Susumu Uchiyama

Susumu Uchiyama
Osaka University | Handai · Department of Biotechnology

Professor

About

354
Publications
38,610
Reads
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6,819
Citations
Introduction
Susumu Uchiyama currently works at the Department of Biotechnology, Osaka University. Susumu does research in Macromolecular Biotechnology, Physical Chemistry of Therapeutic Proteins, and Protein-Protein Interactions Their current project is 'Characterization of proteins in solution.'
Additional affiliations
December 2017 - present
Osaka University
Position
  • Professor (Full)
May 2015 - April 2017
South China University of Technology
Position
  • Professor (Associate)
April 2013 - April 2020
National Institutes of Natural Sciences
Position
  • Professor
Education
April 1996 - March 1999
Osaka University
Field of study
  • Department of Pharmaceutical Sciences
April 1994 - March 1996
Osaka University
Field of study
  • Faculty of Science
April 1989 - March 1994
Nagoya University
Field of study
  • Department of Science

Publications

Publications (354)
Article
Full-text available
The interaction between IgG and Fc gamma receptor IIIa (FcγRIIIa) is essential for mediating immune responses. Recent studies have shown that the antigen binding fragment (Fab) and Fc are involved in IgG-FcγRIII interactions. Here, we conducted bio-layer interferometry (BLI) and isothermal titration calorimetry to measure the kinetic and thermodyna...
Article
Subvisible particles (SVPs) are a critical quality attribute of parenteral and ophthalmic products. United States Pharmacopeia recommends the characterizations of SVPs which are classified into intrinsic, extrinsic, and inherent particles. Flow imaging microscopy (FIM) is useful as an orthogonal method in both the quantification and classification...
Article
Full-text available
Disaggregation of amyloid fibrils is a fundamental biological process required for amyloid propagation. However, due to the lack of experimental systems, the molecular mechanism of how amyloid is disaggregated by cellular factors remains poorly understood. Here, we established a robust in vitro reconstituted system of yeast prion propagation and fo...
Article
BRAC1 associated protein-1 (BAP1) is a major tumor suppressor involved in many cancers. The deubiquitinase (DUB) activity of BAP1 is essential for its nuclear localization, histone remodeling and proteostasis associated with mitochondrial calcium flux. Loss of the DUB activity due to catalytic mutations within the ubiquitin C-terminal hydrolase (UC...
Article
Cancer-specific cell surface antigens are ideal therapeutic targets for monoclonal antibody (mAb)–based therapy. Here, we report that multiple myeloma (MM), an incurable hematological malignancy, can be specifically targeted by an mAb that recognizes a ubiquitously present protein, CD98 heavy chain (hc) (also known as SLC3A2). We screened more than...
Article
Full-text available
Recently, an international randomized controlled clinical trial showed that patients with SARS-CoV-2 infection treated orally with the 3-chymotrypsin-like protease (3CLpro) inhibitor PF-07321332 within three days of symptom onset showed an 89% lower risk of COVID-19-related hospital admission/ death from any cause as compared with the patients who...
Article
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Recombinant adeno-associated virus (rAAV) vectors have proven efficacy as gene therapy vehicles. However, non-specific adsorption of these vectors on solid surfaces is encountered during production, storage, and administration, as well as in quantification processes. Such adsorption has been reported to result in the loss of up to 90% of vector par...
Article
To reduce the risk of infection during intravitreal injections, the external surface of prefilled syringes (PFSs) must be sterilized. Usually, ethylene oxide (EO) gas or vaporized hydrogen peroxide (VHP) is used for sterilization. More recently, nitrogen dioxide (NO2) gas sterilization has been developed. It is known that gas permeability is approx...
Article
Full-text available
LI-cadherin is a member of the cadherin superfamily, which encompasses a group of Ca²⁺-dependent cell adhesion proteins. The expression of LI-cadherin is observed on various types of cells in the human body, such as normal small intestine and colon cells, and gastric cancer cells. Because its expression is not observed on normal gastric cells, LI-c...
Article
Full-text available
The assessment of aggregates is essential in biopharmaceutical development. Although submicron-sized aggregates are considered to have a potential immunogenicity risk, analytical techniques are limited. In this study, we present a new analytical technique using three-dimensional homodyne light detection (3D-HLD). In this system, submicron-sized par...
Article
Full-text available
Protein aggregate formation in prefilled syringes (PFSs) can be influenced by protein adsorption and desorption at the solid–liquid interface. Although inhibition of protein adsorption on the PFS surface can lead to a decrease in the amount of aggregation, the mechanism underlying protein adsorption-mediated aggregation in PFSs is unclear. This stu...
Article
Full-text available
Progesterone receptor membrane component 1 (PGRMC1) is highly expressed in various cancer cells and contributes to tumor progression. We have previously shown that PGRMC1 forms a unique heme-stacking functional dimer to enhance EGF receptor (EGFR) activity required for cancer proliferation and chemoresistance, and the dimer dissociates by carbon mo...
Article
Recombinant adeno-associated virus (rAAV) is a leading platform in human gene therapy. The AAV capsid is composed of three viral proteins (VPs): VP1, VP2, and VP3. To ensure the safety of AAV-based gene therapy products, the stoichiometry of VPs of AAV vector should be carefully monitored. Here, SDS-PAGE, capillary gel electrophoresis (CGE), and li...
Article
Full-text available
During the manufacturing of recombinant adeno-associated virus vectors, it is generally difficult to purify out vectors that lack nucleic acids (empty particles, EPs), contain incomplete nucleic acids (intermediate particles, IPs) or aggregates. These impurities may cause side effects and therefore it is essential to both quantify and reduce them;...
Article
Attractive self-interaction processes in antibody formulations increase the risk of aggregation and extraordinarily elevated viscosity at high protein concentrations. These challenges affect manufacturing and application. This study aimed to understand the self-interaction process of Infliximab as a model system with pronounced attractive self-inte...
Article
Full-text available
IgA antibodies, which are secreted onto the mucosal surface as secretory IgA antibodies (SIgAs), play an important role in preventing influenza virus infection. A recent study reported that anti-hemagglutinin (HA) head-targeting antibodies increase anti-viral functions such as hemagglutination inhibition (HI) and virus neutralization (NT), in addit...
Article
Upscaling the production capacity of inactivated poliovirus vaccines (IPV) is urgently needed to eradicate polio worldwide. For the development of a robust manufacturing process for IPV, the impact of stresses on the properties of the poliovirus during manufacturing needs to be carefully evaluated. In this study, the physicochemical properties of S...
Preprint
Full-text available
Disaggregation of amyloid fibrils is a fundamental biological process required for amyloid propagation. However, due to the lack of experimental systems, the molecular mechanism of how amyloid is disaggregated by cellular factors remains poorly understood. Here, we established a robust, in vitro reconstituted system of yeast prion propagation and f...
Preprint
Full-text available
Background SARS-CoV-2 genome accumulates point mutations in a constant manner. Whether the accumulation of point mutations is correlated with milder manifestations of COVID-19 remains unknown. Methods We performed SARS-CoV-2 genome sequencing in 90 patients with COVID-19 infection treated at a tertiary medical center in Tokyo between March and Aug...
Article
Introduction: Several new biopharmaceutical dosage forms have developed over time, such as lyophilized vial, liquid vial, and liquid prefilled syringe formulations. Due to the research and development of such biopharmaceutical formulations, they can be stored with high stability even at high protein concentrations. This review summarizes major phar...
Article
Full-text available
Xeno nucleic acids, which are synthetic analogues of natural nucleic acids, have potential for use in nucleic acid drugs and as orthogonal genetic biopolymers and prebiotic precursors. Although few acyclic nucleic acids can stably bind to RNA and DNA, serinol nucleic acid (SNA) and L-threoninol nucleic acid (L-aTNA) stably bind to them. Here we dis...
Preprint
Full-text available
LI-cadherin is a member of cadherin superfamily which is a Ca ²⁺ -dependent cell adhesion protein. Its expression is observed on various types of cells in the human body such as normal small intestine and colon cells, and gastric cancer cells. Because its expression is not observed on normal gastric cells, LI-cadherin is a promising target for gast...
Article
Full-text available
Guanosine 5′-monophosphate reductase (GMPR) is involved in the purine salvage pathway and is conserved throughout evolution. Nonetheless, the GMPR of Trypanosoma brucei (TbGMPR) includes a unique structure known as the cystathionine-β-synthase (CBS) domain, though the role of this domain is not fully understood. Here, we show that guanine and adeni...
Article
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We oxidized histidine residues in monoclonal antibody drugs of immunoglobulin gamma 1 (IgG1) using ultraviolet C irradiation (UVC: 200–280 nm), which is known to be potent for sterilization or disinfection. Among the reaction products, we identified asparagine and aspartic acid by mass spectrometry. In the photo-induced oxidation of histidine in an...
Article
Intravitreal injections have become the most commonly performed intraocular treatments worldwide. Because intravitreal injections may induce severe adverse events, such as infectious and noninfectious endophthalmitis, cataract, ocular hypertension, vitreous hemorrhage, or retinal detachment, appropriate awareness of the materials and techniques use...
Article
Full-text available
Isothermal titration calorimetry (ITC) directly provides thermodynamic parameters depicting the energetics of intermolecular interactions in solution. During ITC experiments, a titration syringe with a paddle is continuously rotating to promote a homogeneous mixing. Here, we clarified that the shape of the paddles (flat, corkscrew, and small-pitche...
Article
Serinol nucleic acid (SNA) is promising for nucleic acid‐based drugs due to its affinity to RNA. However, stable self‐hybridization of SNA in short complementary regions hinders hetero‐hybridization with RNA. It is thus crucial to suppress self‐hybridization for promoting SNA‐RNA hybridization. Herein, suitable protocols were developed for the prep...
Article
Serinol nucleic acid (SNA) is a promising candidate for nucleic acid‐based molecular probes and drugs due to its high affinity for RNA. Our previous work revealed that incorporation of 2,6‐diaminpurine (D), which can form three hydrogen bonds with uracil, into SNA increases the melting temperature of SNA‐RNA duplexes. However, D incorporation into...
Article
Full-text available
Banana ripening is a complex molecular process that produces visible changes in the texture, aroma, taste and nutritional content. Ripening is controlled by genetic code, metabolic pathway and associated microbiome. We reported the microbial community structure during banana ripening with alcohol treatment to discover endophytic and epiphytic micro...
Article
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Euryarchaeal genomes encode proteasome-assembling chaperone homologs, PbaA and PbaB, although archaeal proteasome formation is a chaperone-independent process. Homotetrameric PbaB functions as a proteasome activator, while PbaA forms a homopentamer that does not interact with the proteasome. Notably, PbaA forms a complex with PF0014, an archaeal pr...
Article
As reported in the previous commentary (Ishii-Watabe et al., J Pharm Sci 2017), the Japanese biopharmaceutical research group is promoting collaborative multi-laboratory studies to evaluate and standardize new methodologies for biopharmaceutical characterization and quality control. We have conducted the studies and held two annual meetings in 2018...
Article
Full-text available
True understanding of dispersion interaction in solution remains elusive because of difficulty in the precise evaluation of its interaction energy. Here, the effect of substituents with different polarizability on dispersion interactions in water is discussed based on the thermodynamic parameters determined by isothermal titration calorimetry for t...
Article
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Several accessory proteins are required for the assembly of the metal centers in hydrogenases. In NiFe-hydrogenases, CO and CN− are coordinated to the Fe in the NiFe dinuclear cluster of the active center. Though these diatomic ligands are biosynthesized enzymatically, detail mechanisms of their biosynthesis remain unclear. Here, we report the stru...
Article
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The design of injection devices, including pre-filled syringes (PFSs) and auto-injectors, requires an understanding of the optimization of injection conditions. The injection of highly-concentrated biopharmaceuticals can lead to exceptionally high injection forces, due to their high viscosity. To overcome this challenge, a tapered needle has been r...
Article
Aggregation of therapeutic monoclonal antibodies have a potential risk of immunogenicity, requiring minimization of aggregate formation. We have developed a fitting formula for antibody aggregation at 40°C based on physicochemical parameters, including colloidal and conformational stabilities. An IgG1 monoclonal antibody, MAb-T, was formulated in 2...
Article
Full-text available
A novel approach to identify five types of simulated stresses that induce protein aggregation in pre-filled syringe (PFS)-type biopharmaceuticals was developed. Principal components analyses of texture metrics extracted from flow imaging microscopy images were used to define sub-groups of particles. Supervised machine learning methods including con...
Article
Full-text available
The central oscillator generating cyanobacterial circadian rhythms comprises KaiA, KaiB, and KaiC proteins. Their interactions cause KaiC phosphorylation and dephosphorylation cycles over approximately 24 h. KaiB interacts with phosphorylated KaiC in competition with SasA, an output protein harboring a KaiB-homologous domain. Structural data have i...
Article
Full-text available
Most cells active in the immune system express receptors for antibodies which mediate a variety of defensive mechanisms. These receptors interact with the Fc portion of the antibody and are therefore collectively called Fc receptors. Here, using high-speed atomic force microscopy, we observe interactions of human, humanized, and mouse/human-chimeri...
Article
Full-text available
Protein tyrosine phosphatase receptor type Z (PTPRZ) has two receptor isoforms PTPRZ-A and -B, containing tandem intracellular PTP-D1 and -D2 domains, with only D1 being active. Pleiotrophin (PTN) binding to the extracellular PTPRZ region leads to inactivation of its PTPase activity, thereby facilitating oligodendrocyte precursor cell (OPC) differe...
Article
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
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The cyanobacterial clock is controlled via the interplay among KaiA, KaiB, and KaiC, which generate a periodic oscillation of KaiC phosphorylation in the presence of ATP. KaiC forms a homohexamer harboring 12 ATP-binding sites and exerts ATPase activities associated with its autophosphorylation and dephosphorylation. The KaiC nucleotide state is a...
Preprint
Full-text available
Protein tyrosine phosphatase receptor type Z (PTPRZ) has two receptor isoforms (PTPRZ-A and -B) containing tandem PTP-D1 and -D2 domains intracellularly, with only D1 being active. Pleiotrophin (PTN) binding to the extracellular region of PTPRZ leads to the inactivation of PTPase, thereby inducing oligodendrocyte precursor cell (OPC) differentiatio...
Article
Full-text available
Eukaryotic proteasomes harbor heteroheptameric α-rings, each composed of seven different but homologous subunits α1–α7, which are correctly assembled via interactions with assembly chaperones. The human proteasome α7 subunit is reportedly spontaneously assembled into a homotetradecameric double ring, which can be disassembled into single rings via...
Article
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Separation of a homogeneous mixture of different components to reach an ordered out-of-equilibrium state in solution has attracted continuous attention. While this can be achieved using external chemical fuels or photo energy, an alternative energy source is heat. Here we realize a temperature-controlled cycle of transitions between ordered and dis...
Article
Antibody aggregates are a potential risk for immunogenicity; therefore, rational approaches to improve associated aggregation properties need to be developed. Here, we report the amino acid region responsible for aggregation initiation. Two types of therapeutic IgG1 antibody monomer samples were prepared: IgG1 mAb40-3M stored at 40°C for 3 months,...
Article
Full-text available
Phospholipase A2 (PLA2) is one of the representative toxic components of snake venom. PLA2s are categorized into several subgroups according to the amino acid at position 49, which comprises either Asp49, Lys49, Arg49 or Ser49. Previous studies suggested that the Lys49-PLA2 assembles into an extremely stable dimer. Although the behavior on Sodium d...
Article
Full-text available
Several dog allergens cause allergic reactions in humans worldwide. Seven distinct dog allergens, designated Canis familiaris allergen 1 to 7 (Can f 1–Can f 7), have been identified thus far. Can f 6 shows high sequence similarity and cross-reactivity with Fel d 4 and Equ c 1, major cat and horse allergens, respectively. This study was conducted on...
Article
Full-text available
A number of biopharmaceuticals are available as lyophilized formulations along with a prefilled syringe (PFS) containing water for injection (WFI). Submicron- and micron-size droplets of lubricating silicone oil (SO) applied to the inner surface of the PFS barrel might migrate into the WFI, to which protein pharmaceuticals can adsorb, potentially i...
Article
Biopharmaceuticals are often formulated as liquid dosage forms. During manufacturing and storage, protein molecules and active pharmaceutical ingredients form aggregates due to various stresses, including shaking and agitation, as well as by contact with silicone oils coated on pre-fillable syringes. The diameter of protein aggregates ranges from 1...
Article
Full-text available
Insoluble particulate matter test for injections in pharmacopoeia is mandatory for parenteral drug products. In this test using light obscuration, four measurements of at least 5-mL are required. Since therapeutic protein injections of low dosage volumes are getting more popular, reduction of test volumes is desired. In this collaborative study, th...