agent in the case of membrane proteins. Additionally, FSEC can facilitate nanodisc reconstitution by determining the optimal ratio of membrane scaffold protein (MSP), lipids, and target protein. The distinct advantages offered by FSEC indicate that fluorescent proteins can serve as a viable alternative to commonly used affinity tags for both characterization and purification purposes. In this review, I will summarize the advantages of this technique using examples from my own work. It should be noted that this article is not intended to provide an exhaustive review of all available literature, but rather to offer representative examples of FSEC applications.
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Affiliation(s)
- Ali A Kermani
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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7
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Lan T, Dong Y, Jiang L, Zhang Y, Sui X. Analytical approaches for assessing protein structure in protein-rich food: A comprehensive review. Food Chem X 2024; 22:101365. [PMID: 38623506 PMCID: PMC11016869 DOI: 10.1016/j.fochx.2024.101365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024] Open
Abstract
This review focuses on changes in nutrition and functional properties of protein-rich foods, primarily attributed to alterations in protein structures. We provide a comprehensive overview and comparison of commonly used laboratory methods for protein structure identification, aiming to offer readers a convenient understanding of these techniques. The review covers a range of detection technologies employed in food protein analysis and conducts an extensive comparison to identify the most suitable method for various proteins. While these techniques offer distinct advantages for protein structure determination, the inherent complexity of food matrices presents ongoing challenges. Further research is necessary to develop and enhance more robust detection methods to improve accuracy in protein conformation and structure analysis.
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Affiliation(s)
- Tian Lan
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yabo Dong
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Lianzhou Jiang
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yan Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaonan Sui
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
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8
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Raju S, Turner ME, Cao C, Abdul-Samad M, Punwasi N, Blaser MC, Cahalane RM, Botts SR, Prajapati K, Patel S, Wu R, Gustafson D, Galant NJ, Fiddes L, Chemaly M, Hedin U, Matic L, Seidman M, Subasri V, Singh SA, Aikawa E, Fish JE, Howe KL. Multi-omic Landscape of Extracellular Vesicles in Human Carotid Atherosclerotic Plaque Reveals Endothelial Communication Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.599781. [PMID: 38979218 PMCID: PMC11230219 DOI: 10.1101/2024.06.21.599781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background Carotid atherosclerosis is a multifaceted disease orchestrated by a myriad of cell-cell communication that drives progression along a clinical continuum (asymptomatic to symptomatic). Extracellular vesicles (EVs) are lipid bilayer membrane-enclosed cell-derived nanoparticles that represent a new paradigm in cellular communication. Little is known about their biological cargo, cellular origin/destination, and functional roles in human atherosclerotic plaque. Methods EVs were enriched via size exclusion chromatography from human carotid endarterectomy samples dissected into plaque and marginal zones (n= 29 patients, paired plaque and marginal zone; symptomatic n=16, asymptomatic n=13), with further density gradient ultracentrifugation for proteomic analysis. EV cargoes were assessed via whole transcriptome miRNA sequencing and mass spectrometry-based proteomics. EV multi-omics were integrated with publicly available bulk and single cell RNA-sequencing (scRNA-seq) datasets to predict EV cellular origin and ligand-receptor interactions and multi-modal biological network integration of EV-cargo was completed. EV functional impact was assessed with endothelial angiogenesis assays. Results Human carotid plaques contained greater quantities of EVs than adjacent marginal zones. EV-miRNA and protein content was different in diseased plaque versus adjacent marginal zones, with differential functions in key atherogenic pathways. EV cellular origin analysis suggested that tissue EV signatures originated from endothelial cells (EC), smooth muscle cells (SMC), and immune cells. Furthermore, EV signatures from SMCs and immune cells were most enriched in the marginal and plaque zones, respectively. Integrated tissue vesiculomics and scRNA-seq indicated complex EV-vascular cell communication strategies that changed with disease progression and plaque vulnerability (i.e., symptomatic disease). Plaques from symptomatic patients, but not asymptomatic patients, were characterized by increased involvement of endothelial pathways and more complex ligand-receptor interactions, relative to their marginal zones. Plaque-EVs were predicted to mediate communication with ECs. Pathway enrichment analysis delineated a strong endothelial signature with potential roles in angiogenesis and neovascularization - well-known indices of plaque instability. This was corroborated functionally, wherein human carotid symptomatic plaque EVs induced sprouting angiogenesis in comparison to their matched marginal zones. Conclusion Our findings indicate that EVs may drive dynamic changes in plaques through EV-vascular cell communication and effector functions that typify vulnerability to rupture, precipitating symptomatic disease. The discovery of endothelial-directed processes mediated by EVs creates new avenues for novel therapeutics in atherosclerosis.
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9
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Garaudé S, Marone R, Lepore R, Devaux A, Beerlage A, Seyres D, Dell' Aglio A, Juskevicius D, Zuin J, Burgold T, Wang S, Katta V, Manquen G, Li Y, Larrue C, Camus A, Durzynska I, Wellinger LC, Kirby I, Van Berkel PH, Kunz C, Tamburini J, Bertoni F, Widmer CC, Tsai SQ, Simonetta F, Urlinger S, Jeker LT. Selective haematological cancer eradication with preserved haematopoiesis. Nature 2024; 630:728-735. [PMID: 38778101 PMCID: PMC11186773 DOI: 10.1038/s41586-024-07456-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 04/23/2024] [Indexed: 05/25/2024]
Abstract
Haematopoietic stem cell (HSC) transplantation (HSCT) is the only curative treatment for a broad range of haematological malignancies, but the standard of care relies on untargeted chemotherapies and limited possibilities to treat malignant cells after HSCT without affecting the transplanted healthy cells1. Antigen-specific cell-depleting therapies hold the promise of much more targeted elimination of diseased cells, as witnessed in the past decade by the revolution of clinical practice for B cell malignancies2. However, target selection is complex and limited to antigens expressed on subsets of haematopoietic cells, resulting in a fragmented therapy landscape with high development costs2-5. Here we demonstrate that an antibody-drug conjugate (ADC) targeting the pan-haematopoietic marker CD45 enables the antigen-specific depletion of the entire haematopoietic system, including HSCs. Pairing this ADC with the transplantation of human HSCs engineered to be shielded from the CD45-targeting ADC enables the selective eradication of leukaemic cells with preserved haematopoiesis. The combination of CD45-targeting ADCs and engineered HSCs creates an almost universal strategy to replace a diseased haematopoietic system, irrespective of disease aetiology or originating cell type. We propose that this approach could have broad implications beyond haematological malignancies.
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Affiliation(s)
- Simon Garaudé
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Romina Marone
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Rosalba Lepore
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
- Cimeio Therapeutics, Basel, Switzerland
| | - Anna Devaux
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Astrid Beerlage
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
- Department of Hematology, Basel University Hospital, Basel, Switzerland
| | - Denis Seyres
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Alessandro Dell' Aglio
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Darius Juskevicius
- Department of Laboratory Medicine, Diagnostic Hematology, Basel University Hospital, Basel, Switzerland
| | - Jessica Zuin
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Thomas Burgold
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Sisi Wang
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
| | - Varun Katta
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Garret Manquen
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yichao Li
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Clément Larrue
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
| | | | | | | | | | | | | | - Jérôme Tamburini
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Corinne C Widmer
- Department of Hematology, Basel University Hospital, Basel, Switzerland
- Department of Laboratory Medicine, Diagnostic Hematology, Basel University Hospital, Basel, Switzerland
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Federico Simonetta
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Lukas T Jeker
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland.
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland.
- Innovation Focus Cell Therapy, Basel University Hospital, Basel, Switzerland.
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10
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Liau B, Zhang L, Ang MJY, Ng JY, C V SB, Schneider S, Gudihal R, Bae KH, Yang YY. Quantitative analysis of mRNA-lipid nanoparticle stability in human plasma and serum by size-exclusion chromatography coupled with dual-angle light scattering. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 58:102745. [PMID: 38499167 DOI: 10.1016/j.nano.2024.102745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 03/20/2024]
Abstract
Understanding the stability of mRNA loaded lipid nanoparticles (mRNA-LNPs) is imperative for their clinical development. Herein, we propose the use of size-exclusion chromatography coupled with dual-angle light scattering (SEC-MALS) as a new approach to assessing mRNA-LNP stability in pure human serum and plasma. By applying a dual-column configuration to attenuate interference from plasma components, SEC-MALS was able to elucidate the degradation kinetics and physical property changes of mRNA-LNPs, which have not been observed accurately by conventional dynamic light scattering techniques. Interestingly, both serum and plasma had significantly different impacts on the molecular weight and radius of gyration of mRNA-LNPs, suggesting the involvement of clotting factors in desorption of lipids from mRNA-LNPs. We also discovered that a trace impurity (~1 %) in ALC-0315, identified as its O-tert-butyloxycarbonyl-protected form, greatly diminished mRNA-LNP stability in serum. These results demonstrated the potential utility of SEC-MALS for optimization and quality control of LNP formulations.
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Affiliation(s)
- Brian Liau
- Agilent Technologies, 1 Yishun Avenue 7, Singapore 768923, Republic of Singapore.
| | - Li Zhang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore 138668, Republic of Singapore
| | - Melgious Jin Yan Ang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore 138668, Republic of Singapore
| | - Jian Yao Ng
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore 138668, Republic of Singapore
| | - Suresh Babu C V
- Agilent Technologies, 1 Yishun Avenue 7, Singapore 768923, Republic of Singapore
| | - Sonja Schneider
- Agilent Technologies Deutschland GmbH, Hewlett-Packard Strasse 8, 76337 Waldbronn, Germany
| | - Ravindra Gudihal
- Agilent Technologies, 1 Yishun Avenue 7, Singapore 768923, Republic of Singapore
| | - Ki Hyun Bae
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore 138668, Republic of Singapore
| | - Yi Yan Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore 138668, Republic of Singapore.
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11
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Bao Z, Cheng YC, Luo MZ, Zhang JY. Analysis of aggregation profile of glucagon using SEC-HPLC and FFF-MALS methods. PLoS One 2024; 19:e0304086. [PMID: 38771849 PMCID: PMC11108154 DOI: 10.1371/journal.pone.0304086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 05/03/2024] [Indexed: 05/23/2024] Open
Abstract
Recently, the first generic glucagon for injection was approved for the treatment of severe hypoglycemia. Unlike its brand name recombinant glucagon, the generic glucagon is synthetic. Since glucagon has a high propensity to form aggregates in solution, it is essential to assess the aggregation profile of the synthetic glucagon compared to the recombinant glucagon. In this study, two robust separation methods, size-exclusion chromatography (SEC-HPLC) and field-flow fractionation coupled with a multi-angle light scattering detector (FFF-MALS), were employed to characterize generic and brand glucagon aggregation in six lots (three newly released, three expired). The presence of aggregation in samples was determined from the generated chromatograms and analyzed. The study showed that both products have comparable aggregation profiles. The SEC-HPLC demonstrated that in both glucagon versions, the expired lots had a higher percentage of dimers than the newly released lots, but even at expiration, the amount was negligible (∼0.1%). The FFF-MALS method did not detect any dimers or higher molecular weight aggregates. Further evaluation of the detection limit found that FFF-MALS was unable to detect aggregates at amounts lower than 0.5% of total glucagon. The negligible amounts of dimer detected in the generic and brand glucagon indicate that both versions are physically stable and are not prone to aggregation under clinically relevant conditions.
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Affiliation(s)
- Zhongli Bao
- Amphastar Pharmaceuticals, Inc., Rancho Cucamonga, California, California, United States of America
| | - Ya-Chi Cheng
- Amphastar Pharmaceuticals, Inc., Rancho Cucamonga, California, California, United States of America
| | - Mary Ziping Luo
- Amphastar Pharmaceuticals, Inc., Rancho Cucamonga, California, California, United States of America
| | - Jack Yongfeng Zhang
- Amphastar Pharmaceuticals, Inc., Rancho Cucamonga, California, California, United States of America
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12
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Timira V, Chen X, Zhou P, Wu J, Wang T. Potential use of yeast protein in terms of biorefinery, functionality, and sustainability in food industry. Compr Rev Food Sci Food Saf 2024; 23:e13326. [PMID: 38572572 DOI: 10.1111/1541-4337.13326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 04/05/2024]
Abstract
A growing demand for sustainable, alternative protein sources that are nutrient-dense, such as microorganisms, and insects, has gradually evolved. When paired with effective processing techniques, yeast cells contain substantial substances that could supply the population's needs for food, medicine, and fuel. This review article explores the potential of yeast proteins as a sustainable and viable alternative to animal and plant-based protein sources. It highlights the various yeast protein extraction methods including both mechanical and non-mechanical methods. The application of nanoparticles is one example of the fast-evolving technology used to damage microbial cells. SiO2 or Al2O3 nanoparticles break yeast cell walls and disrupt membranes, releasing intracellular bioactive compounds. Succinylation of yeast protein during extraction can increase yeast protein extraction rate, lower RNA concentration, raise yeast protein solubility, increase amino acid content, and improve yeast protein emulsification and foaming capabilities. Combining physical and enzymatic extraction methods generates the most representative pool of mannose proteins from yeast cell walls. Ethanol or isoelectric precipitation purifies mannose proteins. Mannoproteins can be used as foamy replacement for animal-derived components like egg whites due to their emulsification, stability, and foaming capabilities. Yeast bioactive peptide was separated by ultrafiltration after enzymatic hydrolysis of yeast protein and has shown hypoglycemic, hypotensive, and oxidative action in vitro studies. Additionally, the review delves into the physicochemical properties and stability of yeast-derived peptides as well as their applications in the food industry. The article infers that yeast proteins are among the promising sources of sustainable protein, with a wide range of potential applications in the food industry.
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Affiliation(s)
- Vaileth Timira
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xing Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Peng Zhou
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Junjun Wu
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Tao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
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13
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Khalikova M, Jireš J, Horáček O, Douša M, Kučera R, Nováková L. What is the role of current mass spectrometry in pharmaceutical analysis? MASS SPECTROMETRY REVIEWS 2024; 43:560-609. [PMID: 37503656 DOI: 10.1002/mas.21858] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/02/2023] [Accepted: 06/25/2023] [Indexed: 07/29/2023]
Abstract
The role of mass spectrometry (MS) has become more important in most application domains in recent years. Pharmaceutical analysis is specific due to its stringent regulation procedures, the need for good laboratory/manufacturing practices, and a large number of routine quality control analyses to be carried out. The role of MS is, therefore, very different throughout the whole drug development cycle. While it dominates within the drug discovery and development phase, in routine quality control, the role of MS is minor and indispensable only for selected applications. Moreover, its role is very different in the case of analysis of small molecule pharmaceuticals and biopharmaceuticals. Our review explains the role of current MS in the analysis of both small-molecule chemical drugs and biopharmaceuticals. Important features of MS-based technologies being implemented, method requirements, and related challenges are discussed. The differences in analytical procedures for small molecule pharmaceuticals and biopharmaceuticals are pointed out. While a single method or a small set of methods is usually sufficient for quality control in the case of small molecule pharmaceuticals and MS is often not indispensable, a large panel of methods including extensive use of MS must be used for quality control of biopharmaceuticals. Finally, expected development and future trends are outlined.
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Affiliation(s)
- Maria Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Jakub Jireš
- Department of Analytical Chemistry, Faculty of Chemical Engineering, UCT Prague, Prague, Czech Republic
- Department of Development, Zentiva, k. s., Praha, Praha, Czech Republic
| | - Ondřej Horáček
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Michal Douša
- Department of Development, Zentiva, k. s., Praha, Praha, Czech Republic
| | - Radim Kučera
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
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14
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Juković M, Ratkaj I, Kalafatovic D, Bradshaw NJ. Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation. Biophys Chem 2024; 308:107202. [PMID: 38382283 DOI: 10.1016/j.bpc.2024.107202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.
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Affiliation(s)
- Maja Juković
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Ratkaj
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Daniela Kalafatovic
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
| | - Nicholas J Bradshaw
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
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15
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Wachter F, Nowak RP, Ficarro S, Marto J, Fischer ES. Structural characterization of methylation-independent PP2A assembly guides alphafold2Multimer prediction of family-wide PP2A complexes. J Biol Chem 2024; 300:107268. [PMID: 38582449 PMCID: PMC11087950 DOI: 10.1016/j.jbc.2024.107268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 04/08/2024] Open
Abstract
Dysregulation of phosphorylation-dependent signaling is a hallmark of tumorigenesis. Protein phosphatase 2 (PP2A) is an essential regulator of cell growth. One scaffold subunit (A) binds to a catalytic subunit (C) to form a core AC heterodimer, which together with one of many regulatory (B) subunits forms the active trimeric enzyme. The combinatorial number of distinct PP2A complexes is large, which results in diverse substrate specificity and subcellular localization. The detailed mechanism of PP2A assembly and regulation remains elusive and reports about an important role of methylation of the carboxy terminus of PP2A C are conflicting. A better understanding of the molecular underpinnings of PP2A assembly and regulation is critical to dissecting PP2A function in physiology and disease. Here, we combined biochemical reconstitution, mass spectrometry, X-ray crystallography, and functional assays to characterize the assembly of trimeric PP2A. In vitro studies demonstrated that methylation of the carboxy-terminus of PP2A C was dispensable for PP2A assembly in vitro. To corroborate these findings, we determined the X-ray crystal structure of the unmethylated PP2A Aα-B56ε-Cα trimer complex to 3.1 Å resolution. The experimental structure superimposed well with an Alphafold2Multimer prediction of the PP2A trimer. We then predicted models of all canonical PP2A complexes providing a framework for structural analysis of PP2A. In conclusion, methylation was dispensable for trimeric PP2A assembly and integrative structural biology studies of PP2A offered predictive models for all canonical PP2A complexes.
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Affiliation(s)
- Franziska Wachter
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Scott Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jarrod Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
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16
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Salehi M, Negahdari B, Mehryab F, Shekari F. Milk-Derived Extracellular Vesicles: Biomedical Applications, Current Challenges, and Future Perspectives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8304-8331. [PMID: 38587896 DOI: 10.1021/acs.jafc.3c07899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Extracellular vesicles (EVs) are nano to-micrometer-sized sacs that are released by almost all animal and plant cells and act as intercellular communicators by transferring their cargos between the source and target cells. As a safe and scalable alternative to conditioned medium-derived EVs, milk-derived EVs (miEVs) have recently gained a great deal of popularity. Numerous studies have shown that miEVs have intrinsic therapeutic actions that can treat diseases and enhance human health. Additionally, they can be used as natural drug carriers and novel classes of biomarkers. However, due to the complexity of the milk, the successful translation of miEVs from benchtop to bedside still faces several unfilled gaps, especially a lack of standardized protocols for the isolation of high-purity miEVs. In this work, by comprehensively reviewing the bovine miEVs studies, we provide an overview of current knowledge and research on miEVs while highlighting their challenges and enormous promise as a novel class of theranostics. It is hoped that this study will pave the way for clinical applications of miEVs by addressing their challenges and opportunities.
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Affiliation(s)
- Mahsa Salehi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 14177-55469, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran
| | - Babak Negahdari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 14177-55469, Iran
| | - Fatemeh Mehryab
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran 14155-6153, Iran
| | - Faezeh Shekari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran
- Advanced Therapy Medicinal Product Technology Development Center (ATMP-TDC), Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran
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17
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Bashir S, Aiman A, Chaudhary AA, Khan N, Ahanger IA, Sami N, Almugri EA, Ali MA, Khan SUD, Shahid M, Basir SF, Hassan MI, Islam A. Probing protein aggregation through spectroscopic insights and multimodal approaches: A comprehensive review for counteracting neurodegenerative disorders. Heliyon 2024; 10:e27949. [PMID: 38689955 PMCID: PMC11059433 DOI: 10.1016/j.heliyon.2024.e27949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 05/02/2024] Open
Abstract
Aberrant accumulation of protein misfolding can cause aggregation and fibrillation and is one of the primary characteristic features of neurodegenerative diseases. Because they are disordered, misfolded, and aggregated proteins pose a significant setback in drug designing. The structural study of intermediate steps in these kinds of aggregated proteins will allow us to determine the conformational changes as well as the probable pathways encompassing various neurodegenerative disorders. The analysis of protein aggregates involved in neurodegenerative diseases relies on a diverse toolkit of biophysical techniques, encompassing both morphological and non-morphological methods. Additionally, Thioflavin T (ThT) assays and Circular Dichroism (CD) spectroscopy facilitate investigations into aggregation kinetics and secondary structure alterations. The collective application of these biophysical techniques empowers researchers to comprehensively unravel the intricate nature of protein aggregates associated with neurodegeneration. Furthermore, the topics covered in this review have summed up a handful of well-established techniques used for the structural analysis of protein aggregation. This multifaceted approach advances our fundamental understanding of the underlying mechanisms driving neurodegenerative diseases and informs potential therapeutic strategies.
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Affiliation(s)
- Sania Bashir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ayesha Aiman
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Nashrah Khan
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ishfaq Ahmad Ahanger
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Neha Sami
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Eman Abdullah Almugri
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Mohamed A.M. Ali
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
- Department of Biochemistry, Faculty of Science, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Salah-Ud-Din Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic Universi-ty (IMSIU), Riyadh, 11623, Saudi Arabia
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, AlKharj, 11942, Saudi Arabia
| | - Seemi Farhat Basir
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
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18
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Farzam F, Dabirmanesh B. Experimental techniques for detecting and evaluating the amyloid fibrils. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:183-227. [PMID: 38811081 DOI: 10.1016/bs.pmbts.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Amyloid fibrils are insoluble proteins with intricate β-sheet structures associated with various human diseases, including Parkinson's, Alzheimer's, and prion diseases. Proteins can form aggregates when their structure is misfolded, resulting in highly organized amyloid fibrils or amorphous aggregates. The formation of protein aggregates is a promising research field for mitigating diseases and the pharmaceutical and food industries. It is important to monitor and minimize the appearance of aggregates in these protein products. Several methods exist to assess protein aggregation, that includes from basic investigations to advanced biophysical techniques. Physicochemical parameters such as molecular weight, conformation, structure, and dimension are examined to study aggregation. There is an urgent need to develop methods for the detection of protein aggregation and amyloid fibril formation both in vitro and in vivo. This chapter focuses on a comprehensive discussion of the methods used to characterize and evaluate aggregates and amyloid fibrils.
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Affiliation(s)
- Farnoosh Farzam
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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19
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Barrientos RC, Singh AN, Ukaegbu O, Hemida M, Wang H, Haidar Ahmad I, Hu H, Dunn ZD, Appiah-Amponsah E, Regalado EL. Two-Dimensional SEC-SEC-UV-MALS-dRI Workflow for Streamlined Analysis and Characterization of Biopharmaceuticals. Anal Chem 2024; 96:4960-4968. [PMID: 38436624 DOI: 10.1021/acs.analchem.3c05969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
The emergence of complex biological modalities in the biopharmaceutical industry entails a significant expansion of the current analytical toolbox to address the need to deploy meaningful and reliable assays at an unprecedented pace. Size exclusion chromatography (SEC) is an industry standard technique for protein separation and analysis. Some constraints of traditional SEC stem from its restricted ability to resolve complex mixtures and notoriously long run times while also requiring multiple offline separation conditions on different pore size columns to cover a wider molecular size distribution. Two-dimensional liquid chromatography (2D-LC) is becoming an important tool not only to increase peak capacity but also to tune selectivity in a single online method. Herein, an online 2D-LC framework in which both dimensions utilize SEC columns with different pore sizes is introduced with a goal to increase throughput for biomolecule separation and characterization. In addition to improving the separation of closely related species, this online 2D SEC-SEC approach also facilitated the rapid analysis of protein-based mixtures of a wide molecular size range in a single online experimental run bypassing time-consuming deployment of different offline SEC methods. By coupling the second dimension with multiangle light scattering (MALS) and differential refractive index (dRI) detectors, absolute molecular weights of the separated species were obtained without the use of calibration curves. As illustrated in this report for protein mixtures and vaccine processes, this workflow can be used in scenarios where rapid development and deployment of SEC assays are warranted, enabling bioprocess monitoring, purity assessment, and characterization.
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Affiliation(s)
- Rodell C Barrientos
- Analytical Research and Development, MRL, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Andrew N Singh
- Analytical Research and Development, MRL, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Ophelia Ukaegbu
- Analytical Research and Development, MRL, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Mohamed Hemida
- Analytical Research and Development, MRL, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Heather Wang
- Analytical Research and Development, MRL, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Imad Haidar Ahmad
- Analytical Research and Development, MRL, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Hang Hu
- Analytical Research and Development, MRL, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zachary D Dunn
- Analytical Research and Development, MRL, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Emmanuel Appiah-Amponsah
- Analytical Research and Development, MRL, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Erik L Regalado
- Analytical Research and Development, MRL, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
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20
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Cernosek T, Jain N, Dalphin M, Behrens S, Wunderli P. Accelerated development of a SEC-HPLC procedure for purity analysis of monoclonal antibodies using design of experiments. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1235:124037. [PMID: 38335765 DOI: 10.1016/j.jchromb.2024.124037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
The complex structure of biopharmaceutical products poses an inherent need for their thorough characterization to ensure product quality, safety, and efficacy. Analytical size exclusion chromatography (SEC) is a widely used technique throughout the development and manufacturing of monoclonal antibodies (mAbs) which quantifies product size variants such as aggregates and fragments. Aggregate and fragment content are critical quality attributes (CQAs) in mAb products, as higher contents of such size heterogeneities impact product quality. Historically, SEC methods have achieved sufficient separation between the high molecular weight (HMW) species and the main product. In contrast, some low molecular weight (LMW) species are often not sufficiently different in molecular mass from the main product, making it difficult to achieve appropriate resolutions between the two species. This lack of resolution makes it difficult to consistently quantify the LMW species in mAb-based therapeutics. The following work uses a design of experiments (DoE) approach to establish a robust analytical SEC procedure by evaluating SEC column types and mobile phase compositions using two mAb products with different physiochemical properties. The resulting optimized procedure using a Waters™ BioResolve column exhibits an improved ability to resolve and quantify mAb size variants, highlighting improvement in the resolution of the LMW species. Additionally, the addition of L-arginine as a mobile phase additive showed to reduce secondary interactions and was beneficial in increasing the recoveries of the HMW species.
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Affiliation(s)
- Terezie Cernosek
- Catalent Biologics, Madison, WI, USA; Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA.
| | | | | | - Sue Behrens
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
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21
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Lo KJ, Wang MH, Ho CT, Pan MH. Plant-Derived Extracellular Vesicles: A New Revolutionization of Modern Healthy Diets and Biomedical Applications. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2853-2878. [PMID: 38300835 DOI: 10.1021/acs.jafc.3c06867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Plant-derived extracellular vesicles (PDEVs) have recently emerged as a promising area of research due to their potential health benefits and biomedical applications. Produced by various plant species, these EVs contain diverse bioactive molecules, including proteins, lipids, and nucleic acids. Increasing in vitro and in vivo studies have shown that PDEVs have inherent pharmacological activities that affect cellular processes, exerting anti-inflammatory, antioxidant, and anticancer activities, which can potentially contribute to disease therapy and improve human health. Additionally, PDEVs have shown potential as efficient and biocompatible drug delivery vehicles in treating various diseases. However, while PDEVs serve as a potential rising star in modern healthy diets and biomedical applications, further research is needed to address their underlying knowledge gaps, especially the lack of standardized protocols for their isolation, identification, and large-scale production. Furthermore, the safety and efficacy of PDEVs in clinical applications must be thoroughly evaluated. In this review, we concisely discuss current knowledge in the PDEV field, including their characteristics, biomedical applications, and isolation methods, to provide an overview of the current state of PDEV research. Finally, we discuss the challenges regarding the current and prospective issues for PDEVs. This review is expected to provide new insights into healthy diets and biomedical applications of vegetables and fruits, inspiring new advances in natural food-based science and technology.
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Affiliation(s)
- Kai-Jiun Lo
- Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Mu-Hui Wang
- Department of Medical Research, National Taiwan University Hospital, Taipei 100225, Taiwan
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, New Jersey 08901-8520, United States
| | - Min-Hsiung Pan
- Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
- Department of Health and Nutrition Biotechnology, Asia University, Taichung 41354, Taiwan
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22
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Thomas S, Kaur J, Kamboj R, Thangariyal S, Yadav R, Kumar K, Dhania NK. Investigate the efficacy of size exclusion chromatography for the isolation of extracellular vesicles from C. elegans. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1233:123982. [PMID: 38176095 DOI: 10.1016/j.jchromb.2023.123982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
Isolation of Extracellular Vesicles (EVs) has been done extensively in the past using ultracentrifugation, a recent shift has been observed towards precipitation, and exosome isolation kits. These methods often co-elute contaminants of similar size and density which makes their detection and downstream applications quite challenging. As well as the EV yield is also compromised in some methodologies due to aggregate formation. In recent reports, size-exclusion chromatography (SEC) is replacing density gradient-based ultracentrifugation as the gold standard of exosome isolation. It outperforms in yield, purity and does not account for any physical damage to the EVs. We have standardized the methodology for an efficient pure yield of homogenous exosomes of size even smaller than 75 nm in Caenorhabditis elegans homogenate. The paper entails the application and optimization of EV isolation by SEC based on previous studies by optimizing bed size and type of sepharose column employed. We propose that this method is economically feasible in comparison with currently available approaches. A comparative study was conducted to investigate the performance of CL-6B in relation to CL-2B and further, this was combined with ultracentrifugation for higher efficacy. The methodology could be introduced in a clinical setting due to its therapeutic potential and scope. The eluted EVs were studied by flow cytometry, nanotracking and characterized for size and morphology.
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Affiliation(s)
- Sharon Thomas
- Department of Zoology, Faculty of Sciences, University of Delhi, Delhi 110007, India
| | - Jaspreet Kaur
- Department of Zoology, Faculty of Sciences, University of Delhi, Delhi 110007, India
| | - Robinsh Kamboj
- USIC, Faculty of Sciences, University of Delhi, Delhi 110007, India
| | - Swati Thangariyal
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, Delhi 110070, India
| | - Rahul Yadav
- Department of Chemistry, Indian Institute of Technology, New Delhi, Delhi 110016, India
| | - Kamlesh Kumar
- Department of Chemistry, Kirori Mal College, University of Delhi, Delhi 110007, India
| | - Narender K Dhania
- Department of Zoology, Faculty of Sciences, University of Delhi, Delhi 110007, India.
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23
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Bonner SE, van de Wakker SI, Phillips W, Willms E, Sluijter JPG, Hill AF, Wood MJA, Vader P. Scalable purification of extracellular vesicles with high yield and purity using multimodal flowthrough chromatography. JOURNAL OF EXTRACELLULAR BIOLOGY 2024; 3:e138. [PMID: 38939900 PMCID: PMC11080796 DOI: 10.1002/jex2.138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 06/29/2024]
Abstract
Extracellular vesicles (EVs) are cell derived membranous nanoparticles. EVs are important mediators of cell-cell communication via the transfer of bioactive content and as such they are being investigated for disease diagnostics as biomarkers and for potential therapeutic cargo delivery to recipient cells. However, existing methods for isolating EVs from biological samples suffer from challenges related to co-isolation of unwanted materials such as proteins, nucleic acids, and lipoproteins. In the pursuit of improved EV isolation techniques, we introduce multimodal flowthrough chromatography (MFC) as a scalable alternative to size exclusion chromatography (SEC). The use of MFC offers significant advantages for purifying EVs, resulting in enhanced yields and increased purity with respect to protein and nucleic acid co-isolates from conditioned 3D cell culture media. Compared to SEC, significantly higher EV yields with similar purity and preserved functionality were also obtained with MFC in 2D cell cultures. Additionally, MFC yielded EVs from serum with comparable purity to SEC and similar apolipoprotein B content. Overall, MFC presents an advancement in EV purification yielding EVs with high recovery, purity, and functionality, and offers an accessible improvement to researchers currently employing SEC.
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Affiliation(s)
| | - Simonides I. van de Wakker
- Department of Experimental CardiologyUniversity Medical Center Utrecht, Utrecht UniversityUtrechtThe Netherlands
| | - William Phillips
- Department of Biochemistry and ChemistryLa Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Eduard Willms
- Department of Biochemistry and ChemistryLa Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Joost P. G. Sluijter
- Department of Experimental CardiologyUniversity Medical Center Utrecht, Utrecht UniversityUtrechtThe Netherlands
| | - Andrew F. Hill
- Institute for Health and SportVictoria UniversityMelbourneVictoriaAustralia
| | | | - Pieter Vader
- Department of Experimental CardiologyUniversity Medical Center Utrecht, Utrecht UniversityUtrechtThe Netherlands
- CDL ResearchUniversity Medical Center UtrechtUtrechtThe Netherlands
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24
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Chakraborty A, Mitra A, Sahu S, Tawate M, Lad S, Kamaldeep, Rakshit S, Upadhye Bannore T, Gaikwad S, Dhotre G, Ray MK, Damle A, Basu S, Banerjee S. Intricacies in the Preparation of Patient Doses of [ 177Lu]Lu-Rituximab and [ 177Lu]Lu-Trastuzumab Using Low Specific Activity [ 177Lu]LuCl 3: Methodological Aspects. Mol Imaging Biol 2024; 26:61-80. [PMID: 37673943 DOI: 10.1007/s11307-023-01846-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
The development of humanized monoclonal antibodies (MAbs) with Lutetium-177 ([177Lu]Lu3+) has brought a paradigm shift in the arena of targeted therapy of various cancers. [177Lu]Lu-DOTA-Rituximab and [177Lu]Lu-DOTA-Trastuzumab have gained prominence due to their improved therapeutic efficacy in the treatment of lymphoma and breast cancer. The clinical dose formulation of these radiolabeled MAbs, using low specific activity [177Lu]LuCl3, requires extensive optimization of the radiolabeling protocol. The present study merits the development of a single protocol which has been optimized for conjugation of Rituximab and Trastuzumab with p-NCS-benzyl-DOTA and further radiolabeling these immunoconjugates (ICs) with low specific activity [177Lu]LuCl3. Herein, we report a consistent and reproducible protocol for clinical dose formulations of [177Lu]Lu-DOTA-Rituximab and [177Lu]Lu-DOTA-Trastuzumab (~9.25 GBq each, equivalent to ~2 patient doses) with radiochemical yield (RCY) between 84 and 86% and radiochemical purities (RCP) >99%. The in vitro stabilities of both these radioimmunoconjugates (RICs) were retained up to 120 h post-radiolabeling, upon storage with L-ascorbic acid as stabilizer (concentration: ~ 220-240 μg/37MBq) at -20 °C. The ready-to-use formulation of clinical doses[177Lu]Lu-DOTA-Rituximab and [177Lu]Lu-DOTA-Trastuzumab has been successfully achieved by employing a single optimized protocol. While [177Lu]Lu-DOTA-Rituximab has exhibited a high degree of localization in retroperitoneal nodal mass of refractory lymphoma patient, high uptake of [177Lu]Lu-DOTA-Trastuzumab has been observed in metastatic breast carcinoma patient with multiple skeletal metastases.
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Affiliation(s)
- Avik Chakraborty
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Arpit Mitra
- Radiopharmaceuticals Laboratory, Board of Radiation and Isotope Technology, Vashi, Navi Mumbai, India
| | - Sudeep Sahu
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
| | - Megha Tawate
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Sangita Lad
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
| | - Kamaldeep
- Homi Bhabha National Institute, Mumbai, India
- Health Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Sutapa Rakshit
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
| | | | - Sujay Gaikwad
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
| | - Geetanjali Dhotre
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Mukti Kanta Ray
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Archana Damle
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Sandip Basu
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Sharmila Banerjee
- Homi Bhabha National Institute, Mumbai, India.
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410 210, India.
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25
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Gorgzadeh A, Nazari A, Ali Ehsan Ismaeel A, Safarzadeh D, Hassan JAK, Mohammadzadehsaliani S, Kheradjoo H, Yasamineh P, Yasamineh S. A state-of-the-art review of the recent advances in exosome isolation and detection methods in viral infection. Virol J 2024; 21:34. [PMID: 38291452 PMCID: PMC10829349 DOI: 10.1186/s12985-024-02301-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/22/2024] [Indexed: 02/01/2024] Open
Abstract
Proteins, RNA, DNA, lipids, and carbohydrates are only some of the molecular components found in exosomes released by tumor cells. They play an essential role in healthy and diseased cells as messengers of short- and long-distance intercellular communication. However, since exosomes are released by every kind of cell and may be found in blood and other bodily fluids, they may one day serve as biomarkers for a wide range of disorders. In many pathological conditions, including cancer, inflammation, and infection, they play a role. It has been shown that the biogenesis of exosomes is analogous to that of viruses and that the exosomal cargo plays an essential role in the propagation, dissemination, and infection of several viruses. Bidirectional modulation of the immune response is achieved by the ability of exosomes associated with viruses to facilitate immunological escape and stimulate the body's antiviral immune response. Recently, exosomes have received a lot of interest due to their potential therapeutic use as biomarkers for viral infections such as human immunodeficiency virus (HIV), Hepatitis B virus (HBV), Hepatitis C virus (HCV), Epstein-Barr virus (EBV), and SARS-CoV-2. This article discusses the purification procedures and detection techniques for exosomes and examines the research on exosomes as a biomarker of viral infection.
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Affiliation(s)
| | - Ahmad Nazari
- Tehran University of Medical Sciences, Tehran, Iran
| | | | - Diba Safarzadeh
- Vocational School of Health Service, Near East University, Nicosia, Cyprus
| | - Jawad A K Hassan
- National University of Science and Technology, Nasiriyah, Dhi Qar, Iraq
| | | | | | - Pooneh Yasamineh
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Saman Yasamineh
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
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26
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Sutton MN, Glazer SE, Muzzioli R, Yang P, Gammon ST, Piwnica-Worms D. Dimerization of the 4Ig isoform of B7-H3 in tumor cells mediates enhanced proliferation and tumorigenic signaling. Commun Biol 2024; 7:21. [PMID: 38182652 PMCID: PMC10770396 DOI: 10.1038/s42003-023-05736-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/20/2023] [Indexed: 01/07/2024] Open
Abstract
B7-H3 (CD276) has two isoforms (2Ig and 4Ig), no confirmed cognate receptor, and physiological functions that remain elusive. While differentially expressed on many solid tumors correlating with poor survival, mechanisms of how B7-H3 signals in cis (tumor cell) versus in trans (immune cell co-regulator) to elicit pro-tumorigenic phenotypes remain poorly defined. Herein, we characterized a tumorigenic and signaling role for tumor cell-expressed 4Ig-B7-H3, the dominant human isoform, in gynecological cancers that could be abrogated upon CRISPR/Cas9 knockout of B7-H3; tumorigenesis was rescued upon re-expression of 4Ig-B7-H3. Size exclusion chromatography revealed dimerization states for the extracellular domains of both human 4Ig- and murine 2Ig-B7-H3. mEGFP lifetimes of expressed 4Ig-B7-H3-mEGFP fusions determined by FRET-FLIM assays confirmed close-proximity interactions of 4Ig-B7-H3 and identified two distinct homo-FRET lifetime populations, consistent with monomeric and homo-dimer interactions. In live cells, bioluminescence imaging of 4Ig-B7-H3-mediated split luciferase complementation showed dimerization of 4Ig-B7-H3. To separate basal from dimer state activities in the absence of a known receptor, C-terminus (cytosolic) chemically-induced dimerization of 4Ig-B7-H3 increased tumor cell proliferation and cell activation signaling pathways (AKT, Jak/STAT, HIF1α, NF-κβ) significantly above basal expression of 4Ig-B7-H3 alone. These results revealed a new, dimerization-dependent intrinsic tumorigenic signaling role for 4Ig-B7-H3, likely acting in cis, and provide a therapeutically-actionable target for intervention of B7-H3-dependent tumorigenesis.
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Affiliation(s)
- Margie N Sutton
- Department of Cancer Systems Imaging, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sarah E Glazer
- Department of Cancer Systems Imaging, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Riccardo Muzzioli
- Department of Cancer Systems Imaging, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ping Yang
- Department of Cancer Systems Imaging, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Seth T Gammon
- Department of Cancer Systems Imaging, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - David Piwnica-Worms
- Department of Cancer Systems Imaging, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA.
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27
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Singh S, Dansby C, Agarwal D, Bhat PD, Dubey PK, Krishnamurthy P. Exosomes: Methods for Isolation and Characterization in Biological Samples. Methods Mol Biol 2024; 2835:181-213. [PMID: 39105917 DOI: 10.1007/978-1-0716-3995-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Exosomes are small lipid bilayer-encapsulated nanosized extracellular vesicles of endosomal origin. Exosomes are secreted by almost all cell types and are a crucial player in intercellular communication. Exosomes transmit cellular information from donor to recipient cells in the form of proteins, lipids, and nucleic acids and influence several physiological and pathological responses. Due to their capacity to carry a variety of cellular cargo, low immunogenicity and cytotoxicity, biocompatibility, and ability to cross the blood-brain barrier, these nanosized vesicles are considered excellent diagnostic tools and drug-delivery vehicles. Despite their tremendous potential, the progress in therapeutic applications of exosomes is hindered by inadequate isolation techniques, poor characterization, and scarcity of specific biomarkers. The current research in the field is focused on overcoming these limitations. In this chapter, we have reviewed conventional exosome isolation and characterization methods and recent advancements, their advantages and limitations, persistent challenges in exosome research, and future directions.
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Affiliation(s)
- Sarojini Singh
- Department of Biomedical Engineering, Heersink School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Cassidy Dansby
- Department of Biomedical Engineering, Heersink School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Divyanshi Agarwal
- Department of Biomedical Engineering, Heersink School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Purnima Devaki Bhat
- Department of Biomedical Engineering, Heersink School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Praveen Kumar Dubey
- Department of Biomedical Engineering, Heersink School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Prasanna Krishnamurthy
- Department of Biomedical Engineering, Heersink School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL, USA.
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28
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Hossain MA, Sarin R, Donnelly DP, Miller BC, Weiss A, McAlary L, Antonyuk SV, Salisbury JP, Amin J, Conway JB, Watson SS, Winters JN, Xu Y, Alam N, Brahme RR, Shahbazian H, Sivasankar D, Padmakumar S, Sattarova A, Ponmudiyan AC, Gawde T, Verrill DE, Yang W, Kannapadi S, Plant LD, Auclair JR, Makowski L, Petsko GA, Ringe D, Agar NYR, Greenblatt DJ, Ondrechen MJ, Chen Y, Yerbury JJ, Manetsch R, Hasnain SS, Brown RH, Agar JN. Evaluating protein cross-linking as a therapeutic strategy to stabilize SOD1 variants in a mouse model of familial ALS. PLoS Biol 2024; 22:e3002462. [PMID: 38289969 PMCID: PMC10826971 DOI: 10.1371/journal.pbio.3002462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/05/2023] [Indexed: 02/01/2024] Open
Abstract
Mutations in the gene encoding Cu-Zn superoxide dismutase 1 (SOD1) cause a subset of familial amyotrophic lateral sclerosis (fALS) cases. A shared effect of these mutations is that SOD1, which is normally a stable dimer, dissociates into toxic monomers that seed toxic aggregates. Considerable research effort has been devoted to developing compounds that stabilize the dimer of fALS SOD1 variants, but unfortunately, this has not yet resulted in a treatment. We hypothesized that cyclic thiosulfinate cross-linkers, which selectively target a rare, 2 cysteine-containing motif, can stabilize fALS-causing SOD1 variants in vivo. We created a library of chemically diverse cyclic thiosulfinates and determined structure-cross-linking-activity relationships. A pre-lead compound, "S-XL6," was selected based upon its cross-linking rate and drug-like properties. Co-crystallographic structure clearly establishes the binding of S-XL6 at Cys 111 bridging the monomers and stabilizing the SOD1 dimer. Biophysical studies reveal that the degree of stabilization afforded by S-XL6 (up to 24°C) is unprecedented for fALS, and to our knowledge, for any protein target of any kinetic stabilizer. Gene silencing and protein degrading therapeutic approaches require careful dose titration to balance the benefit of diminished fALS SOD1 expression with the toxic loss-of-enzymatic function. We show that S-XL6 does not share this liability because it rescues the activity of fALS SOD1 variants. No pharmacological agent has been proven to bind to SOD1 in vivo. Here, using a fALS mouse model, we demonstrate oral bioavailability; rapid engagement of SOD1G93A by S-XL6 that increases SOD1G93A's in vivo half-life; and that S-XL6 crosses the blood-brain barrier. S-XL6 demonstrated a degree of selectivity by avoiding off-target binding to plasma proteins. Taken together, our results indicate that cyclic thiosulfinate-mediated SOD1 stabilization should receive further attention as a potential therapeutic approach for fALS.
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Affiliation(s)
- Md Amin Hossain
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
- Department of Neurosurgery and Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richa Sarin
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Biogen Inc, Cambridge, Massachusetts, United States of America
| | - Daniel P. Donnelly
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Brandon C. Miller
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Alexandra Weiss
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Luke McAlary
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Joseph P. Salisbury
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Jakal Amin
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Jeremy B. Conway
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Samantha S. Watson
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Jenifer N. Winters
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Yu Xu
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Novera Alam
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Rutali R. Brahme
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Haneyeh Shahbazian
- School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Durgalakshmi Sivasankar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Swathi Padmakumar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Aziza Sattarova
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Aparna C. Ponmudiyan
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Tanvi Gawde
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - David E. Verrill
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Wensheng Yang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Sunanda Kannapadi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Leigh D. Plant
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Jared R. Auclair
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Lee Makowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Gregory A. Petsko
- Ann Romney Center for Neurologic Diseases at Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Departments of Chemistry and Biochemistry, and Rosenstiel Center for Basic Medical Research, Brandeis University, Waltham, Massachusetts, United States of America
| | - Dagmar Ringe
- Departments of Chemistry and Biochemistry, and Rosenstiel Center for Basic Medical Research, Brandeis University, Waltham, Massachusetts, United States of America
| | - Nathalie Y. R. Agar
- Department of Neurosurgery and Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David J. Greenblatt
- School of Medicine, Tufts University, Boston, Massachusetts, United States of America
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Yunqiu Chen
- Biogen Inc, Cambridge, Massachusetts, United States of America
| | - Justin J. Yerbury
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Roman Manetsch
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - S. Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Robert H. Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jeffrey N. Agar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
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29
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Song J, Taraban M, Yu YB, Lu L, Biswas PG, Xu W, Xi H, Bhambhani A, Hu G, Su Y. In-situ biophysical characterization of high-concentration protein formulations using wNMR. MAbs 2024; 16:2304624. [PMID: 38299343 PMCID: PMC10841025 DOI: 10.1080/19420862.2024.2304624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
High-concentration protein formulation is of paramount importance in patient-centric drug product development, but it also presents challenges due to the potential for enhanced aggregation and increased viscosity. The analysis of critical quality attributes often necessitates the transfer of samples from their primary containers together with sample dilution. Therefore, there is a demand for noninvasive, in situ biophysical methods to assess protein drug products directly in primary sterile containers, such as prefilled syringes, without dilution. In this study, we introduce a novel application of water proton nuclear magnetic resonance (wNMR) to evaluate the aggregation propensity of a high-concentration drug product, Dupixent® (dupilumab), under stress conditions. wNMR results demonstrate a concentration-dependent, reversible association of dupilumab in the commercial formulation, as well as irreversible aggregation when exposed to accelerated thermal stress, but gradually reversible aggregation when exposed to freeze and thaw cycles. Importantly, these results show a strong correlation with data obtained from established biophysical analytical tools widely used in the pharmaceutical industry. The application of wNMR represents a promising approach for in situ noninvasive analysis of high-concentration protein formulations directly in their primary containers, providing valuable insights for drug development and quality assessment.
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Affiliation(s)
- Jing Song
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, USA
| | - Marc Taraban
- University of Maryland School of Pharmacy and Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Y. Bruce Yu
- University of Maryland School of Pharmacy and Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Lynn Lu
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc, Rahway, NJ, USA
| | - Pallavi Guha Biswas
- University of Maryland School of Pharmacy and Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Wei Xu
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, USA
| | - Hanmi Xi
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, USA
| | - Akhilesh Bhambhani
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc, Rahway, NJ, USA
| | - Guangli Hu
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc, Rahway, NJ, USA
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, USA
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc, Rahway, NJ, USA
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30
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Thissen J, Klassen MD, Constantinidis P, Hacker MC, Breitkreutz J, Teutenberg T, Fischer B. Online Coupling of Size Exclusion Chromatography to Capillary Enhanced Raman Spectroscopy for the Analysis of Proteins and Biopharmaceutical Drug Products. Anal Chem 2023; 95:17868-17877. [PMID: 38050672 DOI: 10.1021/acs.analchem.3c03991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
The online coupling of size exclusion chromatography (SEC) to capillary enhanced Raman spectroscopy (CERS) based on a liquid core waveguide (LCW) flow cell was applied for the first time to assess the higher-order structure of different proteins. This setup allows recording of Raman spectra of the monomeric protein within complex mixtures, since SEC enables the separation of the monomeric protein from matrix components such as excipients of a biopharmaceutical product and higher molecular weight species (e.g., aggregates). The acquired Raman spectra were used for structural elucidation of well characterized proteins such as bovine serum albumin, hen egg white lysozyme, and β-lactoglobulin and of the monoclonal antibody rituximab in a medicinal product. Additionally, the CERS detection of the disaccharide sucrose, which is used as a stabilizing excipient, was quantified to achieve a limit of detection (LOD) of 120 μg and a limit of quantification (LOQ) of 363 μg injected on the column.
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Affiliation(s)
- Jana Thissen
- Institut für Umwelt & Energie, Technik & Analytik e.V. (IUTA), Bliersheimer Straße 58-60, 47229 Duisburg, Germany
- Institute of Pharmaceutics and Biopharmaceutics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Martin D Klassen
- Institut für Umwelt & Energie, Technik & Analytik e.V. (IUTA), Bliersheimer Straße 58-60, 47229 Duisburg, Germany
| | - Philipp Constantinidis
- Institut für Umwelt & Energie, Technik & Analytik e.V. (IUTA), Bliersheimer Straße 58-60, 47229 Duisburg, Germany
| | - Michael C Hacker
- Institute of Pharmaceutics and Biopharmaceutics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Jörg Breitkreutz
- Institute of Pharmaceutics and Biopharmaceutics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Thorsten Teutenberg
- Institut für Umwelt & Energie, Technik & Analytik e.V. (IUTA), Bliersheimer Straße 58-60, 47229 Duisburg, Germany
| | - Björn Fischer
- Institute of Pharmaceutics and Biopharmaceutics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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31
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Song JG, Baral KC, Kim GL, Park JW, Seo SH, Kim DH, Jung DH, Ifekpolugo NL, Han HK. Quantitative analysis of therapeutic proteins in biological fluids: recent advancement in analytical techniques. Drug Deliv 2023; 30:2183816. [PMID: 36880122 PMCID: PMC10003146 DOI: 10.1080/10717544.2023.2183816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Pharmaceutical application of therapeutic proteins has been continuously expanded for the treatment of various diseases. Efficient and reliable bioanalytical methods are essential to expedite the identification and successful clinical development of therapeutic proteins. In particular, selective quantitative assays in a high-throughput format are critical for the pharmacokinetic and pharmacodynamic evaluation of protein drugs and to meet the regulatory requirements for new drug approval. However, the inherent complexity of proteins and many interfering substances presented in biological matrices have a great impact on the specificity, sensitivity, accuracy, and robustness of analytical assays, thereby hindering the quantification of proteins. To overcome these issues, various protein assays and sample preparation methods are currently available in a medium- or high-throughput format. While there is no standard or universal approach suitable for all circumstances, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay often becomes a method of choice for the identification and quantitative analysis of therapeutic proteins in complex biological samples, owing to its high sensitivity, specificity, and throughput. Accordingly, its application as an essential analytical tool is continuously expanded in pharmaceutical R&D processes. Proper sample preparation is also important since clean samples can minimize the interference from co-existing substances and improve the specificity and sensitivity of LC-MS/MS assays. A combination of different methods can be utilized to improve bioanalytical performance and ensure more accurate quantification. This review provides an overview of various protein assays and sample preparation methods, with particular emphasis on quantitative protein analysis by LC-MS/MS.
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Affiliation(s)
- Jae Geun Song
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Kshitis Chandra Baral
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Gyu-Lin Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Ji-Won Park
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Soo-Hwa Seo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Da-Hyun Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Dong Hoon Jung
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Nonye Linda Ifekpolugo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Hyo-Kyung Han
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
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Rosmeita CN, Budiarti S, Mustopa AZ, Novianti E, Swasthikawati S, Chairunnisa S, Hertati A, Nurfatwa M, Ekawati N, Hasan N. Expression, purification, and characterization of self-assembly virus-like particles of capsid protein L1 HPV 52 in Pichia pastoris GS115. J Genet Eng Biotechnol 2023; 21:126. [PMID: 37981617 PMCID: PMC10657913 DOI: 10.1186/s43141-023-00571-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 10/26/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Cervical cancer caused by the human papillomavirus (HPV) is one of the most frequent malignances globally. HPV 52 is a high-risk cancer-causing genotype that has been identified as the most prevalent type in Indonesia. Virus-like particles (VLP)-based vaccinations against HPV infection could benefit from self-assembled VLP of L1 capsid protein. RESULT The recombinant HPV 52 L1 was expressed in Pichia pastoris on a shake-flask scale with 0.5% methanol induction in this study. The copy number was used to compare the expression level and stability. The colony that survived on a solid medium containing 2000 μg/ml of Zeocin was selected and cultured to express HPV 52 L1. DNA was extracted from the chosen colony, and the copy was determined using qPCR. HPV 52 L1 protein was then purified through fast performance liquid chromatography. Transmission electron microscopy (TEM) evaluation confirmed the VLP self-assembly. The genomic DNA remained intact after 100 generations of serial cultivation under no selective pressure medium conditions, and the protein produced was relatively stable. However, the band intensity was slightly lower than in the parental colony. In terms of copy number, a low copy transformant resulted in low expression but produced a highly stable recombinant clone. Eventually, the L1 protein expressed in Pichia pastoris can self-assemble into VLP. Therefore, recombinant HPV possesses a stable clone and the ability to self-assemble into VLP. CONCLUSION The recombinant L1 HPV 52 protein is successfully expressed in P. pastoris within a size range of approximately 55 kDa and demonstrated favorable stability. The L1 protein expressed in Pichia pastoris successful self-assembled of HPV VLPs, thereby establishing their potential efficacy as a prophylactic vaccine.
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Affiliation(s)
- Chindy Nur Rosmeita
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
- Program of Biotechnology, Graduate School, IPB University, Bogor, Indonesia
| | - Sri Budiarti
- Program of Biotechnology, Graduate School, IPB University, Bogor, Indonesia
- Indonesia Research Center for Bioresources and Biotechnology, IPB University, Bogor, Indonesia
| | - Apon Zaenal Mustopa
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia.
| | - Ela Novianti
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Sri Swasthikawati
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Sheila Chairunnisa
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Ai Hertati
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Maritsa Nurfatwa
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Nurlaili Ekawati
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Nurhasni Hasan
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
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33
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Kumar A, Boradia VM, Mahajan A, Kumaran S, Raje M, Raje CI. Mycobacterium tuberculosis H37Rv enolase (Rv1023)- expression, characterization and effect of host dependent modifications on protein functionality. Biochimie 2023; 214:102-113. [PMID: 37385399 DOI: 10.1016/j.biochi.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/01/2023]
Abstract
Mycobacterium tuberculosis enolase is an essential glycolytic enzyme that catalyzes the conversion of 2, phosphoglycerate (PGA) to phosphoenol pyruvate (PEP). It is also a crucial link between glycolysis and the tricarboxylic acid (TCA) pathway. The depletion of PEP has recently been associated with the emergence of non-replicating drug resistant bacteria. Enolase is also known to exhibit multiple alternate functions, such as promoting tissue invasion via its role as a plasminogen (Plg) receptor. In addition, proteomic studies have identified the presence of enolase in the Mtb degradosome and in biofilms. However, the precise role in these processes has not been elaborated. The enzyme was recently identified as a target for 2-amino thiazoles - a novel class of anti-mycobacterials. In vitro assays and characterization of this enzyme were unsuccessful due to the inability to obtain functional recombinant protein. In the present study, we report the expression and characterization of enolase using Mtb H37Ra as a host strain. Our study demonstrates that the enzyme activity and alternate functions of this protein are significantly impacted by the choice of expression host (Mtb H37Ra or E. coli). Detailed analysis of the protein from each source revealed subtle differences in the post-translational modifications. Lastly, our study confirms the role of enolase in Mtb biofilm formation and describes the potential for inhibiting this process.
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Affiliation(s)
- Ajay Kumar
- Department of Biotechnology National Institute of Pharmaceutical Education and Research (NIPER), Phase X, Sector 67, SAS Nagar, Punjab, 160062, India
| | - Vishant Mahendra Boradia
- Department of Biotechnology National Institute of Pharmaceutical Education and Research (NIPER), Phase X, Sector 67, SAS Nagar, Punjab, 160062, India
| | - Apurwa Mahajan
- Council of Scientific and Industrial Research -Institute of Microbial Technology (CSIR-IMTECH), Sector 39 A, Chandigarh, 160036, India
| | - S Kumaran
- Council of Scientific and Industrial Research -Institute of Microbial Technology (CSIR-IMTECH), Sector 39 A, Chandigarh, 160036, India
| | - Manoj Raje
- Council of Scientific and Industrial Research -Institute of Microbial Technology (CSIR-IMTECH), Sector 39 A, Chandigarh, 160036, India
| | - Chaaya Iyengar Raje
- Department of Biotechnology National Institute of Pharmaceutical Education and Research (NIPER), Phase X, Sector 67, SAS Nagar, Punjab, 160062, India.
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34
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Bock F, Hu A, Cicale V, Larsen SW, Lu X, Østergaard J. Development of UV-Vis Imaging Compatible Chromatographic Matrix with Application for Injectable Formulation Characterization. Anal Chem 2023; 95:15861-15866. [PMID: 37857348 DOI: 10.1021/acs.analchem.3c03648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Transport within human tissue matrices, e.g., the subcutaneous tissue, exhibits some resemblance to chromatographic processes. Here, a porous matrix comprising agarose beads compatible with UV-vis imaging was developed for a parallel piped rectangular flow cell (4 mm light path). Introduction of high-molecular weight dextrans (Mr ∼ 200000 and ∼500000) at 10% (w/v) rendered imaging possible by providing optical clearing of the turbid porous matrix, resulting in improved transmittance as well as resolution (from 400 to 180 μm) at 280 nm, as well as 520 nm. The interplay between diffusive and convective transport at 0 < Pe ≤ 28 was visualized at 280 nm upon injection of dexamethasone suspensions. Real-time UV-vis imaging showed in-flow cell the effect of incorporating ion-exchange resins on the retention of infliximab, lysozyme, and α-lactalbumin. The ion-exchange matrix may serve as a surrogate for polyelectrolytes in the subcutaneous tissue, assessing the potential role of electrostatic interactions of biotherapeutics upon injection. UV-vis imaging of size-exclusion chromatographic matrixes may be of interest in its own right and potentially develop into a characterization tool for injectables.
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Affiliation(s)
- Frederik Bock
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Angela Hu
- Bristol Myers Squibb Company, Drug Product Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Vincent Cicale
- Bristol Myers Squibb Company, Drug Product Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Susan Weng Larsen
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Xujin Lu
- Bristol Myers Squibb Company, Drug Product Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Jesper Østergaard
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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35
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Wu KW, Chen TH, Yang TC, Wang SC, Shameem M, Graham KS. Continuous monitoring of a monoclonal antibody by size exclusion chromatography reveals a correlation between system suitability parameters and column aging. J Pharm Biomed Anal 2023; 235:115622. [PMID: 37540994 DOI: 10.1016/j.jpba.2023.115622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023]
Abstract
Size exclusion chromatography (SEC) is a foundational analytical method to assess product purity of biological molecules. To ensure accurate and reproducible data that meet regulatory agency standards, it is critical to monitor the chromatographic column with efficient and continuous approaches. In this study, 19 SEC columns (Waters Acquity BEH200) were evaluated using an in-house monoclonal antibody made at Regeneron. System suitability parameters (SSPs) were used to monitor the performance of the SEC assay, including USP resolution, USP plate count, USP tailing factor, asymmetry factor, elution time, peak width, and peak height. A general linear model was built and revealed that elution time, peak width, asymmetry factor, and tailing factor increased with injection number, while peak height, resolution, and plate count decreased. After 1000 injections, tailing factor and peak width increased by more than 10%, while resolution and plate count decreased by more than 10% from their respective starting values.
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Affiliation(s)
- Kai-Wei Wu
- Department of Pharmaceutics and Drug Delivery, The University of Mississippi, University, MS 38677, USA
| | - Tse-Hong Chen
- Formulation Development Group, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA.
| | - Teng-Chieh Yang
- Formulation Development Group, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Shao-Chun Wang
- Formulation Development Group, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Mohammed Shameem
- Formulation Development Group, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Kenneth S Graham
- Formulation Development Group, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
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36
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Xu AY, Blanco MA, Castellanos MM, Meuse CW, Mattison K, Karageorgos I, Hatch HW, Shen VK, Curtis JE. Role of Domain-Domain Interactions on the Self-Association and Physical Stability of Monoclonal Antibodies: Effect of pH and Salt. J Phys Chem B 2023; 127:8344-8357. [PMID: 37751332 PMCID: PMC10561141 DOI: 10.1021/acs.jpcb.3c03928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/11/2023] [Indexed: 09/28/2023]
Abstract
Monoclonal antibodies (mAbs) make up a major class of biotherapeutics with a wide range of clinical applications. Their physical stability can be affected by various environmental factors. For instance, an acidic pH can be encountered during different stages of the mAb manufacturing process, including purification and storage. Therefore, understanding the behavior of flexible mAb molecules in acidic solution environments will benefit the development of stable mAb products. This study used small-angle X-ray scattering (SAXS) and complementary biophysical characterization techniques to investigate the conformational flexibility and protein-protein interactions (PPI) of a model mAb molecule under near-neutral and acidic conditions. The study also characterized the interactions between Fab and Fc fragments under the same buffer conditions to identify domain-domain interactions. The results suggest that solution pH significantly influences mAb flexibility and thus could help mAbs remain physically stable by maximizing local electrostatic repulsions when mAbs become crowded in solution. Under acidic buffer conditions, both Fab and Fc contribute to the repulsive PPI observed among the full mAb at a low ionic strength. However, as ionic strength increases, hydrophobic interactions lead to the self-association of Fc fragments and, subsequently, could affect the aggregation state of the mAb.
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Affiliation(s)
- Amy Y. Xu
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Marco A. Blanco
- Discovery
Pharmaceutical Sciences, Merck Research
Laboratories, Merck & Co., Inc, West Point, Pennsylvania 19486, United States
| | - Maria Monica Castellanos
- Institute
for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, United States
- NIST
Center for Neutron Research, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Curtis W. Meuse
- Institute
for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, United States
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Kevin Mattison
- Malvern
Panalytical, Westborough, Massachusetts 01581, United States
| | - Ioannis Karageorgos
- Institute
for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, United States
- Biomolecular
Measurement Division, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Harold W. Hatch
- Chemical
Sciences Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Vincent K. Shen
- Chemical
Sciences Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Joseph E. Curtis
- NIST
Center for Neutron Research, National Institute
of Standards and Technology, Gaithersburg, Maryland 20899, United States
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37
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Campuzano IDG. A Research Journey: Over a Decade of Denaturing and Native-MS Analyses of Hydrophobic and Membrane Proteins in Amgen Therapeutic Discovery. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2413-2431. [PMID: 37643331 DOI: 10.1021/jasms.3c00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Membrane proteins and associated complexes currently comprise the majority of therapeutic targets and remain among the most challenging classes of proteins for analytical characterization. Through long-term strategic collaborations forged between industrial and academic research groups, there has been tremendous progress in advancing membrane protein mass spectrometry (MS) analytical methods and their concomitant application to Amgen therapeutic project progression. Herein, I will describe a detailed and personal account of how electrospray ionization (ESI) native mass spectrometry (nMS), ion mobility-MS (IM-MS), reversed phase liquid chromatographic mass spectrometry (RPLC-MS), high-throughput solid phase extraction mass spectrometry, and matrix-assisted laser desorption ionization mass spectrometry methods were developed, optimized, and validated within Amgen Research, and importantly, how these analytical methods were applied for membrane and hydrophobic protein analyses and ultimately therapeutic project support and progression. Additionally, I will discuss all the highly important and productive collaborative efforts, both internal Amgen and external academic, which were key in generating the samples, methods, and associated data described herein. I will also describe some early and previously unpublished nano-ESI (nESI) native-MS data from Amgen Research and the highly productive University of California Los Angeles (UCLA) collaboration. I will also present previously unpublished examples of real-life Amgen biotherapeutic membrane protein projects that were supported by all the MS (and IM) analytical techniques described herein. I will start by describing the initial nESI nMS experiments performed at Amgen in 2011 on empty nanodisc molecules, using a quadrupole time-of-flight MS, and how these experiments progressed on to the 15 Tesla Fourier transform ion cyclotron resonance MS at UCLA. Then described are monomeric and multimeric membrane protein data acquired in both nESI nMS and tandem-MS modes, using multiple methods of ion activation, resulting in dramatic spectral simplification. Also described is how we investigated the far less established and less published subject, that is denaturing RPLC-MS analysis of membrane proteins, and how we developed a highly robust and reproducible RPLC-MS method capable of effective separation of membrane proteins differing in only the presence or absence of an N-terminal post translational modification. Also described is the evolution of the aforementioned RPLC-MS method into a high-throughput solid phase extraction MS method. Finally, I will give my opinion on key developments and how the area of nMS of membrane proteins needs to evolve to a state where it can be applied within the biopharmaceutical research environment for routine therapeutic project support.
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Affiliation(s)
- Iain D G Campuzano
- Amgen Research, Center for Research Acceleration by Digital Innovation, Molecular Analytics, Thousand Oaks, California 91320, United States
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38
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Liu GY, Zhang Z, Yan Y, Wang S, Li N. Discovery and Characterization of an Acid-Labile Serine-Lysine Cross-Link in Antibody High-Molecular-Weight Species Using a Multipronged Mass Spectrometry Approach. Anal Chem 2023; 95:13813-13821. [PMID: 37674418 PMCID: PMC10515106 DOI: 10.1021/acs.analchem.3c01602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023]
Abstract
Characterizing the cross-links responsible for the covalent high-molecular-weight (HMW) species in therapeutic monoclonal antibodies (mAbs) is of great importance as it not only provides a framework for risk assessment but also offers insights for process improvement. However, owing to the complexity and low abundance, identification of novel and unknown cross-links in mAb products can be very challenging. Here, applying a multipronged MS-based approach, we report the discovery of a novel covalent cross-link formed via an imine bond between lysine and serine residues. In particular, this Ser-Lys cross-link was found to be acid-labile and can be easily overlooked by conventional LC-MS techniques operated at low pH. It is worth noting that although imine-based cross-link has been previously reported in collagen protein cross-linking, this is the first time that a Ser-Lys cross-link has been found in a mAb product that contributes to covalent HMW species formation.
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Affiliation(s)
- Gao-Yuan Liu
- Analytical Chemistry, Regeneron
Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Zhengqi Zhang
- Analytical Chemistry, Regeneron
Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Yuetian Yan
- Analytical Chemistry, Regeneron
Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Shunhai Wang
- Analytical Chemistry, Regeneron
Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Ning Li
- Analytical Chemistry, Regeneron
Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
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Kamaraj S, Vuppu S. Recent Review on the Extraction and Qualitative Assay of Cysteine and Other Amino Acids from Vellore Feather Waste and Molecular Docking Studies of Cysteine for Pharmacological Applications. Mol Biotechnol 2023:10.1007/s12033-023-00862-4. [PMID: 37715883 DOI: 10.1007/s12033-023-00862-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/06/2023] [Indexed: 09/18/2023]
Abstract
Products produced from waste are a relatively recent innovation. Feather substrates are abundant in keratin content and improper disposal can cause ecosystem contamination. However, these pollutants can be transformed into value-added products for industrial application. Physical, chemical and cutting-edge microbiological methods were utilized for decomposing keratin and aid in the identification and estimation of amino acids from poultry feather wastes. These beneficial approaches are receiving more attention due to their retrieval of harmless and value added byproducts. These keratin-based compounds are used widely in pharmaceutical, livestock feed, fertilizer, and a variety of other industrial sectors. Since keratin is primarily consisting of amino acids, it can be utilized to affirm and estimate the amino acids in these feather substrates. This study primarily highlights the various methodologies employed for the qualitative estimation of amino acids in feather waste samples and the inhibitory activity of keratinase enzyme by EDTA and pepstatin in order to accumulate amino acids for drug delivery purpose and their importance in various pharmaceutical industries. In addition to that, molecular docking studies of cysteine with many standard pharmaceutical drugs like acetaminophen, pethidine, methylphenidate, carbamazepine, cillin and amlodipine were performed using autodock to demonstrate how cysteine greatly reduces conventional drug toxicity and its side effects.
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Affiliation(s)
- Sathvika Kamaraj
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Suneetha Vuppu
- School of Biosciences and Technology, Department of Biotechnology, VIT University, Vellore, Tamil Nadu, 632014, India.
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Zhang Y, Liu L, Zhang M, Li S, Wu J, Sun Q, Ma S, Cai W. The Research Progress of Bioactive Peptides Derived from Traditional Natural Products in China. Molecules 2023; 28:6421. [PMID: 37687249 PMCID: PMC10489889 DOI: 10.3390/molecules28176421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/20/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Traditional natural products in China have a long history and a vast pharmacological repertoire that has garnered significant attention due to their safety and efficacy in disease prevention and treatment. Among the bioactive components of traditional natural products in China, bioactive peptides (BPs) are specific protein fragments that have beneficial effects on human health. Despite many of the traditional natural products in China ingredients being rich in protein, BPs have not received sufficient attention as a critical factor influencing overall therapeutic efficacy. Therefore, the purpose of this review is to provide a comprehensive summary of the current methodologies for the preparation, isolation, and identification of BPs from traditional natural products in China and to classify the functions of discovered BPs. Insights from this review are expected to facilitate the development of targeted drugs and functional foods derived from traditional natural products in China in the future.
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Affiliation(s)
- Yanyan Zhang
- College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi 830052, China; (Y.Z.); (Q.S.)
| | - Lianghong Liu
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China; (L.L.); (M.Z.); (S.L.); (J.W.)
| | - Min Zhang
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China; (L.L.); (M.Z.); (S.L.); (J.W.)
| | - Shani Li
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China; (L.L.); (M.Z.); (S.L.); (J.W.)
| | - Jini Wu
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China; (L.L.); (M.Z.); (S.L.); (J.W.)
| | - Qiuju Sun
- College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi 830052, China; (Y.Z.); (Q.S.)
| | - Shengjun Ma
- College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi 830052, China; (Y.Z.); (Q.S.)
| | - Wei Cai
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China; (L.L.); (M.Z.); (S.L.); (J.W.)
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Kubi JA, Brah AS, Cheung KMC, Lee YL, Lee KF, Sze SCW, Qiao W, Yeung KWK. A new osteogenic protein isolated from Dioscorea opposita Thunb accelerates bone defect healing through the mTOR signaling axis. Bioact Mater 2023; 27:429-446. [PMID: 37152710 PMCID: PMC10160600 DOI: 10.1016/j.bioactmat.2023.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/09/2023] Open
Abstract
Delayed bone defect repairs lead to severe health and socioeconomic impacts on patients. Hence, there are increasing demands for medical interventions to promote bone defect healing. Recombinant proteins such as BMP-2 have been recognized as one of the powerful osteogenic substances that promote mesenchymal stem cells (MSCs) to osteoblast differentiation and are widely applied clinically for bone defect repairs. However, recent reports show that BMP-2 treatment has been associated with clinical adverse side effects such as ectopic bone formation, osteolysis and stimulation of inflammation. Here, we have identified one new osteogenic protein, named 'HKUOT-S2' protein, from Dioscorea opposita Thunb. Using the bone defect model, we have shown that the HKUOT-S2 protein can accelerate bone defect repair by activating the mTOR signaling axis of MSCs-derived osteoblasts and increasing osteoblastic biomineralization. The HKUOT-S2 protein can also modulate the transcriptomic changes of macrophages, stem cells, and osteoblasts, thereby enhancing the crosstalk between the polarized macrophages and MSCs-osteoblast differentiation to facilitate osteogenesis. Furthermore, this protein had no toxic effects in vivo. We have also identified HKUOT-S2 peptide sequence TKSSLPGQTK as a functional osteogenic unit that can promote osteoblast differentiation in vitro. The HKUOT-S2 protein with robust osteogenic activity could be a potential alternative osteoanabolic agent for promoting osteogenesis and bone defect repairs. We believe that the HKUOT-S2 protein may potentially be applied clinically as a new class of osteogenic agent for bone defect healing.
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Affiliation(s)
- John Akrofi Kubi
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong S.A.R., PR China
- Shenzhen Key Laboratory for Innovative Technology in Orthopaedic Trauma, HKU-Shenzhen Hospital, Shenzhen, 518053, PR China
| | - Augustine Suurinobah Brah
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong S.A.R., PR China
- Shenzhen Key Laboratory for Innovative Technology in Orthopaedic Trauma, HKU-Shenzhen Hospital, Shenzhen, 518053, PR China
| | - Kenneth Man Chee Cheung
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong S.A.R., PR China
- Shenzhen Key Laboratory for Innovative Technology in Orthopaedic Trauma, HKU-Shenzhen Hospital, Shenzhen, 518053, PR China
| | - Yin Lau Lee
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, HKU, 21 Sassoon Road, Hong Kong S.A.R, PR China
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, HKU- Shenzhen Hospital, Shenzhen, PR China
| | - Kai-Fai Lee
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, HKU, 21 Sassoon Road, Hong Kong S.A.R, PR China
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, HKU- Shenzhen Hospital, Shenzhen, PR China
| | - Stephen Cho Wing Sze
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong S.A.R, PR China
- Golden Meditech Center for NeuroRegeneration Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong S.A.R, PR China
| | - Wei Qiao
- Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, Hong Kong S.A.R, PR China
| | - Kelvin Wai-Kwok Yeung
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong S.A.R., PR China
- Shenzhen Key Laboratory for Innovative Technology in Orthopaedic Trauma, HKU-Shenzhen Hospital, Shenzhen, 518053, PR China
- Corresponding author.Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong S.A.R, PR China
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Zheng J, Yang J, Zhao F, Peng B, Wang Y, Fang M. CIL-ExPMRM: An Ultrasensitive Chemical Isotope Labeling Assisted Pseudo-MRM Platform to Accelerate Exposomic Suspect Screening. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:10962-10973. [PMID: 37469223 DOI: 10.1021/acs.est.3c01830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Exposome is the future of next-generation environmental health to establish the association between environmental exposure and diseases. However, due to low concentrations of exposure chemicals, exposome has been hampered by lacking an effective analytical platform to characterize its composition. In this study, by combining the benefit of chemical isotope labeling and pseudo-multiple reaction monitoring (CIL-pseudo-MRM), we have developed one highly sensitive and high-throughput platform (CIL-ExPMRM) by isotope labeling urinary exposure biomarkers. Dansyl chloride (DnsCl), N-methylphenylethylamine (MPEA), and their isotope-labeled forms were used to derivatize polar hydroxyl and carboxyl compounds, respectively. We have programmed a series of scripts to optimize MRM transition parameters, curate the MRM database (>70,000 compounds), predict accurate retention time (RT), and automize dynamic MRMs. This was followed by an automated MRM peak assignment, peak alignment, and statistical analysis. A computational pipeline was eventually incorporated into a user-friendly website interface, named CIL-ExPMRM (http://www.exposomemrm.com/). The performance of this platform has been validated with a relatively low false positive rate (10.7%) across instrumental platforms. CIL-ExPMRM has systematically overcome key bottlenecks of exposome studies to some extent and outperforms previous methods due to its independence of MS/MS availability, accurate RT prediction, and collision energy optimization, as well as the ultrasensitivity and automated robust intensity-based quantification. Overall, CIL-ExPMRM has great potential to advance the exposomic studies based on urinary biomarkers.
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Affiliation(s)
- Jie Zheng
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, 639798 Singapore
| | - Junjie Yang
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Fanrong Zhao
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Bo Peng
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Yulan Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, 639798 Singapore
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
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Ventouri IK, Veelders S, Passamonti M, Endres P, Roemling R, Schoenmakers PJ, Somsen GW, Haselberg R, Gargano AFG. Micro-flow size-exclusion chromatography for enhanced native mass spectrometry of proteins and protein complexes. Anal Chim Acta 2023; 1266:341324. [PMID: 37244657 DOI: 10.1016/j.aca.2023.341324] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/29/2023] [Accepted: 05/03/2023] [Indexed: 05/29/2023]
Abstract
Size-exclusion chromatography (SEC) employing aqueous mobile phases with volatile salts at neutral pH combined with native mass spectrometry (nMS) is a valuable tool to characterize proteins and protein aggregates in their native state. However, the liquid-phase conditions (high salt concentrations) frequently used in SEC-nMS hinder the analysis of labile protein complexes in the gas phase, necessitating higher desolvation-gas flow and source temperature, leading to protein fragmentation/dissociation. To overcome this issue, we investigated narrow SEC columns (1.0 mm internal diameter, I.D.) operated at 15-μL/min flow rates and their coupling to nMS for the characterization of proteins, protein complexes and higher-order structures (HOS). The reduced flow rate resulted in a significant increase in the protein-ionization efficiency, facilitating the detection of low-abundant impurities and HOS up to 230 kDa (i.e., the upper limit of the Orbitrap-MS instrument used). More-efficient solvent evaporation and lower desolvation energies allowed for softer ionization conditions (e.g., lower gas temperatures), ensuring little or no structural alterations of proteins and their HOS during transfer into the gas phase. Furthermore, ionization suppression by eluent salts was decreased, permitting the use of volatile-salt concentrations up to 400 mM. Band broadening and loss of resolution resulting from the introduction of injection volumes exceeding 3% of the column volume could be circumvented by incorporating an online trap-column containing a mixed-bed ion-exchange (IEX) material. The online IEX-based solid-phase extraction (SPE) or "trap-and-elute" set-up provided on-column focusing (sample preconcentration). This allowed the injection of large sample volumes on the 1-mm I.D. SEC column without compromising the separation. The enhanced sensitivity attained by the micro-flow SEC-MS, along with the on-column focusing achieved by the IEX precolumn, provided picogram detection limits for proteins.
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Affiliation(s)
- Iro K Ventouri
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands.
| | - Sharene Veelders
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands
| | - Marta Passamonti
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands
| | - Patrick Endres
- Tosoh Bioscience GmbH, Im Leuschnerpark 4, 64347, Griesheim, Germany
| | - Regina Roemling
- Tosoh Bioscience GmbH, Im Leuschnerpark 4, 64347, Griesheim, Germany
| | - Peter J Schoenmakers
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands
| | - Govert W Somsen
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Division of Bioanalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV Amsterdam, the Netherlands
| | - Rob Haselberg
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Division of Bioanalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV Amsterdam, the Netherlands
| | - Andrea F G Gargano
- Analytical Chemistry group, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands; Centre for Analytical Sciences Amsterdam, van't Hoff Insititute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, the Netherlands.
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Surappa S, Multani P, Parlatan U, Sinawang PD, Kaifi J, Akin D, Demirci U. Integrated "lab-on-a-chip" microfluidic systems for isolation, enrichment, and analysis of cancer biomarkers. LAB ON A CHIP 2023; 23:2942-2958. [PMID: 37314731 PMCID: PMC10834032 DOI: 10.1039/d2lc01076c] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The liquid biopsy has garnered considerable attention as a complementary clinical tool for the early detection, molecular characterization and monitoring of cancer over the past decade. In contrast to traditional solid biopsy techniques, liquid biopsy offers a less invasive and safer alternative for routine cancer screening. Recent advances in microfluidic technologies have enabled handling of liquid biopsy-derived biomarkers with high sensitivity, throughput, and convenience. The integration of these multi-functional microfluidic technologies into a 'lab-on-a-chip' offers a powerful solution for processing and analyzing samples on a single platform, thereby reducing the complexity, bio-analyte loss and cross-contamination associated with multiple handling and transfer steps in more conventional benchtop workflows. This review critically addresses recent developments in integrated microfluidic technologies for cancer detection, highlighting isolation, enrichment, and analysis strategies for three important sub-types of cancer biomarkers: circulating tumor cells, circulating tumor DNA and exosomes. We first discuss the unique characteristics and advantages of the various lab-on-a-chip technologies developed to operate on each biomarker subtype. This is then followed by a discussion on the challenges and opportunities in the field of integrated systems for cancer detection. Ultimately, integrated microfluidic platforms form the core of a new class of point-of-care diagnostic tools by virtue of their ease-of-operation, portability and high sensitivity. Widespread availability of such tools could potentially result in more frequent and convenient screening for early signs of cancer at clinical labs or primary care offices.
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Affiliation(s)
- Sushruta Surappa
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
| | - Priyanka Multani
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
| | - Ugur Parlatan
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
| | - Prima Dewi Sinawang
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Jussuf Kaifi
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65212, USA
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA
| | - Demir Akin
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
- Center for Cancer Nanotechnology Excellence for Translational Diagnostics (CCNE-TD), School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
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Kumar P, Vyas P, Faisal SM, Chang YF, Akif M. Crystal structure of a variable region segment of Leptospira host-interacting outer surface protein, LigA, reveals the orientation of Ig-like domains. Int J Biol Macromol 2023:125445. [PMID: 37336372 DOI: 10.1016/j.ijbiomac.2023.125445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
Leptospiral immunoglobulin-like (Lig) protein family is a surface-exposed protein from the pathogenic Leptospira. The Lig protein family has been identified as an essential virulence factor of L. interrogan. One of the family members, LigA, contains 13 homologous tandem repeats of bacterial Ig-like (Big) domains in its extracellular portion. It is crucial in binding with the host's Extracellular matrices (ECM) and complement factors. However, its vital role in the invasion and evasion of pathogenic Leptospira, structural details, and domain organization of the extracellular portion of this protein are not explored thoroughly. Here, we described the first high-resolution crystal structure of a variable region segment (LigA8-9) of LigA at 1.87 Å resolution. The structure showed some remarkably distinctive aspects compared with the most closely related Immunoglobulin superfamily (IgSF) members. The structure illustrated the relative orientation of two domains and highlighted the role of the linker region in the domain orientation. We also observed an apparent electron density of Ca2+ ions coordinated with a proper interacting geometry within the protein. Molecular dynamic simulations demonstrated the involvement of a linker salt bridge in providing rigidity between the two domains. Our study proposes an overall arrangement of Ig-like domains in the LigA protein. The structural understanding of the extracellular portion of LigA and its interaction with the ECM provides insight into developing new therapeutics directed toward leptospirosis.
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Affiliation(s)
- Pankaj Kumar
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | - Pallavi Vyas
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Gachibowli, Hyderabad, Telangana, India
| | - Syed M Faisal
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Gachibowli, Hyderabad, Telangana, India
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Mohd Akif
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India.
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De Figueiredo I, Bartenlian B, Van der Rest G, Pallandre A, Halgand F. Proteomics Methodologies: The Search of Protein Biomarkers Using Microfluidic Systems Coupled to Mass Spectrometry. Proteomes 2023; 11:proteomes11020019. [PMID: 37218924 DOI: 10.3390/proteomes11020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/29/2023] [Accepted: 05/07/2023] [Indexed: 05/24/2023] Open
Abstract
Protein biomarkers have been the subject of intensive studies as a target for disease diagnostics and monitoring. Indeed, biomarkers have been extensively used for personalized medicine. In biological samples, these biomarkers are most often present in low concentrations masked by a biologically complex proteome (e.g., blood) making their detection difficult. This complexity is further increased by the needs to detect proteoforms and proteome complexity such as the dynamic range of compound concentrations. The development of techniques that simultaneously pre-concentrate and identify low-abundance biomarkers in these proteomes constitutes an avant-garde approach to the early detection of pathologies. Chromatographic-based methods are widely used for protein separation, but these methods are not adapted for biomarker discovery, as they require complex sample handling due to the low biomarker concentration. Therefore, microfluidics devices have emerged as a technology to overcome these shortcomings. In terms of detection, mass spectrometry (MS) is the standard analytical tool given its high sensitivity and specificity. However, for MS, the biomarker must be introduced as pure as possible in order to avoid chemical noise and improve sensitivity. As a result, microfluidics coupled with MS has become increasingly popular in the field of biomarker discovery. This review will show the different approaches to protein enrichment using miniaturized devices and the importance of their coupling with MS.
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Affiliation(s)
- Isabel De Figueiredo
- Institut de Chimie Physique, Université Paris Saclay, Avenue Jean Perrin, F91400 Orsay, France
| | - Bernard Bartenlian
- Centre des Nanosciences et Nanotechnologies, Université Paris Saclay, 10 Boulevard Thomas Gobert, F91120 Palaiseau, France
| | - Guillaume Van der Rest
- Institut de Chimie Physique, Université Paris Saclay, Avenue Jean Perrin, F91400 Orsay, France
| | - Antoine Pallandre
- Institut de Chimie Physique, Université Paris Saclay, Avenue Jean Perrin, F91400 Orsay, France
| | - Frédéric Halgand
- Institut de Chimie Physique, Université Paris Saclay, Avenue Jean Perrin, F91400 Orsay, France
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Ventouri IK, Chang W, Meier F, Drexel R, Somsen GW, Schoenmakers PJ, de Spiegeleer B, Haselberg R, Astefanei A. Characterizing Non-covalent Protein Complexes Using Asymmetrical Flow Field-Flow Fractionation On-Line Coupled to Native Mass Spectrometry. Anal Chem 2023; 95:7487-7494. [PMID: 37146101 DOI: 10.1021/acs.analchem.2c05049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We report an online analytical platform based on the coupling of asymmetrical flow field-flow fractionation (AF4) and native mass spectrometry (nMS) in parallel with UV-absorbance, multi-angle light scattering (MALS), and differential-refractive-index (UV-MALS-dRI) detectors to elucidate labile higher-order structures (HOS) of protein biotherapeutics. The technical aspects of coupling AF4 with nMS and the UV-MALS-dRI multi-detection system are discussed. The "slot-outlet" technique was used to reduce sample dilution and split the AF4 effluent between the MS and UV-MALS-dRI detectors. The stability, HOS, and dissociation pathways of the tetrameric biotherapeutic enzyme (anticancer agent) l-asparaginase (ASNase) were studied. ASNase is a 140 kDa homo-tetramer, but the presence of intact octamers and degradation products with lower molecular weights was indicated by AF4-MALS/nMS. Exposing ASNase to 10 mM NaOH disturbed the equilibrium between the different non-covalent species and led to HOS dissociation. Correlation of the information obtained by AF4-MALS (liquid phase) and AF4-nMS (gas phase) revealed the formation of monomeric, tetrameric, and pentameric species. High-resolution MS revealed deamidation of the main intact tetramer upon exposure of ASNase to high pH (NaOH and ammonium bicarbonate). The particular information retrieved from ASNase with the developed platform in a single run demonstrates that the newly developed platform can be highly useful for aggregation and stability studies of protein biopharmaceuticals.
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Affiliation(s)
- Iro Konstantina Ventouri
- Analytical Chemistry Group, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
- Centre of Analytical Sciences Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
| | - Wayne Chang
- Analytical Chemistry Group, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
| | - Florian Meier
- Postnova Analytics GmbH, Rankinestraße 1, 86899 Landsberg, Germany
| | - Roland Drexel
- Postnova Analytics GmbH, Rankinestraße 1, 86899 Landsberg, Germany
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre of Analytical Sciences Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
| | - Peter J Schoenmakers
- Analytical Chemistry Group, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
- Centre of Analytical Sciences Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
| | - Bart de Spiegeleer
- Drug Quality and Registration (DruQuaR) Group, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Rob Haselberg
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre of Analytical Sciences Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
| | - Alina Astefanei
- Analytical Chemistry Group, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
- Centre of Analytical Sciences Amsterdam, Science Park, 904, 1098 XH Amsterdam, The Netherlands
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48
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Gao Y, Shelling AN, Porter D, Leung E, Wu Z. Stability of trastuzumab during nanomedicine formulation using SEC-HPLC coupled with polyacrylamide gel electrophoresis. Pharm Dev Technol 2023; 28:288-298. [PMID: 36912800 DOI: 10.1080/10837450.2023.2191277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
The anti-HER2 antibody trastuzumab has been proven to be an effective targeting ligand for drug delivery. This study investigates the structural integrity of trastuzumab under different stress factors in formulation development and its long-term stability. A validated size exclusion high performance liquid chromatographic (SEC-HPLC) method was first developed. The stability of trastuzumab (0.21-21 mg/ml) under stress conditions (mechanical, freeze-and-thaw, pH and temperature) and long-term storage in the presence of formulation excipients were monitored for up to 12 months, using both the SEC-HPLC method and sodium-dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). The anti-proliferation activity of the reconstituted antibody stored at 4 °C against HER2+ BT-474 breast cells was also monitored over 12 months. The developed SEC-HPLC method was sensitive and accurate. Solutions of trastuzumab were resistant to mechanical stress and repeated freeze-and-thaw; but were unstable under acidic (pH 2.0 and 4.0) and alkaline (pH 10.0 and 12.0) environments. The samples degraded over 5 days at 60 °C, and within 24 h at 75 °C. Low temperature (-80 °C or 4 °C) and low concentration (0.21 mg/ml) favoured the long-term stability. The anti-proliferation activity was conserved at 4 °C for at least 12 months. This study provided valuable stability information in developing trastuzumab involved nano-formulation as well as in clinical settings.
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Affiliation(s)
- Yu Gao
- School of Pharmacy, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Andrew N Shelling
- Department of Obstetrics and Gynaecology, School of Medicine, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - David Porter
- Auckland Regional Cancer and Blood Service, Auckland City Hospital, Auckland, New Zealand
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Zimei Wu
- School of Pharmacy, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
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49
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Huynh CM, Arribas Díez I, Thi HKL, Jensen ON, Sellergren B, Irgum K. Terminally Phosphorylated Triblock Polyethers Acting Both as Templates and Pore-Forming Agents for Surface Molecular Imprinting of Monoliths Targeting Phosphopeptides. ACS OMEGA 2023; 8:8791-8803. [PMID: 36910939 PMCID: PMC9996590 DOI: 10.1021/acsomega.3c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
The novel process reported here described the manufacture of monolithic molecularly imprinted polymers (MIPs) using a terminally functionalized block copolymer as the imprinting template and pore-forming agent. The MIPs were prepared through a step-growth polymerization process using a melamine-formaldehyde precondensate in a biphasic solvent system. Despite having a relatively low imprinting factor, the use of MIP monolith in liquid chromatography demonstrated the ability to selectively target desired analytes. An MIP capillary column was able to separate monophosphorylated peptides from a tryptic digest of bovine serum albumin. Multivariate data analysis and modeling of the phosphorylated and nonphosphorylated peptide retention times revealed that the number of phosphorylations was the strongest retention contributor for peptide retention on the monolithic MIP capillary column.
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Affiliation(s)
- Chau Minh Huynh
- Department
of Chemistry, Umeå University, S-901 87 Umeå, Sweden
| | - Ignacio Arribas Díez
- Department
of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical
Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Hien Kim Le Thi
- Department
of Chemistry, Umeå University, S-901 87 Umeå, Sweden
| | - Ole N. Jensen
- Department
of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical
Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Börje Sellergren
- Faculty
of Health and Society, Department of Biomedical Science, Malmö University, S-205 06 Malmö, Sweden
| | - Knut Irgum
- Department
of Chemistry, Umeå University, S-901 87 Umeå, Sweden
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50
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Jalaludin I, Lubman DM, Kim J. A guide to mass spectrometric analysis of extracellular vesicle proteins for biomarker discovery. MASS SPECTROMETRY REVIEWS 2023; 42:844-872. [PMID: 34747512 DOI: 10.1002/mas.21749] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/21/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Exosomes (small extracellular vesicles) in living organisms play an important role in processes such as cell proliferation or intercellular communication. Recently, exosomes have been extensively investigated for biomarker discoveries for various diseases. An important aspect of exosome analysis involves the development of enrichment methods that have been introduced for successful isolation of exosomes. These methods include ultracentrifugation, size exclusion chromatography, polyethylene glycol-based precipitation, immunoaffinity-based enrichment, ultrafiltration, and asymmetric flow field-flow fractionation among others. To confirm the presence of exosomes, various characterization methods have been utilized such as Western blot analysis, atomic force microscopy, electron microscopy, optical methods, zeta potential, visual inspection, and mass spectrometry. Recent advances in high-resolution separations, high-performance mass spectrometry and comprehensive proteome databases have all contributed to the successful analysis of exosomes from patient samples. Herein we review various exosome enrichment methods, characterization methods, and recent trends of exosome investigations using mass spectrometry-based approaches for biomarker discovery.
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Affiliation(s)
- Iqbal Jalaludin
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Jeongkwon Kim
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, Republic of Korea
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