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研 究 業 績 / Publications

　　#同等貢献 (equal contribution), *責任著者 (corresponding author)

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  1. Honcharuk, V., Zainab, A., Horimoto, Y., Takemoto, K., Diez, D., Kawaoka, S., and Vandenbon, A. (2025). DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments. Nucl. Acid. Res. gkaf1117

  2. Prabhune, N., Du, Y., Zainab, A., Ebihara, S., Takeoka, S., Kawaoka, S*., and Vandenbon, A*. (2025). Mining spatial transcriptomics datasets using DeepSpaceDB. J. Vis. Exp. 223

  3. Iwasaki, T., Shirota, H., Hishinuma, E., Kawaoka, S., Matsukawa, N., Kasahara, Y., Ouchi, K., Imai, H., Saijo, Ken., Komine, K., Takahashi, M., Ishioka, C., Koshiba, S., and Kawakami, H. (2025). Plasma Lysophosphatidylcholine levels correlate with prognosis and immunotherapy response in squamous cell carcinoma. Int. J. Mol. Sci. 26: 7528.

  4. Maeshima, Y., Kataoka, R.T., Vandenbon, A., Hirata, M., Takeuchi, Y., Suzuki, Y., Fukui, Y., Kawashima, M., Takada, M., Ibi, Y., Haga, H., Morita, S., Toi, M., Kawaoka, S*., and Kawaguchi, K*. (2024). Intra-patient spatial comparison of non-metastatic and metastatic lymph nodes reveals the reduction of CD169+ macrophages by metastatic breast cancers. eBioMedicine, accepted.

  5. Oguchi, A., Suzuki, A., Komatsu, S., Yoshitomi, H., Bhagat, S., Son, R., Bonnal, R.J.P., Kojima, S., Koido, M., Takeuchi, K., Myouzen, K., Inoue, G., Hirai, T., Sano, H., Takegami, Y., Konishi, R., Sekito, S., Inoue, T., Kere, J., Takeda, S., Takaori-Kondo, A., Endo, I., ., Kawaji, H., Ishigaki, K., Ueno, H., Hayashizaki, Y., Pagani, M., Carninci, P., Yanagita, M., ITEC consortium, Parrish, N., Terao, C., Yamamoto, K., and Murakawa, Y. (2024). An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases. Science, 385, eadd8394.

  6. Nakamura, Y#., Saldajeno, D.P#., Kawaguchi, K., and Kawaoka, S*. (2024). Progressive, multi-organ, and multi-layered nature of cancer cachexia. Cancer Sci., 115, 715-722

  7. Saldajeno, D.P#., Kawaoka, S#., Masuda, N., Tanaka, S., Bando, H., Nishimura, T., Kadoya, T., Yamanaka, T., Imoto, S., Velaga, R.V., Tamura, N., Aruga, T., Ikeda, K., Maeshima, Y., Takada, M., Suzuki, E., Ueno, T., Ogawa, S., Haga, H., Ohno, S., Morita, S., Kawaguchi, K., and Toi, M. (2024). Time-series blood cytokine profiles correlate with treatment responses in triple-negative breast cancer patients. Br J Cancer

  8. ​Nakamura, Y., Yoda, M., Izumi, Y., Kashima, Y., Takahashi, M., Nakatani, K., Bamba, M., He, C., Konishi, R., Vandenbon, A., Suzuki, Y., Toi, M., Kawaguchi, K*., and Kawaoka, S*. (2023). Low albumin status accompanies multi-layered immunosuppressive phenotypes in metastatic breast cancer patients. bioRxiv.

  9. Yoda, M., Mizuno, R., Izumi, Y., Takahashi, M., Nakao, M., Bamba, T., and Kawaoka, S*. (2023). Nicotinamide-N-methyltransferase regulates lipid metabolism via SAM and 1-methylnicotinamide in the AML12 hepatocyte cell line. J Biochem. 

  10. He, C#., Konishi, R#., Harata, A., Nakamura, Y., Mizuno, R., Yoda, M., Toi, M., Kawaguchi, K*., and Kawaoka, S*. (2023). Serum amyloid alpha 1-2 are not required for liver inflammation in the 4T1 breast cancer model. Front Immunol. 14, 300.

  11. Vandenbon, A#*., Mizuno, R#., Konishi, R#., Onishi, M#., Masuda, K., Kobayashi Y., Kawamoto, H., Suzuki, A., He, C., Nakamura, Y., Kawaguchi, K., Toi, M., Shimizu, M., Tanaka, Y., Suzuki, Y*., and Kawaoka, S*. (2023). Murine breast cancers disorganize hepatic transcriptome in a zonated manner. Commun Biol. 6, 97 

  12. Nagahata, Y., Masuda, K., Nishimura, Y., Ikawa, T., Kawaoka, S., Kitawaki, T., Nannya, Y., Ogawa, S., Satou, Y., Suga, H., Takaori-Kondo, A., and Kawamoto, H. (2022). Tracing the evolutionary history of blood cells back to a unicellular organism. Blood 140, 2611.

  13. Mizuno, R., Hojo, H., Takahashi, M., Kashio, S., Enya, S., Nakao, M., Konishi, R., Yoda, M., Harata, A., Hamanishi, J., Kawamoto, H., Mandai, M., Suzuki, Y., Miura, M., Bamba, T., Izumi, Y., and Kawaoka, S*. (2022). Remote solid cancers rewire hepatic nitrogen metabolism via host nicotinamide-N-methyltransferase. Nat Commun 13, 3346.

  14. Hojo, M.A., Masuda, K., Hojo, H., Nagahata, Y., Yasuda, K., Ohara, D., Takeuchi, Y., Hirota, K., Suzuki, Y., Kawamoto, H., and Kawaoka, S*. (2019). Identification of a genomic enhancer that enforces proper apoptosis induction in thymic negative selection. Nat Commun 10, 2603.

  15.  Enya, S., Kawakami, K., Suzuki, Y., and Kawaoka, S*. (2018). A novel zebrafish intestinal tumor model reveals a role for cyp7a1-dependent tumor-liver crosstalk in causing adverse effects on the host. Dis Model Mech 11.

  16. Hojo, H., Enya, S., Arai, M., Suzuki, Y., Nojiri, T., Kangawa, K., Koyama, S., and Kawaoka, S*. (2017). Remote reprogramming of hepatic circadian transcriptome by breast cancer. Oncotarget 8, 34128-34140.

  17. Wang, E., Kawaoka, S., Roe, J.S., Shi, J., Hohmann, A.F., Xu, Y., Bhagwat, A.S., Suzuki, Y., Kinney, J.B., and Vakoc, C.R. (2015). The transcriptional cofactor TRIM33 prevents apoptosis in B lymphoblastic leukemia by deactivating a single enhancer. Elife 4, e06377.

  18. Shoji, K., Hara, K., Kawamoto, M., Kiuchi, T., Kawaoka, S., Sugano, S., Shimada, T., Suzuki, Y., and Katsuma, S. (2014). Silkworm HP1a transcriptionally enhances highly expressed euchromatic genes via association with their transcription start sites. Nucleic Acids Res 42, 11462-71.

  19. Kiuchi, T., Koga, H., Kawamoto, M., Shoji, K., Sakai, H., Arai, Y., Ishihara, G., Kawaoka, S., Sugano, S., Shimada, T., Suzuki, Y., Suzuki, M.G., and Katsuma, S. (2014). A single female-specific piRNA is the primary determiner of sex in the silkworm. Nature 509, 633-6.

  20. Kawaoka, S., Katsuma, S., and Tomari, Y. (2014). Making piRNAs in vitro. Methods Mol Biol 1093, 35-46.

  21. Wang, E#., Kawaoka, S#., Yu, M., Shi, J., Ni, T., Yang, W., Zhu, J., Roeder, R.G., and Vakoc, C.R. (2013). Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia. Proc Natl Acad Sci U S A 110, 3901-3906.

  22. Suetsugu, Y., Futahashi, R., Kanamori, H., Kadono-Okuda, K., Sasanuma, S., Narukawa, J., Ajimura, M., Jouraku, A., Namiki, N., Shimomura, M., Sezutsu, H., Osanai-Futahashi, M., Suzuki, M.G., Daimon, T., Shinoda, T., Taniai, K., Asaoka, K., Niwa, R., Kawaoka, S., Katsuma, S., Tamura, T., Noda, H., Kasahara, M., Sugano, S., Suzuki, Y., Fujiwara, H., Kataoka, H., Arunkumar, K.P., Tomar, A., Nagaraju, J., Goldsmith, M.R., Feng, O., Xia, Q., Yamamoto, K., Shimada, T., Mita, K. (2013). Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori. G3 (Bethesda) 3, 1481-1492.

  23. Shoji, K., Kiuchi, T., Hara, K., Kawamoto, M., Kawaoka, S., Arimura, S., Tsutsumi, N., Sugano, S., Suzuki, Y., Shimada, T., and Katsuma, S. (2013). Characterization of a novel chromodomain-containing gene from the silkworm, Bombyx mori. Gene 527, 649-654.

  24. Shi, J., Whyte, W.A., Zepeda-Mendoza, C.J., Milazzo, J.P., Shen, C., Roe, J.S., Minder, J.L., Mercan, F., Wang, E., Eckersley-Maslin, M.A., Campbell, A.E., Kawaoka, S., Shareef, S., Zhu, S., Kendall, J., Muhar, M., Haslinger, C., Yu, M., Roeder, R.G., Wigler, M.H., Blobel, G.A., Zuber, J., Spector, D.L., Young, R.A., and Vakoc, C.R. (2013). Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes Dev 27, 2648-2662.

  25. Kawaoka, S#*., Hara, K#., Shoji, K., Kobayashi, M., Shimada, T., Sugano, S., Tomari, Y., Suzuki, Y., and Katsuma, S*. (2013). The comprehensive epigenome map of piRNA clusters. Nucleic Acids Res 41, 1581-1590.

  26. Izumi, N#., Kawaoka, S#., Yasuhara, S., Suzuki, Y., Sugano, S., Katsuma, S., and Tomari, Y. (2013). Hsp90 facilitates accurate loading of precursor piRNAs into PIWI proteins. RNA 19, 896-901.

  27. Kawaoka, S#., Mitsutake, H#., Kiuchi, T., Kobayashi, M., Yoshikawa, M., Suzuki, Y., Sugano, S., Shimada, T., Kobayashi, J., Tomari, Y., and Katsuma, S. (2012). A role for transcription from a piRNA cluster in de novo piRNA production. RNA 18, 265-273.

  28. Hara, K., Fujii, T., Suzuki, Y., Sugano, S., Shimada, T., Katsuma, S*., and Kawaoka, S*. (2012). Altered expression of testis-specific genes, piRNAs, and transposons in the silkworm ovary masculinized by a W chromosome mutation. BMC Genomics 13, 119.

  29. Kawaoka, S., Kadota, K., Arai, Y., Suzuki, Y., Fujii, T., Abe, H., Yasukochi, Y., Mita, K., Sugano, S., Shimizu, K., Tomari, Y., Shimada, T., and Katsuma, S. (2011). The silkworm W chromosome is a source of female-enriched piRNAs. RNA 17, 2144-2151.

  30. Kawaoka, S., Izumi, N., Katsuma, S., and Tomari, Y. (2011). 3' end formation of PIWI-interacting RNAs in vitro. Mol Cell 43, 1015-1022.

  31. Kawaoka, S., Arai, Y., Kadota, K., Suzuki, Y., Hara, K., Sugano, S., Shimizu, K., Tomari, Y., Shimada, T., and Katsuma, S. (2011). Zygotic amplification of secondary piRNAs during silkworm embryogenesis. RNA 17, 1401-1407.

  32. Niwa, R., Namiki, T., Ito, K., Shimada-Niwa, Y., Kiuchi, M., Kawaoka, S., Kayukawa, T., Banno, Y., Fujimoto, Y., Shigenobu, S., Kobayashi, S., Shimada, T., Katsuma, S., and Shinoda, T. (2010). Non-molting glossy/shroud encodes a short-chain dehydrogenase/reductase that functions in the 'Black Box' of the ecdysteroid biosynthesis pathway. Development 137, 1991-1999.

  33. Kawaoka, S., Katsuma, S., Meng, Y., Hayashi, N., Mita, K., and Shimada, T. (2009). Identification and characterization of globin genes from two lepidopteran insects, Bombyx mori and Samia cynthia ricini. Gene 431, 33-38.

  34. Kawaoka, S., Hayashi, N., Suzuki, Y., Abe, H., Sugano, S., Tomari, Y., Shimada, T., and Katsuma, S. (2009). The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes. RNA 15, 1258-1264.

  35. Meng, Y., Omuro, N., Funaguma, S., Daimon, T., Kawaoka, S., Katsuma, S., and Shimada, T. (2008). Prominent down-regulation of storage protein genes after bacterial challenge in eri-silkworm, Samia cynthia ricini. Arch Insect Biochem Physiol 67, 9-19.

  36. Kawaoka, S., Minami, K., Katsuma, S., Mita, K., and Shimada, T. (2008). Developmentally synchronized expression of two Bombyx mori Piwi subfamily genes, SIWI and BmAGO3 in germ-line cells. Biochem Biophys Res Commun 367, 755-760.

  37. Kawaoka, S., Katsuma, S., Daimon, T., Isono, R., Omuro, N., Mita, K., and Shimada, T. (2008). Functional analysis of four Gloverin-like genes in the silkworm, Bombyx mori. Arch Insect Biochem Physiol 67, 87-96.

  38. Kawaoka, S., Hayashi, N., Katsuma, S., Kishino, H., Kohara, Y., Mita, K., and Shimada, T. (2008). Bombyx small RNAs: genomic defense system against transposons in the silkworm, Bombyx mori. Insect Biochem Mol Biol 38, 1058-1065.

  39. Katsuma, S., Kawaoka, S., Mita, K., and Shimada, T. (2008). Genome-wide survey for baculoviral host homologs using the Bombyx genome sequence. Insect Biochem Mol Biol 38, 1080-1086.

  40. Katsuma, S., Fujii, T., Kawaoka, S., and Shimada, T. (2008). Bombyx mori nucleopolyhedrovirus SNF2 global transactivator homologue (Bm33) enhances viral pathogenicity in B. mori larvae. J Gen Virol 89, 3039-3046.

  41. International Silkworm Genome Consortium. (2008). The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem Mol Biol 38, 1036-1045.

  42. 河岡慎平. (2024). がん悪液質再考: 最新研究に基づく定義の拡張. 実験医学. 3月号. 42, 4: 509-514.

  43. Cortez Natalia Erika、河岡慎平、Fabio Penna (2024). Cancer Cachexia: from bench to bedside. 実験医学. 3月号. 42, 4: 515-521.

  44. 中村有輝、小西理予、河岡慎平. (2024).がん患者における病的代謝・免疫変化の俯瞰. 実験医学. 3月号. 42, 4: 541-546.

  45. 小西理予、河岡慎平. (2023). エンハンサーRNA. 脳科学辞典

  46. 河岡慎平. (2023). がんが宿主の肝臓に異常をもたらすメカニズム. 医学のあゆみ. 284:23805-23806.

  47. 河岡慎平. (2023). がんに起因する宿主の病態生理に関わる代謝メカニズム. 生化学. 95: 91-95.

  48. 水野林、小林由佳、河岡慎平. (2021). 10xVisiumによる空間トランスクリプトーム解析. 実験医学. 39, 14: 2200-2204.

  49. 小西理予、河岡慎平. (2020). エンハンサーを利用した細胞の制御. 実験医学. 38, 17:100-106.

  50. 北條広朗、水野林、河岡慎平. (2020). マルチオミクスを活用したがん悪液質の理解. 実験医学. 38, 8:1300-1305.

  51. 河岡慎平、佐藤匠徳. (2017). iOrgansテクノロジーによる生体ビッグデータ構築とその活用による疾患の予測診断・先制治療・創薬. 学術の動向.  2017年7月号 p83-p87

  52. 荒井未来、河岡慎平. (2016). エンハンサーとエンハンサーRNA. DOJIN BIOSCIENCEシリーズ ノンコーディングRNA.

  53. 河岡慎平、泊幸秀. (2011). カイコ発: piRNAがつくられるしくみ. ライフサイエンス新着論文レビュー.

  54. 河岡慎平、嶋田透、勝間進. (2011). カイコの生殖巣に存在するsmall RNAの特性と機能． 蚕糸・昆虫バイオテック. 77(3): 219-225.

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