研究者詳細 - 松井　佑介

論文 - 松井　佑介

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理学療法におけるデータサイエンスとAIの利活用と課題理学療法の教育分野におけるデータサイエンスとAIの利活用と課題招待有り査読有り

松井佑介

理学療法 2022年4月

理学療法におけるデータサイエンスとAIの利活用と課題理学療法の教育分野におけるデータサイエンスとAIの利活用と課題招待有り

松井佑介

理学療法 39 巻 ( 4 ) 頁： 336 - 342 2022年4月

Meta-analysis integrated with multi-omics data analysis to elucidate pathogenic mechanisms of age-related knee osteoarthritis in mice. 査読有り国際共著国際誌 Open Access

Hirotaka Iijima, Gabrielle Gilmer, Kai Wang, Sruthi Sivakumar, Christopher Evans, Yusuke Matsui, Fabrisia Ambrosio

The journals of gerontology. Series A, Biological sciences and medical sciences 77 巻 ( 7 ) 頁： 1321 - 1334 2022年1月

記述言語：英語掲載種別：研究論文（学術雑誌）

Increased mechanistic insight into the pathogenesis of knee osteoarthritis (KOA) is needed to develop efficacious disease-modifying treatments. Though age-related pathogenic mechanisms are most relevant to the majority of clinically-presenting KOA, the bulk of our mechanistic understanding of KOA has been derived using surgically induced post-traumatic OA (PTOA) models. Here, we took an integrated approach of meta-analysis and multi-omics data analysis to elucidate pathogenic mechanisms of age-related KOA in mice. Protein-level data were integrated with transcriptomic profiling to reveal inflammation, autophagy, and cellular senescence as primary hallmarks of age-related KOA. Importantly, the molecular profiles of cartilage aging were unique from those observed following PTOA, with less than 3% overlap between the two models. At the nexus of the three aging hallmarks, Advanced Glycation End-Product (AGE)/Receptor for AGE emerged as the most statistically robust pathway associated with age-related KOA. This pathway was further supported by analysis of mass spectrometry data. Notably, the change in AGE-RAGE signaling over time was exclusively observed in male mice, suggesting sexual dimorphism in the pathogenesis of age-induced KOA in murine models. Collectively, these findings implicate dysregulation of AGE-RAGE signaling as a sex-dependent driver of age-related KOA.

DOI： 10.1093/gerona/glab386

PubMed

Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin. 招待有り査読有り

Dai Shimizu, Kenzui Taniue, Yusuke Matsui, Hiroshi Haeno, Hiromitsu Araki, Fumihito Miura, Mitsuko Fukunaga, Kenji Shiraishi, Yuji Miyamoto, Seiichi Tsukamoto, Aya Komine, Yuta Kobayashi, Akihiro Kitagawa, Yukihiro Yoshikawa, Kuniaki Sato, Tomoko Saito, Shuhei Ito, Takaaki Masuda, Atsushi Niida, Makoto Suzuki, Hideo Baba, Takashi Ito, Nobuyoshi Akimitsu, Yasuhiro Kodera, Koshi Mimori

Cancer gene therapy 2021年11月

Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin. 査読有り国際誌

Cancer gene therapy 29 巻 ( 5 ) 頁： 428 - 436 2021年11月

記述言語：英語掲載種別：研究論文（学術雑誌）

The accurate and early diagnosis and classification of cancer origin from either tissue or liquid biopsy is crucial for selecting the appropriate treatment and reducing cancer-related mortality. Here, we established the CAncer Cell-of-Origin (CACO) methylation panel using the methylation data of the 28 types of cancer in The Cancer Genome Atlas (7950 patients and 707 normal controls) as well as healthy whole blood samples (95 subjects). We showed that the CACO methylation panel had high diagnostic potential with high sensitivity and specificity in the discovery (maximum AUC = 0.998) and validation (maximum AUC = 1.000) cohorts. Moreover, we confirmed that the CACO methylation panel could identify the cancer cell type of origin using the methylation profile from liquid as well as tissue biopsy, including primary, metastatic, and multiregional cancer samples and cancer of unknown primary, independent of the methylation analysis platform and specimen preparation method. Together, the CACO methylation panel can be a powerful tool for the classification and diagnosis of cancer.

DOI： 10.1038/s41417-021-00401-w

PubMed

Increased BUB1B/BUBR1 expression contributes to aberrant DNA repair activity leading to resistance to DNA-damaging agents. 招待有り査読有り Open Access

Kazumasa Komura, Teruo Inamoto, Takuya Tsujino, Yusuke Matsui, Tsuyoshi Konuma, Kazuki Nishimura, Taizo Uchimoto, Takeshi Tsutsumi, Tomohisa Matsunaga, Ryoichi Maenosono, Yuki Yoshikawa, Kohei Taniguchi, Tomohito Tanaka, Hirofumi Uehara, Koichi Hirata, Hajime Hirano, Hayahito Nomi, Yoshinobu Hirose, Fumihito Ono, Haruhito Azuma

Oncogene 2021年9月

Increased BUB1B/BUBR1 expression contributes to aberrant DNA repair activity leading to resistance to DNA-damaging agents. 査読有り国際誌 Open Access

Oncogene 40 巻 ( 43 ) 頁： 6210 - 6222 2021年9月

記述言語：英語掲載種別：研究論文（学術雑誌）

There has been accumulating evidence for the clinical benefit of chemoradiation therapy (CRT), whereas mechanisms in CRT-recurrent clones derived from the primary tumor are still elusive. Herein, we identified an aberrant BUB1B/BUBR1 expression in CRT-recurrent clones in bladder cancer (BC) by comprehensive proteomic analysis. CRT-recurrent BC cells exhibited a cell-cycle-independent upregulation of BUB1B/BUBR1 expression rendering an enhanced DNA repair activity in response to DNA double-strand breaks (DSBs). With DNA repair analyses employing the CRISPR/cas9 system, we revealed that cells with aberrant BUB1B/BUBR1 expression dominantly exploit mutagenic nonhomologous end joining (NHEJ). We further found that phosphorylated ATM interacts with BUB1B/BUBR1 after ionizing radiation (IR) treatment, and the resistance to DSBs by increased BUB1B/BUBR1 depends on the functional ATM. In vivo, tumor growth of CRT-resistant T24R cells was abrogated by ATM inhibition using AZD0156. A dataset analysis identified FOXM1 as a putative BUB1B/BUBR1-targeting transcription factor causing its increased expression. These data collectively suggest a redundant role of BUB1B/BUBR1 underlying mutagenic NHEJ in an ATM-dependent manner, aside from the canonical activity of BUB1B/BUBR1 on the G2/M checkpoint, and offer novel clues to overcome CRT resistance.

DOI： 10.1038/s41388-021-02021-y

Open Access

PubMed

RoDiCE: robust differential protein co-expression analysis for cancer complexome. 招待有り査読有り国際誌 Open Access

Yusuke Matsui, Yuichi Abe, Kohei Uno, Satoru Miyano

Bioinformatics (Oxford, England) 2021年9月

記述言語：英語掲載種別：研究論文（学術雑誌）

MOTIVATION: The full spectrum of abnormalities in cancer-associated protein complexes remains largely unknown. Comparing the co-expression structure of each protein complex between tumor and healthy cells may provide insights regarding cancer-specific protein dysfunction. However, the technical limitations of mass spectrometry-based proteomics, including contamination with biological protein variants, causes noise that leads to non-negligible over- (or under-) estimating co-expression. RESULTS: We propose a robust algorithm for identifying protein complex aberrations in cancer based on differential protein co-expression testing. Our method based on a copula is sufficient for improving identification accuracy with noisy data compared to conventional linear correlation-based approaches. As an application, we use large-scale proteomic data from renal cancer to show that important protein complexes, regulatory signaling pathways and drug targets can be identified. The proposed approach surpasses traditional linear correlations to provide insights into higher-order differential co-expression structures. AVAILABILITY AND IMPLEMENTATION: https://github.com/ymatts/RoDiCE. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI： 10.1093/bioinformatics/btab612

PubMed

Pre-stimulus alpha oscillation and post-stimulus cortical activity differ in localization between consciously perceived and missed near-threshold somatosensory stimuli. 招待有り査読有り国際誌 Open Access

Jun-Ichi Uemura, Aiko Hoshino, Go Igarashi, Yusuke Matsui, Makoto Chishima, Minoru Hoshiyama

The European journal of neuroscience 54 巻 ( 4 ) 頁： 5518 - 5530 2021年8月

記述言語：英語掲載種別：研究論文（学術雑誌）

Conscious perception of a near-threshold (NT) stimulus is characterized by the pre- and post-stimulus brain state. However, the power of pre-stimulus neural oscillations and strength of post-stimulus cortical activity that lead to conscious perception have rarely been examined in individual cortical areas. This is because most previous electro- and magnetoencephalography (EEG and MEG, respectively) studies involved scalp- and sensor-level analyses. Therefore, we recorded MEG during a continuous NT somatosensory stimulus detection task and applied the reconstructed source data in order to identify cortical areas where the post-stimulus cortical activity and pre-stimulus alpha oscillation predict the conscious perception of NT somatosensory stimuli. We found that the somatosensory hierarchical processing areas, prefrontal areas and cortical areas belonging to the default mode network showed stronger cortical activity for consciously perceived trials in the post-stimulus period, but the cortical activity in primary somatosensory area (SI) is independent of conscious perception during the early stage of NT stimulus processing. In addition, we revealed that the pre-stimulus alpha oscillation only in SI is predictive of conscious perception. These findings suggest that the bottom-up stream of somatosensory information flow following SI and pre-stimulus alpha activity fluctuation in SI as a top-down modulation are crucial constituents of conscious perception.

DOI： 10.1111/ejn.15388

PubMed

An in vitro coculture system of human peripheral blood mononuclear cells with hepatocellular carcinoma-derived cells for predicting drug-induced liver injury 査読有り国際誌

Oda Shingo, Uchida Yuka, Aleo Michael D., Koza-Taylor Petra H., Matsui Yusuke, Hizue Masanori, Marroquin Lisa D., Whritenour Jessica, Uchida Eri, Yokoi Tsuyoshi

ARCHIVES OF TOXICOLOGY 95 巻 ( 1 ) 頁： 149 - 168 2020年8月

EXOSC9 depletion attenuates P-body formation, stress resistance, and tumorigenicity of cancer cells 査読有り国際誌 Open Access

Yoshino Seiko, Matsui Yusuke, Fukui Yuya, Seki Masahide, Yamaguchi Kiyoshi, Kanamori Akane, Saitoh Yurika, Shimamura Teppei, Suzuki Yutaka, Furukawa Yoichi, Kaneko Shuichi, Seiki Motoharu, Murakami Yoshinori, Inoue Jun-ichiro, Sakamoto Takeharu

SCIENTIFIC REPORTS 10 巻 ( 1 ) 頁： 9275 - 9275 2020年6月

Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells 査読有り国際誌 Open Access

Higashijima Yoshiki, Matsui Yusuke, Shimamura Teppei, Nakaki Ryo, Nagai Nao, Tsutsumi Shuichi, Abe Yohei, Link Verena M., Osaka Mizuko, Yoshida Masayuki, Watanabe Ryo, Tanaka Toshihiro, Taguchi Akashi, Miura Mai, Ruan Xiaoan, Li Guoliang, Inoue Tsuyoshi, Nangaku Masaomi, Kimura Hiroshi, Furukawa Tetsushi, Aburatani Hiroyuki, Wada Youichiro, Ruan Yijun, Glass Christopher K., Kanki Yasuharu

EMBO JOURNAL 39 巻 ( 7 ) 頁： e103949 2020年4月

Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-Wild-Type Diffuse Astrocytic Gliomas. 査読有り国際誌 Open Access

Fumiharu Ohka, Keiko Shinjo, Shoichi Deguchi, Yusuke Matsui, Yusuke Okuno, Keisuke Katsushima, Miho Suzuki, Akira Kato, Noboru Ogiso, Akane Yamamichi, Kosuke Aoki, Hiromichi Suzuki, Shinya Sato, Nirmala Arul Rayan, Shyam Prabhakar, Jonathan Göke, Teppei Shimamura, Reo Maruyama, Satoru Takahashi, Akio Suzumura, Hiroshi Kimura, Toshihiko Wakabayashi, Hui Zong, Atsushi Natsume, Yutaka Kondo

Cancer research 79 巻 ( 19 ) 頁： 4814 - 4827 2019年10月

記述言語：英語掲載種別：研究論文（学術雑誌）

Gliomas are classified by combining histopathologic and molecular features, including isocitrate dehydrogenase (IDH) status. Although IDH-wild-type diffuse astrocytic glioma (DAG) shows a more aggressive phenotype than IDH-mutant type, lack of knowledge regarding relevant molecular drivers for this type of tumor has hindered the development of therapeutic agents. Here, we examined human IDH-wild-type DAGs and a glioma mouse model with a mosaic analysis with double markers (MADM) system, which concurrently lacks p53 and NF1 and spontaneously develops tumors highly comparable with human IDH-wild-type DAG without characteristic molecular features of glioblastoma (DAG-nonMF). During tumor formation, enhancer of zeste homolog (EZH2) and the other polycomb repressive complex 2 (PRC2) components were upregulated even at an early stage of tumorigenesis, together with an increased number of genes with H3K27me3 or H3K27me3 and H3K4me3 bivalent modifications. Among the epigenetically dysregulated genes, frizzled-8 (Fzd8), which is known to be a cancer- and stem cell reprogramming-related gene, was gradually silenced during tumorigenesis. Genetic and pharmacologic inhibition of EZH2 in MADM mice showed reactivation of aberrant H3K27me3 target genes, including Fzd8, together with significant reduction of tumor size. Our study clarifies a pathogenic molecular pathway of IDH-wild-type DAG-nonMF that depends on EZH2 activity and provides a strong rationale for targeting EZH2 as a promising therapeutic approach for this type of glioma. SIGNIFICANCE: EZH2 is involved in the generation of IDH-wild-type diffuse astrocytic gliomas and is a potential therapeutic target for this type of glioma. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/79/19/4814/F1.large.jpg.

DOI： 10.1158/0008-5472.CAN-19-1272

PubMed

A network of networks approach for modeling interconnected brain tissue-specific networks. 査読有り Open Access

Kawakubo H, Matsui Y, Kushima I, Ozaki N, Shimamura T

Bioinformatics (Oxford, England) 35 巻 ( 17 ) 頁： 3092 - 3101 2019年9月

Tumor subclonal progression model for cancer hallmark acquisition 査読有り

Y MATSUI, S MIYANO, T SHIMAMURA

Lecture Notes in Bioinformatics 10834 巻頁： 115 - 123 2019年

GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics 査読有り

T SHIMAMURA, Y MATSUI, S MIYANO

Lecture Notes in Bioinformatics 10834 巻頁： 124 - 137 2019年

A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer. 査読有り国際誌 Open Access

Tomoko Saito, Atsushi Niida, Ryutaro Uchi, Hidenari Hirata, Hisateru Komatsu, Shotaro Sakimura, Shuto Hayashi, Sho Nambara, Yosuke Kuroda, Shuhei Ito, Hidetoshi Eguchi, Takaaki Masuda, Keishi Sugimachi, Taro Tobo, Haruto Nishida, Tsutomu Daa, Kenichi Chiba, Yuichi Shiraishi, Tetsuichi Yoshizato, Masaaki Kodama, Tadayoshi Okimoto, Kazuhiro Mizukami, Ryo Ogawa, Kazuhisa Okamoto, Mitsutaka Shuto, Kensuke Fukuda, Yusuke Matsui, Teppei Shimamura, Takanori Hasegawa, Yuichiro Doki, Satoshi Nagayama, Kazutaka Yamada, Mamoru Kato, Tatsuhiro Shibata, Masaki Mori, Hiroyuki Aburatani, Kazunari Murakami, Yutaka Suzuki, Seishi Ogawa, Satoru Miyano, Koshi Mimori

Nature communications 9 巻 ( 1 ) 頁： 2884 - 2884 2018年7月

記述言語：英語掲載種別：研究論文（学術雑誌）

Advanced colorectal cancer harbors extensive intratumor heterogeneity shaped by neutral evolution; however, intratumor heterogeneity in colorectal precancerous lesions has been poorly studied. We perform multiregion whole-exome sequencing on ten early colorectal tumors, which contained adenoma and carcinoma in situ. By comparing with sequencing data from advanced colorectal tumors, we show that the early tumors accumulate a higher proportion of subclonal driver mutations than the advanced tumors, which is highlighted by subclonal mutations in KRAS and APC. We also demonstrate that variant allele frequencies of subclonal mutations tend to be higher in early tumors, suggesting that the subclonal mutations are subject to selective sweep in early tumorigenesis while neutral evolution is dominant in advanced ones. This study establishes that the evolutionary principle underlying intratumor heterogeneity shifts from Darwinian to neutral evolution during colorectal tumor progression.

DOI： 10.1038/s41467-018-05226-0

Open Access

Web of Science

PubMed

ER stress signaling promotes the survival of cancer "Persister Cells" tolerant to EGFR tyrosine Kinase inhibitors 査読有り Open Access

Hideki Terai, Shunsuke Kitajima, Danielle S. Potter, Yusuke Matsui, Laura Gutierrez Quiceno, Ting Chen, Tae-Jung Kim, Maria Rusan, Tran C. Thai, Federica Piccioni, Katherine A. Donovan, Nicholas Kwiatkowski, Kunihiko Hinohara, Guo Wei, Nathanael S. Gray, Eric S. Fischer, Kwok-Kin Wong, Teppei Shimamura, Anthony Letai, Peter S. Hammerman, David A. Barbie

Cancer Research 78 巻 ( 4 ) 頁： 1044 - 1057 2018年2月

Identification of Cardiomyocyte-Fated Progenitors from Human-Induced Pluripotent Stem Cells Marked with CD82 査読有り Open Access

Masafumi Takeda, Yasuharu Kanki, Hidetoshi Masumoto, Shunsuke Funakoshi, Takeshi Hatani, Hiroyuki Fukushima, Akashi Izumi-Taguchi, Yusuke Matsui, Teppei Shimamura, Yoshinori Yoshida, Jun K. Yamashita

Cell Reports 22 巻 ( 2 ) 頁： 546 - 556 2018年

ハイブリッドサイエンスの新時代〜生命科学とデータ科学を繋ぐ〜ゲノムワイドCRISPRスクリーニングによるEGFR-TKI+転写阻害剤相乗作用の分子機構の理解

寺井秀樹, Potter Danielle, 北嶋俊輔, 松井佑介, Kim Tae-Jung, Rusan Maria, Thai Tran, Piccioni Federica, Donovan Katherine, Kwiatkowski Nicholas, 日野原邦彦, Wei Guo, Gray Nathanael, Fischer Eric, 島村徹平, Letai Anthony, Hammerman Peter, Barbie David

生命科学系学会合同年次大会 2017年度巻頁： [1PW08 - 6] 2017年12月

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論文 - 松井　佑介