Intra-single cell analysis clarifies the mechanism of bone remodeling and improves prognosis of hip fractures

• Project/Area Number: 22KK0272
• Research Category: Fund for the Promotion of Joint International Research (Fostering Joint International Research (A))
• Allocation Type: Multi-year Fund
• Review Section: Basic Section 56020:Orthopedics-related
• Research Institution: The University of Tokyo
• Principal Investigator: Okada Hiroyuki 東京大学, 大学院医学系研究科(医学部), 助教 (10883481)
• Project Period (FY): 2022 – 2024
• Project Status: Completed (Fiscal Year 2024)
• Budget Amount: ¥15,470,000 (Direct Cost: ¥11,900,000、Indirect Cost: ¥3,570,000)
• Keywords: 破骨細胞 / 骨免疫 / １細胞解析 / トランスクリプトーム / 1細胞内解析 / リアルワールドデータ / 次世代シーケンサー / 骨代謝

Outline of Research at the Start

我々が開発したiSC-seq(intra-single cell sequencing)により同一細胞「内」にまで存在する遺伝子発現不均一性エピジェネティクス制御機構を解明する。
骨リモデリングに関わる多細胞系を理解し、新たな骨折修復促進因子を同定する。
1細胞内解析技術をコア技術として、国際的共同研究を加速する。骨形成側の主に骨細胞の知見と、骨吸収側の破骨細胞の知見をマッチさせることによって、骨リモデリングに関わる多細胞系の全容解明につなげる。

Outline of Final Research Achievements

The intracellular analysis technique, iSCseq, has enabled gene expression analysis at subcellular resolution within living cells. In osteoclast research; studies involving multinucleated giant cells responsible for bone resorption; cell differentiation and cell fusion have previously been discussed interchangeably. However, iSCseq now allows these processes to be separately addressed. This advancement provides foundational insights necessary for developing osteoporosis therapies specifically targeting cell fusion.

To enhance international recognition of iSCseq technology as a method for capturing gene expression dynamics in living cells, we delivered oral presentations at the American Society for Bone and Mineral Research (ASBMR) and the American Society for Cell Biology (Cell Bio), receiving positive feedback. Moving forward, we will continue our global outreach efforts, promoting this Japanese-origin sequencing technology internationally.

Academic Significance and Societal Importance of the Research Achievements

超高齢社会日本において、骨粗しょう症を背景とした骨脆弱性骨折は増加の一途を辿っている。特に骨折後の二次骨折予防は喫緊の課題である。しかし、急速に骨量を改善し、かつ腎不全などの併存疾患があっても安全に使用できる薬剤は、現時点では存在しておらず、骨粗鬆症治療の案メットニーズになっていた。
本研究で開発した手法により骨吸収を担う破骨細胞の新たな細胞融合機序が明らかになる可能性が高い。新たな骨粗鬆症薬開発の基盤となる研究プラットフォーム開発を本国際共同研究で推進することができた。

Research Products

• [Int'l Joint Research] Harvard University(米国) (2023)
• [Journal Article] Synergistic effects of estrogen deficiency and articular disk derangement on condylar bone loss (2025)
  • Author(s): Kazuhiro Shibusaka、Soichiro Negishi、Nobuhiro Sakai、Youngkwan Kim、Hiroyuki Okada、Fumiko Yano
  • Journal Title: Journal of Oral Biosciences Volume: 67 Issue: 1 Pages: 100616-100616
  • DOI: 10.1016/j.job.2025.100616
  • Peer Reviewed
• [Journal Article] Modeling vascular dynamics at the initial stage of endochondral ossification on a microfluidic chip using a human embryonic-stem-cell-derived organoid (2025)
  • Author(s): Kesharwani Abhiraj、Tani Shoichiro、Nishikawa Masaki、Sakai Yasuyuki、Okada Hiroyuki、Ohba Shinsuke、Chung Ung-il、Hojo Hironori
  • Journal Title: Regenerative Therapy Volume: 28 Pages: 90-100
  • DOI: 10.1016/j.reth.2024.11.018
  • Peer Reviewed / Open Access
• [Journal Article] CD34hi subset of synovial fibroblasts contributes to fibrotic phenotype of human knee osteoarthritis (2025)
  • Author(s): Miyahara J、Omata Y、Chijimatsu R、Okada H、Ishikura H、Higuchi J、Tachibana N、Nagata K、Tani S、Kono K、Kawaguchi K、Yamagami R、Inui H、Taketomi S、Iwanaga Y、Terashima A、Yano F、Seki M、Suzuki Y、Baron R、Tanaka S、Saito T
  • Journal Title: JCI Insight Volume: 10 Issue: 2
  • DOI: 10.1172/jci.insight.183690
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Osteogenic differentiation capabilities of multiarm PEG hydrogels: involvement of gel-gel-phase separation in cell differentiation (2024)
  • Author(s): Si Jinyan、Ishikawa Shohei、Nepal Shant、Okada Hiroyuki、Chung Ung-il、Sakai Takamasa、Hojo Hironori
  • Journal Title: Polymer Journal Volume: 57 Issue: 4 Pages: 407-417
  • DOI: 10.1038/s41428-024-00955-0
  • Peer Reviewed
• [Journal Article] Exploring the role of DNMT1 in dental papilla cell fate specification during mouse tooth germ development through integrated single-cell transcriptomics and bulk RNA sequencing (2024)
  • Author(s): Eldeeb Dahlia、Okada Hiroyuki、Suzuki Yutaka、Seki Masahide、Tanaka Junichi、Mishima Kenji、Chung Ung-il、Ohba Shinsuke、Hojo Hironori
  • Journal Title: Journal of Oral Biosciences Volume: 66 Issue: 3 Pages: 530-538
  • DOI: 10.1016/j.job.2024.06.010
  • Peer Reviewed
• [Journal Article] Baricitinib ameliorates inflammatory and neuropathic pain in collagen antibody-induced arthritis mice by modulating the IL-6/JAK/STAT3 pathway and CSF-1 expression in dorsal root ganglion neurons (2024)
  • Author(s): Makabe Kenta、Okada Hiroyuki、Tachibana Naohiro、Ishikura Hisatoshi、Ito Norihito、Tanaka Masaru、Chijimatsu Ryota、Terashima Asuka、Yano Fumiko、Asaka Meiko、Yanagihara Dai、Taketomi Shuji、Matsumoto Takumi、Tanaka Sakae、Omata Yasunori、Saito Taku
  • Journal Title: Arthritis Research & Therapy Volume: 26 Issue: 1 Pages: 121-121
  • DOI: 10.1186/s13075-024-03354-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Practical Compass of Single-Cell RNA-Seq Analysis (2023)
  • Author(s): Okada Hiroyuki、Chung Ung-il、Hojo Hironori
  • Journal Title: Current Osteoporosis Reports Volume: - Issue: 5 Pages: 433-440
  • DOI: 10.1007/s11914-023-00840-4
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] intra-single cell sequencing (iSCseq) spotlights transcriptomic and epigenetic heterogeneity inside multinucleated osteoclast (2022)
  • Author(s): Okada Hiroyuki、Terui Yuta、Omata Yasunori、Seki Masahide、Tani Shoichiro、Miyahara Junya、Makabe Kenta、Terashima Asuka、Kanazawa Sanshiro、Hosonuma Masahiro、Yano Fumiko、Kajiya Hiroshi、Saito Taku、Suzuki Yutaka、Okabe Koji、Baron Roland、Tanaka Sakae、Chung Ung-il、Hojo Hironori
  • Journal Title: bioRxiv Volume: 0 Pages: 0-0
  • DOI: 10.1101/2022.09.05.506360
  • Open Access / Int'l Joint Research
• [Journal Article] Offset nail fixation for intertrochanteric fractures improves reduction and lag screw position (2022)
  • Author(s): Matsubara Takehiro、Soma Kazuhito、Yamada Ikufumi、Fujita Hiroshi、Yoshitani Junya、Oka Hiroyuki、Okada Hiroyuki、Tanaka Sakae
  • Journal Title: PLOS ONE Volume: 17 Issue: 11 Pages: 0276903-0276903
  • DOI: 10.1371/journal.pone.0276903
  • Peer Reviewed / Open Access
• [Journal Article] Runx2 and Runx3 differentially regulate articular chondrocytes during surgically induced osteoarthritis development (2022)
  • Author(s): Nagata K, Hojo H, Chang SH, Okada H, Chijimatsu R, Omata Y, Mori D, Makii Y, Kawata M, Kaneko T, Iwanaga Y, Nakamoto H, Maenohara Y, Tachibana N, Ishikura H, Higuchi J, Taniguchi Y, Ohba S, Chung Ul, Tanaka S, Saito T
  • Journal Title: Nature Communications Volume: 13 Issue: 1 Pages: 6187-6204
  • DOI: 10.1038/s41467-022-33744-5
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Runx2 regulates chromatin accessibility to direct the osteoblast program at neonatal stages (2022)
  • Author(s): Hojo Hironori, Saito Taku, He Xinjun, Guo Qiuyu, Onodera Shoko, Azuma Toshifumi, Koebis Michinori, Nakao Kazuki, Aiba Atsu, Seki Masahide, Suzuki Yutaka, Okada Hiroyuki, Tanaka Sakae, Chung Ung-il, McMahon Andrew P., Ohba Shinsuke
  • Journal Title: Cell Reports Volume: 40 Issue: 10 Pages: 111315-111315
  • DOI: 10.1016/j.celrep.2022.111315
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] RSPO2 defines a distinct undifferentiated progenitor in the tendon/ligament and suppresses ectopic ossification (2022)
  • Author(s): Tachibana N、Chijimatsu R、Okada H、Oichi T、Taniguchi Y、Maenohara Y、Miyahara J、Ishikura H、Iwanaga Y、Arino Y、Nagata K、Nakamoto H、Kato S、Doi T、Matsubayashi Y、Oshima Y、Terashima A、Omata Y、Yano F、Maeda S、Ikegawa S、Seki M、Suzuki Y、Tanaka S、Saito T
  • Journal Title: Science Advances Volume: 8 Issue: 33 Pages: 2138-2154
  • DOI: 10.1126/sciadv.abn2138
  • Peer Reviewed / Open Access
• [Journal Article] Hematopoietic-Mesenchymal Signals Regulate the Properties of Mesenchymal Stem Cells (2022)
  • Author(s): Kanazawa Sanshiro、Okada Hiroyuki、Riu Dan、Mabuchi Yo、Akazawa Chihiro、Iwata Junichi、Hoshi Kazuto、Hikita Atsuhiko
  • Journal Title: International Journal of Molecular Sciences Volume: 23 Issue: 15 Pages: 8238-8238
  • DOI: 10.3390/ijms23158238
  • Peer Reviewed / Open Access
• [Journal Article] Single-cell RNA sequencing unravels heterogeneity of skeletal progenitors and cell-cell interactions underlying the bone repair process (2022)
  • Author(s): Nakayama Mika、Okada Hiroyuki、Seki Masahide、Suzuki Yutaka、Chung Ung-il、Ohba Shinsuke、Hojo Hironori
  • Journal Title: Regenerative Therapy Volume: 21 Pages: 9-18
  • DOI: 10.1016/j.reth.2022.05.001
  • Peer Reviewed / Open Access
• [Journal Article] Interspecies Single‐Cell RNA‐Seq Analysis Reveals the Novel Trajectory of Osteoclast Differentiation and Therapeutic Targets (2022)
  • Author(s): Omata Yasunori、Okada Hiroyuki、Uebe Steffen、Izawa Naohiro、Ekici Arif B.、Sarter Kerstin、Saito Taku、Schett Georg、Tanaka Sakae、Zaiss Mario M.
  • Journal Title: JBMR Plus Volume: 6 Issue: 7 Pages: 10631-10645
  • DOI: 10.1002/jbm4.10631
  • Peer Reviewed / Open Access
• [Presentation] 硬組織をマルチオミクスで掘ってみた新世界 (2025)
  • Author(s): 岡田寛之, 他
  • Organizer: iSeminar
  • Invited
• [Presentation] 1 生細胞内シーケンスから破骨細胞の成り立ちを考える (2024)
  • Author(s): 岡田寛之, 他
  • Organizer: 筋・骨・リウマチ3学会合同若手研究会
• [Presentation] Advancing single cell technology: iSCseq drives living subcellular transcriptomic profiling in osteoclast (2024)
  • Author(s): Hiroyuki Okada, et al.
  • Organizer: Nature Conference “Spatiotemporal regulation of metabolism”
  • Int'l Joint Research
• [Presentation] Advancing Single-Cell Technology: Exploring Diverse Osteoclast Subsets (2024)
  • Author(s): Hiroyuki Okada, et al.
  • Organizer: SSBH 2024
  • Int'l Joint Research / Invited
• [Presentation] Bioadaptive injection base produced by multiomics (2024)
  • Author(s): Hiroyuki Okada, et al.
  • Organizer: 第9回日本骨免疫学会
• [Presentation] 生きた細胞内シーケンスで迫る破骨細胞内ネットワーク (2024)
  • Author(s): 岡田寛之, 他
  • Organizer: 第42回日本骨代謝学会
  • Invited
• [Presentation] Osteocyte Subsets through the Lens of Subcellular Spatial and Interspecies Single Cell Atlas-level Transcriptomics for Bone (2024)
  • Author(s): Hiroyuki Okada, et al.
  • Organizer: ASBMR 2024 Annual Meeting
  • Int'l Joint Research
• [Presentation] 面倒なシングルセル解析はChatGPTにやらせよう (2024)
  • Author(s): 岡田寛之
  • Organizer: NGS expo 2024
  • Invited
• [Presentation] マルチオミクスがバイオアダプティブ注射基剤を創出する (2024)
  • Author(s): 岡田寛之, 他
  • Organizer: NGS expo 2024
• [Presentation] 年齢別好発部位を「見える化」する骨折リアルワールドデータ (2024)
  • Author(s): 岡田寛之, 他
  • Organizer: 第26回日本骨粗鬆症学会
• [Presentation] Bioadaptive Injection Base Created by Multiomics (2024)
  • Author(s): Hiroyuki Okada, et al.
  • Organizer: 1st Asia&Pacific Bioinformatics Joint Conference ～JSBi, GIW, InCoB, APBC, and ISCB-Asia～
  • Int'l Joint Research
• [Presentation] バイオアダプティブ注射基剤を創出するマルチオミクス (2024)
  • Author(s): 岡田寛之, 他
  • Organizer: 第97回日本生化学会
• [Presentation] 2種のサブセルラートランスクリプトームで硬組織を深掘り (2024)
  • Author(s): 岡田寛之, 他
  • Organizer: 第47回日本分子生物学会
  • Invited
• [Presentation] Bone-deep insights from Single Cell and Subcellular Spatial Transcriptomics (2024)
  • Author(s): Hiroyuki Okada, et al.
  • Organizer: KSBMR-JSBMR-ANZBMS-ISBMR-ICMRS Joint Webinar: Innovative Solutions in MSF
  • Int'l Joint Research / Invited
• [Presentation] Inclusive Living Subcellular Sequencing by iSCseq Rendering Physical, Physiological and Pathological Features in Osteoclast Diversity. (2024)
  • Author(s): H. Okada, Y. Terui, Y. Omata, M. Seki, S. Tani, A. Terashima, S. Kanazawa, M. Hosonuma, J. Miyahara, K. Makabe, S. Onodera, F. Yano, H. Kajiya, F. Gori, T. Saito, K. Okabe, Y. Suzuki, R. Baron, U. Chung, S. Tanaka, H. Hojo.
  • Organizer: Gordon Research Conference “Bones and Teeth” 2024
  • Int'l Joint Research
• [Presentation] Inclusive living subcellular sequencing spotlights physical physiological and human pathological features in osteoimmune diversity. (2024)
  • Author(s): Hiroyuki Okada, Yuta Terui, Asuka Terashima, Masahide Seki, Sanshiro Kanazawa, Francesca Gori, Taku Saito, Yutaka Suzuki, Roland Baron, Ung-il Chung, Sakae Tanaka, Hironori Hojo.
  • Organizer: AGBT 2024
  • Int'l Joint Research
• [Presentation] Inclusive living subcellular sequencing clarifies physical physiological and human pathological features in osteoimmune diversity. (2024)
  • Author(s): Okada H, Terui Y, Terashima A, Gori F, Suzuki Y, Baron R, Chung UI, Tanaka S, Hojo H.
  • Organizer: Discover BMB 24
  • Int'l Joint Research
• [Presentation] 破骨細胞のデジタルハック; シングルセルを超えてサブセルラーへ (2023)
  • Author(s): 岡田 寛之, 照井 悠太, 小俣 康徳, 関 真秀, 谷 彰一郎, 宮原 潤也, 真壁 健太, 寺島 明日香, 金澤 三四朗, 細沼 雅弘, 矢野 文子, 小野寺 晶子, 鍛治屋 浩, 斎藤 琢, 鈴木 穣, 岡部 幸司, Roland Baron, 田中 栄, 鄭 雄一, 北條 宏徳
  • Organizer: 第8回日本骨免疫学会
  • Invited
• [Presentation] SS2000は生サブセルラーシーケンスを可能に (2023)
  • Author(s): 岡田 寛之
  • Organizer: 第75回日本細胞生物学会
  • Invited
• [Presentation] 運動器発のサブセルラーシーケンスで細胞生物学の常識に挑む (2023)
  • Author(s): 岡田 寛之, 照井 悠太, 小俣 康徳, 関 真秀, 谷 彰一郎, 宮原 潤也, 真壁 健太, 寺島 明日香, 金澤 三四朗, 細沼 雅弘, 矢野 文子, 小野寺 晶子, 鍛治屋 浩, 斎藤 琢, 鈴木 穣, 岡部 幸司, Roland Baron, 田中 栄, 鄭 雄一, 北條 宏徳
  • Organizer: 第41回日本骨代謝学会
  • Invited
• [Presentation] Subcellular sequencing by iSCseq connects transcriptomics with morphological, physical, and physiological findings (2023)
  • Author(s): Hiroyuki Okada, Yuta Terui, Masahide Seki, Yutaka Suzuki, Roland Baron, Ung-il Chung, Sakae Tanaka, Hironori Hojo
  • Organizer: Cell symposia “The conceptual power of single cell biology” 2023
  • Int'l Joint Research
• [Presentation] Interventional and integrative subcellular sequencing (i2scseq) clarifies the multi differentiation stages embedded inside mature osteoclast (2023)
  • Author(s): Hiroyuki Okada *, Yuta Terui , Yasunori Omata, Masahide Seki , Shoichiro Tani, Junya Miyahara, Kenta Makabe, Asuka Terashima, Sanshiro Kanazawa, Masahiro Hosonuma, Shoko Onodera, Fumiko Yano, Hiroshi Kajiya, Taku Saito, Yutaka Suzuki, Koji Okabe, Roland Baron, Sakae Tanaka, Ung-il Chung, Hironori Hojo
  • Organizer: ASBMR 2023
  • Int'l Joint Research
• [Presentation] 1生細胞内シーケンスで多核巨細胞の遺伝子発現制御に挑む (2023)
  • Author(s): 岡田 寛之, 照井 悠太, 小俣 康徳, 関 真秀, 谷 彰一郎, 宮原 潤也, 真壁 健太, 寺島 明日香, 金澤 三四朗, 細沼 雅弘, 矢野 文子, 小野寺 晶子, 鍛治屋 浩, 斎藤 琢, 鈴木 穣, 岡部 幸司, Roland Baron, 田中 栄, 鄭 雄一, 北條 宏徳
  • Organizer: 第96回日本生化学会
  • Invited
• [Presentation] Subcellular sampling and sequencing by iSCseq connects transcriptomics with morphological, physical, and physiological findings in osteoimmunology. (2023)
  • Author(s): Hiroyuki Okada *, Yuta Terui , Yasunori Omata, Masahide Seki , Shoichiro Tani, Junya Miyahara, Kenta Makabe, Asuka Terashima, Sanshiro Kanazawa, Masahiro Hosonuma, Shoko Onodera, Fumiko Yano, Hiroshi Kajiya, Taku Saito, Yutaka Suzuki, Koji Okabe, Roland Baron, Sakae Tanaka, Ung-il Chung, Hironori Hojo.
  • Organizer: Cold Spring Harbor Laboratory Meeting “Single Cell Analyses 2023”
  • Int'l Joint Research
• [Presentation] Subcellular sequencing connects transcriptomics with physical and physiological findings. (2023)
  • Author(s): H. Okada, Y. Terui, Y. Omata, M. Seki, S. Tani, A. Terashima, S. Kanazawa, M. Hosonuma, J. Miyahara, K. Makabe, S. Onodera, F. Yano, H. Kajiya, F. Gori, T. Saito, K. Okabe, Y. Suzuki, R. Baron, U. Chung, S. Tanaka, H. Hojo.
  • Organizer: Cell Bio 2023
  • Int'l Joint Research
• [Presentation] The gene expression and epigenetic regulation of individual nuclei within the same multinucleated osteoclast is heterogeneous: Evidence from Intra-single cell sequencing (iscSeq) (2022)
  • Author(s): Hiroyuki Okada
  • Organizer: 第45回日本分子生物学会年会
• [Presentation] intra-single cell sequencing( iSC-seq )による破骨細胞の多核間制御メカニズム解明 (2022)
  • Author(s): Hiroyuki Okada
  • Organizer: 第9回日本リウマチ学会ベーシックリサーチカンファ
• [Presentation] The gene expression and epigenetic regulation of individual nuclei within the same osteoclast is heterogeneous: Evidence from Intra-single cell sequencing (iscSeq) (2022)
  • Author(s): Hiroyuki Okada
  • Organizer: 第95回日本生化学大会
• [Presentation] intra-single cell sequencing（iSC-seq）による破骨細胞の多核間制御メカニズム解明 (2022)
  • Author(s): Hiroyuki Okada
  • Organizer: NGSexpo2022
• [Presentation] The gene expression and epigenetic regulation of individual nuclei within the same osteoclast is heterogeneous: Evidence from Intra-single cell sequencing (iscSeq) (2022)
  • Author(s): Hiroyuki Okada
  • Organizer: ASBMR2022
  • Int'l Joint Research
• [Presentation] 1細胞骨アトラス作成とその利活用 (2022)
  • Author(s): Hiroyuki Okada
  • Organizer: 第40回日本骨代謝学会
• [Presentation] 1細胞骨アトラスによるskeletal diseases病因解明 (2022)
  • Author(s): Hiroyuki Okada
  • Organizer: 第7回日本骨免疫学会
• [Presentation] 病的骨折の手術は骨軟部腫瘍専門医がするべきなのか？ Surgery for Pathological limb fracture should be performed by all the orthopaedic surgeons (2022)
  • Author(s): Hiroyuki Okada
  • Organizer: 第95回日本整形外科学会
  • Invited
• [Remarks] 東京大学医学系研究科疾患生命工学センター 臨床医工学部門
  • URL: https://www.cdbim.m.u-tokyo.ac.jp/research/laboratory04/