Research

1. Shimoyama M, Nakada-Tsukui K, Nozaki T. EhRacM differentially regulates macropinocytosis and motility in the enteric protozoan parasite Entamoeba histolytica. PLoS Pathog. 20(11):e1012364. https://doi.org/10.1371/journal.ppat.1012364 (2024)

2. Kawataki S, Kubota Y, Katayama K, Imoto S, Takekawa M. GADD45beta-MTK1 signaling axis mediates oncogenic stress-induced activation of the p38 and JNK pathways. Cancer Sci. https://doi.org/10.1111/cas.16389 (2024)

3. Kuwata T, Kaku Y, Biswas S, Matsumoto K, Shimizu M, Kawanami Y, Uraki R, Okazaki K, Minami R, Nagasaki Y, Nagashima M, Yoshida I, Sadamasu K, Yoshimura K, Ito M, Kiso M, Yamayoshi S, Imai M, Ikeda T, Sato K, Toyoda M, Ueno T, Inoue T, Tanaka Y, Kimura KT, Hashiguchi T, Sugita Y, Noda T, Morioka H, Kawaoka Y, Matsushita S, Genotype to Phenotype Japan (G2P-Japan) Consortium. Induction of IGHV3-53 public antibodies with broadly neutralising activity against SARS-CoV-2 including Omicron subvariants in a Delta breakthrough infection case. EBioMedicine. 110:105439. https://doi.org/10.1016/j.ebiom.2024.105439 (2024)

4. Gu C, Maemura T, Guan L, Eisfeld AJ, Biswas A, Kiso M, Uraki R, Ito M, Trifkovic S, Wang T, Babujee L, Presler RJ, Dahn R, Suzuki Y, Halfmann PJ, Yamayoshi S, Neumann G, Kawaoka Y. A human isolate of bovine H5N1 is transmissible and lethal in animal models. Nature. https://doi.org/10.1038/s41586-024-08254-7 (2024)

5. Yajima H, Nomai T, Okumura K, Maenaka K, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito J, Hashiguchi T, Sato K. Molecular and structural insights into SARS-CoV-2 evolution: from BA.2 to XBB subvariants. mBio. 15(10):e0322023–23. Epub 2024 Sep 16. https://doi.org/10.1128/mbio.03220-23 (2024)

6. Chiba S, Kiso M, Yamada S, Someya K, Onodera Y, Yamaguchi A, Matsunaga S, Uraki R, Iwatsuki-Horimoto K, Yamayoshi S, Takeshita F, Kawaoka Y. An mRNA vaccine candidate encoding H5HA clade 2.3.4.4b protects mice from clade 2.3.2.1a virus infection. NPJ Vaccines. 9(1):189–9. https://doi.org/10.1038/s41541-024-00988-9 (2024)

7. Chiba S, Kiso M, Yamada S, Someya K, Onodera Y, Yamaguchi A, Matsunaga S, Jounai N, Yamayoshi S, Takeshita F, Kawaoka Y. Protective effects of an mRNA vaccine candidate encoding H5HA clade 2.3.4.4b against the newly emerged dairy cattle H5N1 virus. eBioMedicine. 109:105408. https://doi.org/10.1016/j.ebiom.2024.105408 (2024) 

8. Yaku H, Takahashi K, Okada H, Kobiyama K, Shiokawa M, Uza N, Kodama Y, Ishii KJ, Seno H. Near-infrared photoimmunotherapy as a complementary modality to in situ vaccine in a preclinical pancreatic cancer model. Biochem Biophys Res Commun. 737:150534. https://doi.org/10.1016/j.bbrc.2024.150534 (2024)

9. Jiang H, Santos HJ, Nozaki T. Tetraspanin-enriched microdomains play an important role in pathogenesis in the protozoan parasite Entamoeba histolytica. PLoS Pathog. 20(10):e1012151. https://doi.org/10.1371/journal.ppat.1012151 (2024)

10. Wulansari D, Jeelani G, Yazaki E, Nozaki T. Identification and characterization of archaeal-type FAD synthase as a novel tractable drug target from the parasitic protozoa Entamoeba histolytica. mSphere. 9(9):e0034724–24. Epub 2024 Aug 27. https://doi.org/10.1128/msphere.00347-24 (2024)

11. Kiso M, Uraki R, Yamayoshi S, Imai M, Kawaoka Y. Drug susceptibility and the potential for drug-resistant SARS-CoV-2 emergence in immunocompromised animals. Iscience. 27(9):110729. https://doi.org/10.1016/j.isci.2024.110729 (2024)

12. Miyauchi K, Kimura S, Akiyama N, Inoue K, Ishiguro K, Vu T, Srisuknimit V, Koyama K, Hayashi G, Soma A, Nagao A, Shirouzu M, Okamoto A, Waldor MK, Suzuki T. A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis. Nat Chem Biol. https://doi.org/10.1038/s41589-024-01726-x (2024)

13. Tanaka T, Hososhima S, Yamashita Y, Sugimoto T, Nakamura T, Shigemura S, Iida W, Sano FK, Oda K, Uchihashi T, Katayama K, Furutani Y, Tsunoda SP, Shihoya W, Kandori H, Nureki O. The high-light-sensitivity mechanism and optogenetic properties of the bacteriorhodopsin-like channelrhodopsin GtCCR4. Mol Cell. 84(18) https://doi.org/10.1016/j.molcel.2024.08.016 (2024)

14. Muraoka D, Moi ML, Muto O, Nakatsukasa T, Deng S, Takashima C, Yamaguchi R, Sawada S, Hayakawa H, Nguyen TTN, Haseda Y, Soga T, Matsushita H, Ikeda H, Akiyoshi K, Harada N. Low-frequency CD8(+) T cells induced by SIGN-R1(+) macrophage-targeted vaccine confer SARS-CoV-2 clearance in mice. NPJ Vaccines. 9(1):173–6. https://doi.org/10.1038/s41541-024-00961-6 (2024)

15. Inoue T, Baba Y, Kurosaki T. BCR signaling in germinal center B cell selection. Trends Immunol. 45(9):693–704. https://doi.org/10.1016/j.it.2024.07.005 (2024)

16. Neumann G, Kawaoka Y. Highly pathogenic H5N1 avian influenza virus outbreak in cattle: the knowns and unknowns. Nature Reviews Microbiology. 22(9):525–526. https://doi.org/10.1038/s41579-024-01087-1 (2024)

17. Takashita E, Ichikawa M, Fujisaki S, Morita H, Nagata S, Miura H, Watanabe S, Hasegawa H, Kawaoka Y. Antiviral susceptibility of SARS-CoV-2 and influenza viruses from 3 co-infecte d pe diatric patients. International Journal of Infectious Diseases. 146:107134. https://doi.org/10.1016/j.ijid.2024.107134 (2024)

18. Liu S, Maruzuru Y, Takeshima K, Koyanagi N, Kato A, Kawaguchi Y. Impact of the interaction between herpes simplex virus 1 ICP22 and FACT on viral gene expression and pathogenesis. J Virol. 98(8):e0073724–24. Epub 2024 Jul 17. https://doi.org/10.1128/jvi.00737-24 (2024)

19. Manabe S, Iwamoto S, Nagatoishi S, Hoshinoo A, Mitani A, Sumiyoshi W, Kinoshita T, Yamaguchi Y, Tsumoto K. Systematic Preparation of a 66-IgG Library with Symmetric and Asymmetric Homogeneous Glycans and Their Functional Evaluation. J Am Chem Soc. 146(33):23426–23436. https://doi.org/10.1021/jacs.4c06558 (2024)

20. Mizutani T, Ishizaka A. Poliovirus capsid protein VP3 can penetrate vascular endothelial cells. FEBS Lett. 598(15):1909–1918. https://doi.org/10.1002/1873-3468.14974 (2024)

21. Huynh NC, Ling R, Komagamine M, Shi T, Tsukasaki M, Matsuda K, Okamoto K, Asano T, Muro R, Pluemsakunthai W, Kollias G, Kaneko Y, Takeuchi T, Tanaka S, Komatsu N, Takayanagi H. Oncostatin M-driven macrophage-fibroblast circuits as a drug target in autoimmune arthritis. Inflamm Regen. 44(1):36-0. https://doi.org/10.1186/s41232-024-00347-0 (2024)

22. Ishizaka A, Koga M, Mizutani T, Suzuki Y, Matano T, Yotsuyanagi H. Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy. BMC Microbiol. 24(1):274-0. https://doi.org/10.1186/s12866-024-03431-0 (2024)

23. Kato A, Iwasaki R, Takeshima K, Maruzuru Y, Koyanagi N, Natsume T, Kusano H, Adachi S, Kawano S, Kawaguchi Y. Identification of a novel neurovirulence factor encoded by the cryptic orphan gene UL31.6 of herpes simplex virus 1. J Virol. 98(7):e0074724-24. Epub 2024 May 31. https://doi.org/10.1128/jvi.00747-24 (2024)

24. Iijima N, Hayashi T, Niino M, Miyamoto Y, Oka M, Ishii KJ. Tridecylcyclohexane in incomplete Freund's adjuvant is a critical component in inducing experimental autoimmune diseases. Eur J Immunol. :e2350957. https://doi.org/10.1002/eji.202350957 (2024)

25. Eisfeld AJ, Biswas A, Guan L, Gu C, Maemura T, Trifkovic S, Wang T, Babujee L, Dahn R, Halfmann PJ, Barnhardt T, Neumann G, Suzuki Y, Thompson A, Swinford AK, Dimitrov KM, Poulsen K, Kawaoka Y. Pathogenicity and transmissibility of bovine H5N1 influenza virus. Nature. https://doi.org/10.1038/s41586-024-07766-6 (2024)

26. Guan L, Eisfeld AJ, Pattinson D-PD, Gu C, Biswas A, Maemura T, Trifkovic S, Babujee L, Presler RJ, Dahn R, Halfmann PJ, Barnhardt T, Neumann G, Thompson A, Swinford AK, Dimitrov KM, Poulsen K, Kawaoka Y. Cow's Milk Containing Avian Influenza A(H5N1) Virus - Heat Inactivation and Infectivity in Mice. N Engl J Med. 391(1):87-90. https://doi.org/10.1056/NEJMc2405495 (2024)

27. Nakane T, Nakagawa R, Ishiguro S, Okazaki S, Mori H, Shuto Y, Yamashita K, Yachie N, Nishimasu H, Nureki O. Structure and engineering of Brevibacillus laterosporus Cas9. Commun Biol. 7(1):803-z. https://doi.org/10.1038/s42003-024-06422-z (2024)

28. Inoue T, Matsumoto Y, Kawai C, Ito M, Nada S, Okada M, Kurosaki T. Csk restrains BCR-mediated ROS production and contributes to germinal center selection and affinity maturation. J Exp Med. 221(7):e20231996. doi: 10.1084/jem.20231996. Epub 2024 May 16. https://doi.org/10.1084/jem.20231996 (2024)

29. Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O. Structural basis for pegRNA-guided reverse transcription by a prime editor. Nature. 631(8019):224–231. https://doi.org/10.1038/s41586-024-07497-8 (2024)

30. Asano R, Nakakido M, Perez JF, Ise T, Caaveiro JMM, Nagata S, Tsumoto K. Crystal structures of human CD40 in complex with monoclonal antibodies dacetuzumab and bleselumab. Biochem Biophys Res Commun. 714:149969. https://doi.org/10.1016/j.bbrc.2024.149969 (2024)

31. Iwama A, Kise R, Akasaka H, Sano FK, Oshima HS, Inoue A, Shihoya W, Nureki O. Structure and dynamics of the pyroglutamylated RF-amide peptide QRFP receptor GPR103. Nat Commun. 15(1):4769-5. https://doi.org/10.1038/s41467-024-49030-5 (2024)

32. Lee MSJ, Matsuo-Dapaah J, Del Rosario Zorrilla C, Omatsu Y, Nagasawa T, Uemura S, Iwama A, Ishii KJ, Coban C. Acute malaria suppresses the B lymphocytic niche in the bone marrow through the alteration of CXCL12-abundant reticular cells. Int Immunol. 36(7):339–352. https://doi.org/10.1093/intimm/dxae012 (2024)

33. Fujita S, Plianchaisuk A, Deguchi S, Ito H, Nao N, Wang L, Nasser H, Tamura T, Kimura I, Kashima Y, Suzuki R, Suzuki S, Kida I, Tsuda M, Oda Y, Hashimoto R, Watanabe Y, Uriu K, Yamasoba D, Guo Z, Hinay AAJ, Kosugi Y, Chen L, Pan L, Kaku Y, Chu H, Donati F, Temmam S, Eloit M, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Suzuki Y, Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito J, Ikeda T, Tanaka S, Matsuno K, Fukuhara T, Takayama K, Sato K. Virological characteristics of a SARS-CoV-2-related bat coronavirus, BANAL-20-236. EBioMedicine. 104:105181. https://doi.org/10.1016/j.ebiom.2024.105181 (2024)

34. Ito S, Matsunaga R, Nakakido M, Komura D, Katoh H, Ishikawa S, Tsumoto K. High-throughput system for the thermostability analysis of proteins. Protein Sci. 33(6):e5029. https://doi.org/10.1002/pro.5029 (2024)

35. Shimizu K, Kawakami C, Matsuzaki Y, Fujisaki S, Nagata S, Morita H, Watanabe K, Miura H, Momoki T, Saikusa M, Ozawa H, Kumazaki M, Usuku S, Tanaka N, Senda R, Okubo I, Watanabe S, Hasegawa H, Kawaoka Y, Takashita E. Monitoring Influenza C and D Viruses in Patients With Respiratory Diseases in Japan, January 2018 to March 2023. Influenza Other Respir Viruses. 18(6):e13345. https://doi.org/10.1111/irv.13345 (2024)

36. Yoshioka D, Nakamura T, Kubota Y, Takekawa M. Formation of the NLRP3 inflammasome inhibits stress granule assembly by multiple mechanisms. J Biochem. 175(6):629-641. https://doi.org/10.1093/jb/mvae009 (2024)

37. Setoguchi R, Sengiku T, Kono H, Kawakami E, Kubo M, Yamamoto T, Hori S. Memory CD8 T cells are vulnerable to chronic IFN-gamma signals but not to CD4 T cell deficiency in MHCII-deficient mice. Nat Commun. 15(1):4418-4. https://doi.org/10.1038/s41467-024-48704-4 (2024)

38. Kitai Y, Watanabe O, Ohmiya S, Kisu T, Ota R, Kawakami K, Katoh H, Fukuzawa K, Takeda M, Nishimura H. Detailed analysis of low temperature inactivation of respiratory syncytial virus. Sci Rep. 14(1):11823-z. https://doi.org/10.1038/s41598-024-62658-z (2024)

39. Yamamoto K, Nagatoishi S, Nakakido M, Kuroda D, Tsumoto K. Functional insights of Tyr37 in framework region 2 directly contributing to the binding affinities and dissociation kinetics in single-domain V H H antibodies. Biochem Biophys Res Commun. 709:149839. https://doi.org/10.1016/j.bbrc.2024.149839 (2024)

40. Muehlemann B, Wilks SH, Baracco L, Bekliz M, Carreno JM, Corman VM, Davis-Gardner ME, Dejnirattisai W, Diamond MS, Douek DC, Drosten C, Eckerle I, Edara V, Ellis M, Fouchier RAM, Frieman M, Godbole S, Haagmans B, Halfmann PJ, Henry AR, Jones TC, Katzelnick LC, Kawaoka Y, Kimpel J, Krammer F, Lai L, Liu C, Lusvarghi S, Meyer B, Mongkolsapaya J, Montefiori DC, Mykytyn A, Netzl A, Pollett S, Roessler A, Screaton GR, Shen X, Sigal A, Simon V, Subramanian R, Supasa P, Suthar MS, Tuereli S, Wang W, Weiss CD, Smith DJ. Comparative analysis of SARS-CoV-2 neutralization titers reveals consistency between human and animal model serum and across assays. Science Translational Medicine. 16(747):eadl1722. https://doi.org/10.1126/scitranslmed.adl1722 (2024)

41. Wang W, Harimurti S, Inoue D, Nayeem MOG, Wang J, Okuda C, Hashizume D, Lee S, Fukuda K, Yokota T, Someya T. Janus Membrane-Based Wearable pH Sensor with Sweat Absorption, Gas Permeability, and Self-Adhesiveness. Acs Applied Materials & Interfaces. 16(21):27065–27074. https://doi.org/10.1021/acsami.4c02189 (2024)

42. Akiyama N, Ishiguro K, Yokoyama T, Miyauchi K, Nagao A, Shirouzu M, Suzuki T. Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine. Nature Structural & Molecular Biology. 31(5) https://doi.org/10.1038/s41594-024-01238-1 (2024)

43. Sasaki I, Fukuda-Ohta Y, Nakai C, Wakaki-Nishiyama N, Okamoto C, Okuzaki D, Morita S, Kaji S, Furuta Y, Hemmi H, Kato T, Yamamoto A, Tosuji E, Saitoh S, Tanaka T, Hoshino K, Fukuda S, Miyake K, Kuroda E, Ishii KJ, Iwawaki T, Furukawa K, Kaisho T. A stress sensor, IRE1α, is required for bacterial-exotoxin-induced interleukin-1β production in tissue-resident macrophages. Cell Rep. 43(4):113981. https://doi.org/10.1016/j.celrep.2024.113981 (2024)

44. Tolentino JE, Lytras S, Ito J, Sato K. Recombination analysis on the receptor switching event of MERS-CoV and its close relatives: implications for the emergence of MERS-CoV. Virol J. 21(1):84-2. https://doi.org/10.1186/s12985-024-02358-2 (2024)

45. Goto M, Takahashi H, Yoshida R, Itamiya T, Nakano M, Nagafuchi Y, Harada H, Shimizu T, Maeda M, Kubota A, Toda T, Hatano H, Sugimori Y, Kawahata K, Yamamoto K, Shoda H, Ishigaki K, Ota M, Okamura T, Fujio K. Age-associated CD4(+) T cells with B cell-promoting functions are regulated by ZEB2 in autoimmunity. Sci Immunol. 9(93):eadk1643. https://doi.org/10.1126/sciimmunol.adk1643 (2024)

46. Onishi S, Uchiyama K, Sato K, Okada C, Kobayashi S, Hamada K, Nishizawa T, Nureki O, Ogata K, Sengoku T. Structure of the human Bre1 complex bound to the nucleosome. Nat Commun. 15(1):2580-8. https://doi.org/10.1038/s41467-024-46910-8 (2024)

47. Katayama M, Murakami S, Ishida H, Matsugo H, Sekine W, Ohira K, Takenaka-Uema A, Horimoto T. Antigenic commonality and divergence of hemagglutinin-esterase-fusion protein among influenza D virus lineages revealed using epitope mapping. J Virol. 98(3):e0190823-23. Epub 2024 Feb 12. https://doi.org/10.1128/jvi.01908-23 (2024)

48. Shihoya W, Iwama A, Sano FK, Nureki O. Cryo-EM advances in GPCR structure determination. J Biochem. https://doi.org/10.1093/jb/mvae029 (2024)

49. Serafini N, Di Santo JP. Group 3 innate lymphoid cells: A trained Gutkeeper. Immunol Rev. https://doi.org/10.1111/imr.13322 (2024)

50. Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K. Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport. Nat Commun. 15(1):2404-1. https://doi.org/10.1038/s41467-024-46747-1 (2024)

51. Halfmann PJ, Iwatsuki-Horimoto K, Kuroda M, Hirata Y, Yamayoshi S, Iida S, Uraki R, Ito M, Ueki H, Furusawa Y, Sakai-Tagawa Y, Kiso M, Armbrust T, Spyra S, Maeda K, Wang Z, Imai M, Suzuki T, Kawaoka Y. Characterization of Omicron BA.4.6, XBB, and BQ.1.1 subvariants in hamsters. Commun Biol. 7(1):331-w. https://doi.org/10.1038/s42003-024-06015-w (2024)

52. Inada T, Beckmann R. Mechanisms of Translation-coupled Quality Control. J Mol Biol. 436(6):168496. https://doi.org/10.1016/j.jmb.2024.168496 (2024)

53. Song I, Yang J, Saito M, Hartanto T, Nakayama Y, Ichinohe T, Fukuda S. Prebiotic inulin ameliorates SARS-CoV-2 infection in hamsters by modulating the gut microbiome. NPJ Sci Food. 8(1):18-z. https://doi.org/10.1038/s41538-024-00248-z (2024)

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News Release　Study reveals the 3D structure of a protein involved in genome editing

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