Publications

1. Atsushi Kuno, Hiroaki Sakaue, Sachiko Koizumi, Azusa Tomioka, Saho Mizukado, Yuki Yamaguchi, Mitsuko Fukuhara, Yasuo Tsunaka, Hiroyuki Kaji, Susumu Uchiyama.

   Analytical dissection of minor glycoforms and glycoprotein associations in rAAV preparations by multimodal glycoproteomics
   Anal Bioanal Chem .2025 Sep;417(23):5155-5170.

2. Yuki Yamaguchi, Saki Shimojo, Risa Shibuya, Karin Bandoh, Aoba Matsushita, Mitsuko Fukuhara, Yasuo Tsunaka, Tetsuo Torisu, Susumu Uchiyama.

   Direct Identification and Quantification of Recombinant Adeno-Associated Virus in Crude Cell Lysate and Conditioned Medium by Mass Photometry
   Anal Chem .2025 May 20;97(19):10405-10416.

3. Kiichi Hirohata, Shinichiro Kino, Takuya Yamane, Karin Bandoh, Takeshi Bamba, Shawn M Sternisha, Tetsuo Torisu, Mitsuko Fukuhara, Yuki Yamaguchi, Susumu Uchiyama.

   Use of cesium chloride density gradient ultracentrifugation for the purification and characterization of recombinant adeno-associated virus
   Eur Biophys J .2025 May 19.

4. Yuki Yamaguchi, Saki Shimojo, Tomohiko Ikeda, Mitsuko Fukuhara, Yasuo Tsunaka, Risa Shibuya, Mark Allen Vergara Rocafort, Ryoji Nakatsuka, Kiichi Hirohata, Tetsuo Torisu, Susumu Uchiyama.

   Unfolding of viral protein 1 N-termini facilitates genome ejection from recombinant adeno-associated virus serotype 8
   Mol Ther Methods Clin Dev.2025 Apr 24;33(2):101480.

5. Hiroko Shibata, Satoshi Saitoh, Masato Kiyoshi , Yu Hayashi, Kazue Inaba, Shinji Katsura, Maho Sakurai, Yuka Komine, Shinji Okabe, Naomi Ohbayashi, Youko Kita, Hirokazu Kito, Masako Nakano, Kana Miyamoto, Akira Maruyama, Yuya Miyahara, Masanori Noda, Yasuyo Nozawa, Kazutaka Shimbo, Shota Kojima, Shinya Honda, Tetsuo Torisu, Susumu Uchiyama, Akiko Ishii-Watabe.

   Survey and Establishment of Points to Consider for Application of Analytical Techniques to Evaluate Protein Aggregates and Insoluble Particles in Biopharmaceuticals: Experiences in Japan Biopharmaceutical Consortium
   AAPS J.2025 Apr 3;27(3):75.

6. Rio Okada, Kosei Shibata, Risa Shibuya, Tetsuo Torisu, Susumu Uchiyama 

   Hierarchical clustering of therapeutic proteins based on agitation-induced aggregation propensity and its relation to physicochemical parameters
   European Journal of Pharmaceutical Sciences Volume 208, 1 May 2025, 107060

7. Nakatsuka R, Yamaguchi Y, Hirohata K, Shimojo S, Murakami M, Rocafort MAV, Tsunaka Y, Fukuhara M, Torisu T, Uchiyama S.

   Multimass Analysis of Adeno-Associated Virus Vectors by Orbitrap-Based Charge Detection Mass Spectrometry
   Anal Chem (2024) Oct 22;96(42):17037-17046.

8. Yamaguchi Y, Ishii K, Koizumi S, Sakaue H, Maruno T, Fukuhara M, Shibuya R, Tsunaka Y, Matsushita A, Bandoh K, Torisu T, Murata-Kishimoto C, Tomioka A, Mizukado S, Kaji H, Kashiwakura Y, Ohmori T, Kuno A, Uchiyama S.

   Glycosylation of recombinant adeno-associated virus serotype 6.
   Mol Ther Methods Clin Dev(2024) Apr 25;32(2):101256.

9. Nishiumi H, Hirohata K, Fukuhara M, Matsushita A, Tsunaka Y, Rocafort MAV, Maruno T, Torisu T, Uchiyama S.

   Combined 100 keV Cryo-Electron Microscopy and Image Analysis Methods to Characterize the Wider Adeno-Associated Viral Products
   J Pharm Sci.(2024) Jul;113(7):1804-1815.

10. Tran THN, Takada R, Krayukhina E, Maruno T, Mii Y, Uchiyama S, Takada S.

    Soluble Frizzled-related proteins promote exosome-mediated Wnt re-secretion
    Commun Biol(2024) Mar 1;7(1):254.

11. Onishi T, Nonaka M, Maruno T, Yamaguchi Y, Fukuhara M, Torisu T, Maeda M, Abbatiello S, Haris A, Richardson K, Giles K, Preece S, Yamano-Adachi N, Omasa T, Uchiyama S.

    Enhancement of recombinant adeno-associated virus activity by improved stoichiometry and homogeneity of capsid protein assembly
    Mol Ther Methods Clin Dev(2023) Oct 24;31:101142.

12. Kurinomaru T, Takeda K, Onaka M, Kuruma Y, Takahata K, Takahashi K, Sakurai H, Sasaki A, Noda N, Honda S, Shibuya R, Ikeda T, Okada R, Torisu T, Uchiyama S.

    Optimization of Flow Imaging Microscopy Setting Using Spherical Beads with Optical Properties Similar to Those of Biopharmaceuticals
    J Pharm Sci(2023) Dec;112(12):3248-3255.

13. Yui A, Kuroda D, Maruno T, Nakakido M, Nagatoishi S, Uchiyama S, Tsumoto K

    Molecular mechanism underlying the increased risk of colorectal cancer metastasis caused by single nucleotide polymorphisms in LI-cadherin gene
    Sci Rep(2023) Apr 20;13(1):6493.

14. Maruno T, Ishii K, Torisu T, Uchiyama S.

    Size Distribution Analysis of the Adeno-Associated Virus Vector by the c(s) Analysis of Band Sedimentation Analytical Ultracentrifugation with Multiwavelength Detection
    J Pharm Sci(2022) Oct 29:S0022-3549(22)00480-4.

15. Takeda K, Noda M, Maruno T, Uchiyama S.

    Critical Calibration of Mass Photometry for Higher-Mass Samples Such as Adeno-Associated Virus Vectors
    J Pharm Sci(2022) Nov 9:S0022-3549(22)00505-6.

16. Oki H, Kawahara K, Iimori M, Imoto Y, Nishiumi H, Maruno T, Uchiyama S, Muroga Y, Yoshida A, Yoshida T, Ohkubo T, Matsuda S, Iida T, Nakamura S.

    Structural basis for the toxin-coregulated pilus-dependent secretion of Vibrio cholerae colonization factor
    Sci Adv(2022) Oct 14;8(41):eabo3013.

17. Nishiumi H, Deiringer N, Krause N, Yoneda S, Torisu T, Menzen T, Friess W, Uchiyama S.

    Utility of Three Flow Imaging Microscopy Instruments for Image Analysis in Evaluating four Types of Subvisible Particle in Biopharmaceuticals
    J Pharm Sci(2022) Nov;111(11):3017-3028.

18. Shibata H, Terabe M, Shibano Y, Saitoh S, Takasugi T, Hayashi Y, Okabe S, Yamaguchi Y, Yasukawa H, Suetomo H, Miyanabe K, Ohbayashi N, Akimaru M, Saito S, Ito D, Nakano A, Kojima S, Miyahara Y, Sasaki K, Maruno T, Noda M, Kiyoshi M, Harazono A, Torisu T, Uchiyama S, Ishii-Watabe A.

    A Collaborative Study on the Classification of Silicone Oil Droplets and Protein Particles Using Flow Imaging Method.
    J Pharm Sci(2022) Oct;111(10):2745-2757.

19. Puri S, Chen SN, Chiu YH, Draczkowski P, Ko KT, Yang TJ, Wang YS, Uchiyama S, Hsu SD.

    Impacts of Cancer-associated Mutations on the Structure-Activity Relationship of BAP1
    J Mol Biol(2022) May 15;434(9):167553.

20. Nakagawa Y, Shen HC, Komi Y, Sugiyama S, Kurinomaru T, Tomabechi Y, Krayukhina E, Okamoto K, Yokoyama T, Shirouzu M, Uchiyama S, Inaba M, Niwa T, Sako Y, Taguchi H, Tanaka M.

    Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system.
    Nat Chem Biol(2022) Mar;18(3):321-331.

21. Abe K, Kabe Y, Uchiyama S, Iwasaki YW, Ishizu H, Uwamino Y, Takenouchi T, Uno S, Ishii M, Maruno T, Noda M, Murata M, Hasegawa N, Saya H, Kitagawa Y, Fukunaga K, Amagai M, Siomi H, Suematsu M, Kosaki K; Keio Donner Project.

    Pro108Ser mutation of SARS-CoV-2 3CLpro reduces the enzyme activity and ameliorates the clinical severity of COVID-19.
    Sci Rep(2022) Jan 25;12(1):1299.

22. Fujiwara S, Ueda T, Ishii N, Abe Y, Hayashihara-Kakuhou K, Takeda K, Kurinomaru T, Fukuhara A, Uchiyama S, Carpenter JF.

    Chemical-gas Sterilization of External Surface of Polymer-based Prefilled Syringes and Its Effect on Stability of Model Therapeutic Protein.
    J Pharm Sci(2022) Jan;111(1):41-50.

23. Fukuhara A, Anzai Y, Osawa K, Umeda M, Minemura H, Shiramizu N, Yokoyama M, Uchiyama S.

    Plate Reader-Based Analytical Method for the Size Distribution of Submicron-Sized Protein Aggregates Using Three-Dimensional Homodyne Light Detection.
    J Pharm Sci(2021) Dec;110(12):3803-3810.

24. Yoneda S, Maruno T, Mori A, Hioki A, Nishiumi H, Okada R, Murakami M, Zekun W, Fukuhara A, Itagaki N, Harauchi Y, Adachi S, Okuyama K, Sawaguchi T, Torisu T, Uchiyama S.

    Influence of Protein Adsorption on Aggregation in Prefilled Syringes.
    J Pharm Sci(2021) Nov;110(11):3568-3579.

25. Kabe Y, Koike I, Yamamoto T, Hirai M, Kanai A, Furuhata R, Tsugawa H, Harada E, Sugase K, Hanadate K, Yoshikawa N, Hayashi H, Noda M, Uchiyama S, Yamazaki H, Tanaka H, Kobayashi T, Handa H, Suematsu M.

    Glycyrrhizin Derivatives Suppress Cancer Chemoresistance by Inhibiting Progesterone Receptor Membrane Component 1.
    Cancers (Basel)(2021) Jun 29;13(13):3265.

26. Gambe-Gilbuena A, Shibano Y, Krayukhina E, Torisu T, Uchiyama S.

    Automatic Identification of the Stress Sources of Protein Aggregates Using Flow Imaging Microscopy Images.
    J Pharm Sci(2020) Jan;109(1):614-623.

27. Oyama H, Koga H, Tadokoro T, Maenaka K, Shiota A, Yokoyama M, Noda M, Torisu T, Uchiyama S.

    Relation of Colloidal and Conformational Stabilities to Aggregate Formation in a Monoclonal Antibody.
    J Pharm Sci(2020) Jan;109(1):308-315.

28. Krayukhina E, Fukuhara A, Uchiyama S.

    Assessment of the Injection Performance of a Tapered Needle for Use in Prefilled Biopharmaceutical Products.
    J Pharm Sci(2020) Jan;109(1):515-523.

29. Noda M, Ishii K, Yamauchi M, Oyama H, Tadokoro T, Maenaka K, Torisu T, Uchiyama S.

    Identification of IgG1 Aggregation Initiation Region by Hydrogen Deuterium Mass Spectrometry.
    J Pharm Sci(2019) Jul;108(7):2323-2333.

30. Krayukhina E, Yokoyama M, Hayashihara KK, Maruno T, Noda M, Watanabe H, Uchihashi T, Uchiyama S.

    An Assessment of the Ability of Submicron- and Micron-Size Silicone Oil Droplets in Dropped Prefillable Syringes to Invoke Early- and Late-Stage Immune Responses.
    J Pharm Sci(2019) Jul;108(7):2278-2287.

31. Harazono A, Shibata H, Kiyoshi M, Muto T, Fukuda J, Torisu T, Saitoh S, Nishimura H, Uchiyama S, Ishii-Watabe A.

    Interlaboratory comparison about feasibility of insoluble particulate matter test for injections with reduced test volume in light obscuration method.
    Biologicals(2019) Jan;57:46-49.

32. Yoneda S, Niederleitner B, Wiggenhorn M, Koga H, Totoki S, Krayukhina E, Friess W, Uchiyama S.

    Quantitative laser diffraction (qLD) for a quantification of protein aggregates – comparison with resonant mass measurement, nano-particle tracking, flow imaging and light obscuration.
    J Pharm Sci(2019) Jan;108(1):755-762.

33. Takada R, Mii Y, Krayukhina E, Maruyama Y, Mio K, Sasaki Y, Shinkawa T, Pack CG, Sako C, Uchiyama S, Takada S.

    Assembly of protein complexes restricts diffusion of Wnt3a proteins.
    Commun Biol(2018) Oct 10;1:165.

34. Kiyoshi M, Shibata H, Harazono A, Torisu T, Maruno T, Akimaru M, Asano Y, Hirokawa M, Ikemoto K, Itakura Y, Iwura T, Kikitsu A, Kumagai T, Mori N, Murase H, Nishimura H, Oda A, Ogawa T, Ojima T, Okabe S, Saito S, Saitoh S, Suetomo H, Takegami K, Takeuchi M, Yasukawa H, Uchiyama S, Ishii-Watabe A.

    Collaborative Study For Analysis Of Subvisible Particles Using Flow Imaging And Light Obscuration: Experiences In Japanese Biopharmaceutical Consortium.
    J Pharm Sci(2018) Aug 16. pii: S0022-3549(18)30505-7.

35. Maruno T, Watanabe H, Yoneda S, Uchihashi T, Adachi S, Arai K, Sawaguchi T, Uchiyama S.

    Sweeping of Adsorbed Therapeutic Protein on Prefillable Syringes Promotes Micron Aggregate Generation.
    J Pharm Sci(2018) Jun;107(6):1521-1529.

36. Uchiyama S, Noda M, Krayukhina E.

    Sedimentation velocity analytical ultracentrifugation for characterization of therapeutic antibodies.
    Biophys Rev(2018) Apr;10(2):259-269.

37. Yanaka S, Yamazaki T, Yogo R, Noda M, Uchiyama S, Yagi H, Kato K.

    NMR Detection of Semi-Specific Antibody Interactions in Serum Environments.
    Molecules(2017) Sep 27;22(10).

38. Krayukhina E, Noda M, Ishii K, Maruno T, Wakabayashi H, Tada M, Suzuki T, Ishii-Watabe A, Kato M, Uchiyama S.

    Analytical ultracentrifugation with fluorescence detection system reveals differences in complex formation between recombinant human TNF and different biological TNF antagonists in various environments.
    MAbs(2017) May/Jun;9(4):664-679.

39. Oda M, Tanabe Y, Noda M, Inaba S, Krayukhina E, Fukada H, Uchiyama S.

    Structural and binding properties of laminarin revealed by analytical ultracentrifugation and calorimetric analyses.
    Carbohydr Res(2016) Aug 5;431:33-8.

40. Toma-Fukai S, Kim JD, Park KE, Kuwabara N, Shimizu N, Krayukhina E, Uchiyama S, Fukamizu A, Shimizu T.

    Novel helical assembly in arginine methyltransferase 8.
    J Mol Biol(2016) Mar 27;428(6):1197-1208.

41. Kita S, Matsubara H, Kasai Y, Tamaoki T, Okabe Y, Fukuhara H, Kamishikiryo J, Krayukhina E, Uchiyama S, Ose T, Kuroki K, Maenaka K.

    Crystal structure of extracellular domain of human lectin-like transcript 1 (LLT1), the ligand for natural killer receptor-P1A.
    Eur J Immunol(2015) Jun;45(6):1605-13.

42. Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E, Uchiyama S, Miyake K, Shimizu T.

    Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9.
    Nature(2015) Apr 30;520(7549):702-5.

43. Han W, Yamauchi M, Hasegawa U, Noda M, Fukui K, van der Vlies AJ, Uchiyama S, Uyama H.

    Pepsin immobilization on an aldehyde-modified polymethacrylate monolith and its application for protein analysis.
    J Biosci Bioeng(2015) May;119(5):505-10.

44. Krayukhina E, Tsumoto K, Uchiyama S, Fukui K.

    Effects of syringe material and silicone oil lubrication on the stability of pharmaceutical proteins.
    J Pharm Sci(2015) Feb;104(2):527-35.