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Vázquez-Domínguez I, Anido AA, Duijkers L, Hoppenbrouwers T, Hoogendoorn ADM, Koster C, Collin RWJ, Garanto A. Efficacy, biodistribution and safety comparison of chemically modified antisense oligonucleotides in the retina. Nucleic Acids Res 2024:gkae686. [PMID: 39119918 DOI: 10.1093/nar/gkae686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 06/25/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Antisense oligonucleotides (AONs) are a versatile tool for treating inherited retinal diseases. However, little is known about how different chemical modifications of AONs can affect their biodistribution, toxicity, and uptake in the retina. Here, we addressed this question by comparing splice-switching AONs with three different chemical modifications commonly used in a clinical setting (2'O-methyl-phosphorothioate (2-OMe/PS), 2'O-methoxyethyl-phosphoriate (2-MOE/PS), and phosphorodiamidite morpholino oligomers (PMO)). These AONs targeted genes exclusively expressed in certain types of retinal cells. Overall, studies in vitro and in vivo in C57BL/6J wild-type mouse retinas showed that 2-OMe/PS and 2-MOE/PS AONs have comparable efficacy and safety profiles. In contrast, octa-guanidine-dendrimer-conjugated in vivo PMO-oligonucleotides (ivPMO) caused toxicity. This was evidenced by externally visible ocular phenotypes in 88.5% of all ivPMO-treated animals, accompanied by severe alterations at the morphological level. However, delivery of unmodified PMO-AONs did not cause any toxicity, although it clearly reduced the efficacy. We conducted the first systematic comparison of different chemical modifications of AONs in the retina. Our results showed that the same AON sequence with different chemical modifications displayed different splicing modulation efficacies, suggesting the 2'MOE/PS modification as the most efficacious in these conditions. Thereby, our work provides important insights for future clinical applications.
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Affiliation(s)
| | - Alejandro Allo Anido
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Lonneke Duijkers
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Tamara Hoppenbrouwers
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Anita D M Hoogendoorn
- Radboud university medical center, Amalia Children's Hospital, Department of Pediatrics, Nijmegen, The Netherlands
| | - Céline Koster
- Departments of Human Genetics and Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Rob W J Collin
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Alejandro Garanto
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
- Radboud university medical center, Amalia Children's Hospital, Department of Pediatrics, Nijmegen, The Netherlands
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Date M, Miyamoto A, Honjo T, Shiokawa T, Tada H, Okada N, Futami J. Hydrophobicity and molecular mass-based separation method for autoantibody discovery from mammalian total cellular proteins. Protein Sci 2023; 32:e4771. [PMID: 37638851 PMCID: PMC10503409 DOI: 10.1002/pro.4771] [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: 05/25/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 08/29/2023]
Abstract
Serum autoantibody profiles are unique to individuals and reflect the level and history of autoimmunity and tumor immunity. The identification of autoantibody biomarkers is critical for the development of immune monitoring systems for immune-related disorders. Here, we present a practical method for large-scale autoantibody discovery using total cellular proteins from cultured mammalian cells. We found that nucleic acid-free and fully denatured water-soluble total cellular proteins from mammalian cells were superior, allowing precise separation by reversed-phase HPLC after preparing a large set of homogeneous total cellular proteins. After separating the proteins based on hydrophobicity, the fractionated samples were subjected to molecular mass analysis using conventional SDS-PAGE. The resulting two-dimensional gel electrophoresis was successfully employed for immune blotting and LC-MS/MS analysis. All procedures, including TRIzol-based total cellular protein extraction, solubilization of denatured proteins, reversed-phase HPLC separation, and SDS-PAGE, were highly reproducible and easily scalable. We propose this novel two-dimensional gel electrophoresis system as an alternative proteomics-based methodology suitable for large-scale autoantibody discovery.
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Affiliation(s)
- Mirei Date
- Graduate School of Interdisciplinary Science and Engineering in Health SystemsOkayama UniversityOkayamaJapan
| | - Ai Miyamoto
- Graduate School of Interdisciplinary Science and Engineering in Health SystemsOkayama UniversityOkayamaJapan
| | - Tomoko Honjo
- Graduate School of Interdisciplinary Science and Engineering in Health SystemsOkayama UniversityOkayamaJapan
| | - Tsugumi Shiokawa
- Division of Instrumental Analysis, Department of Instrumental Analysis and Cryogenics, Advanced Science Research CenterOkayama UniversityOkayamaJapan
| | - Hiroko Tada
- Division of Instrumental Analysis, Department of Instrumental Analysis and Cryogenics, Advanced Science Research CenterOkayama UniversityOkayamaJapan
| | - Nobuhiro Okada
- Graduate School of Interdisciplinary Science and Engineering in Health SystemsOkayama UniversityOkayamaJapan
| | - Junichiro Futami
- Graduate School of Interdisciplinary Science and Engineering in Health SystemsOkayama UniversityOkayamaJapan
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Miyamoto A, Honjo T, Masui M, Kinoshita R, Kumon H, Kakimi K, Futami J. Engineering Cancer/Testis Antigens With Reversible S-Cationization to Evaluate Antigen Spreading. Front Oncol 2022; 12:869393. [PMID: 35600379 PMCID: PMC9115381 DOI: 10.3389/fonc.2022.869393] [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: 02/04/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Serum autoantibody to cancer/testis antigens (CTAs) is a critical biomarker that reflects the antitumor immune response. Quantitative and multiplexed anti-CTA detection arrays can assess the immune status in tumors and monitor therapy-induced antitumor immune reactions. Most full-length recombinant CTA proteins tend to aggregate. Cysteine residue-specific S-cationization techniques facilitate the preparation of water-soluble and full-length CTAs. Combined with Luminex technology, we designed a multiple S-cationized antigen-immobilized bead array (MUSCAT) assay system to evaluate multiple serum antibodies to CTAs. Reducible S-alkyl-disulfide-cationized antigens in cytosolic conditions were employed to develop rabbit polyclonal antibodies as positive controls. These control antibodies sensitively detected immobilized antigens on beads and endogenous antigens in human lung cancer-derived cell lines. Rabbit polyclonal antibodies successfully confirmed the dynamic ranges and quantitative MUSCAT assay results. An immune monitoring study was conducted using the serum samples on an adenovirus−mediated REIC/Dkk−3 gene therapy clinical trial that showed a successful clinical response in metastatic castration-resistant prostate cancer. Autoantibody responses were closely related to clinical outcomes. Notably, upregulation of anti-CTA responses was monitored before tumor regression. Thus, quantitative monitoring of anti-CTA antibody biomarkers can be used to evaluate the cancer-immunity cycle. A quality-certified serum autoantibody monitoring system is a powerful tool for developing and evaluating cancer immunotherapy.
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Affiliation(s)
- Ai Miyamoto
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
| | - Tomoko Honjo
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
| | - Mirei Masui
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
| | - Rie Kinoshita
- Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hiromi Kumon
- Innovation Center Okayama for Nanobio-targeted Therapy, Okayama University, Okayama, Japan.,Niimi University, Niimi, Japan
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan
| | - Junichiro Futami
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
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Kimura S, Imamura K, Futami J. A suitable and effective stepwise oxidative refolding procedure for highly-cationic tetrameric avidin in nucleic acid free conditions. Biotechnol Prog 2020; 36:e3031. [PMID: 32463160 DOI: 10.1002/btpr.3031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/17/2020] [Accepted: 05/26/2020] [Indexed: 11/06/2022]
Abstract
Optimized conditions are needed to refold recombinant proteins from bacterial inclusion bodies into their biologically active conformations. In this study, we found two crucial requirements for efficient refolding of cationic tetrameric chicken avidin. The first step is to eliminate nucleic acid contaminants from the bacterial inclusion body. The electrostatic interactions between the remaining nucleic acids and proteins strongly enhanced protein aggregation during the refolding process. The cysteine specific reversible S-cationization procedure was successfully employed for large-scale preparation of nucleic acid free denatured protein without purification tag system. The second step is the intramolecular disulfide formation prior to refolding in dialysis removing denaturant. Disulfide intact monomeric avidin showed efficient formation of biologically active tetrameric conformation during the refolding process. Using this optimized refolding procedure, highly cationic avidin derivative designed as an intracellular delivery carrier of biotinylated protein was successfully prepared.
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Affiliation(s)
- Shuichiro Kimura
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Koreyoshi Imamura
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Junichiro Futami
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
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Futami J, Miyamoto A, Hagimoto A, Suzuki S, Futami M, Tada H. Evaluation of irreversible protein thermal inactivation caused by breakage of disulphide bonds using methanethiosulphonate. Sci Rep 2017; 7:12471. [PMID: 28963503 PMCID: PMC5622167 DOI: 10.1038/s41598-017-12748-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 09/15/2017] [Indexed: 01/09/2023] Open
Abstract
Many extracellular globular proteins have evolved to possess disulphide bonds in their native conformations, which aids in thermodynamic stabilisation. However, disulphide bond breakage by heating leads to irreversible protein denaturation through disulphide-thiol exchange reactions. In this study, we demonstrate that methanethiosulphonate (MTS) specifically suppresses the heat-induced disulphide-thiol exchange reaction, thus improving the heat-resistance of proteins. In the presence of MTS, small globular proteins that contain disulphides can spontaneously refold from heat-denatured states, maintaining wild-type disulphide pairing. Because the disulphide-thiol exchange reaction is triggered by the generation of catalytic amounts of perthiol or thiol, rapid and specific perthiol/thiol protection by MTS reagents prevents irreversible denaturation. Combining MTS reagents with another additive that suppresses chemical modifications, glycinamide, further enhanced protein stabilisation. In the presence of these additives, reliable remnant activities were observed even after autoclaving. However, immunoglobulin G and biotin-binding protein, which are both composed of tetrameric quaternary structures, failed to refold from heat-denatured states, presumably due to chaperon requirements. Elucidation of the chemical modifications involved in irreversible thermoinactivation is useful for the development of preservation buffers with optimum constitutions for specific proteins. In addition, the impact of disulphide bond breakage on the thermoinactivation of proteins can be evaluated using MTS reagents.
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Affiliation(s)
- Junichiro Futami
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
| | - Ai Miyamoto
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Atsushi Hagimoto
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Shigeyuki Suzuki
- Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Midori Futami
- Department of Biomedical Engineering, Faculty of Engineering, Okayama University of Science, Okayama, 700-0005, Japan
| | - Hiroko Tada
- Division of Instrumental Analysis, Department of Instrumental Analysis and Cryogenics, Advanced Science Research Center, Okayama University, Okayama, 700-8530, Japan
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