2025

• Wang W*, Kumegawa K*, Chapman O, Shiraishi R, Xiao Z, Okonechnikov K, Pfister S. M., Feng W, Uesaka N, Hoshino M, Chavez L, Maruyama R¶, Kawauchi D¶.
  Chromatin Modification Abnormalities by CHD7 and KMT2C Loss Promote Medulloblastoma Progression.
  Cell Rep in press. (*co-first, ¶co-corresponding)
  

2024

• Okazaki F, Yorozu A, Sekiguchi S, Niinuma T, Maruyama R, Kitajima H, Yamamoto E, Ishiguro K, Toyota M, Hatanaka Y, Nishiyama K, Ogi K, Kai M, Takano K, Ichimiya S, Miyazaki A, Suzuki H.
  AEBP1 is a negative regulator of skeletal muscle cell differentiation in oral squamous cell carcinoma.
  Sci Rep 2024;14:27425.
  

• Sakimoto Y*, Kumegawa K*, Matsui S, Yamaguchi T, Mukai T, Okabayashi K, Seiichi M, Kitagawa Y, Akiyoshi T, Maruyama R¶.
  Single-cell RNA-seq analysis of cancer-endothelial cell interactions in primary tumor and peritoneal metastasis from a single patient with colorectal cancer.
  BJC Reports 2024;2:88.(*co-first)
  

• Otsuji K, Takahashi Y, Osako T, Kobayashi T, Takano T, Saeki S, Yang L, Baba S, Kumegawa K, Suzuki H, Noda T, Takeuchi K, Ohno S, Ueno T, Maruyama R¶.
  Serial single-cell RNA sequencing unveils drug resistance and metastatic traits in stage IV breast cancer.
  NPJ Precis Oncol 2024;8;222.
  

• Shiraishi R*, Cancila G*, Kumegawa K*, Torrejon J, Basili I, Bernardi F, da Silva P. B. G., Wang W, Chapman O, Yang L, Jami M, Nishitani K, Arai Y, Xiao Z, Yu H, Lo Re V, Marsaud V, Talbot J, Lombard B, Loew D, Jingu M, Okonechnikov K, Sone M, Motohashi N, Aoki Y, Pfister S. M., Chavez L, Hoshino M, Maruyama R¶, Ayrault O¶, Kawauchi D¶.
  Cancer-Specific Epigenome Identifies Oncogenic Hijacking by Nuclear Factor I Family Proteins for Medulloblastoma Progression.
  Dev Cell 2024;59:2302-2319.e12. (*co-first, ¶co-corresponding)

• Gotoh O, Sugiyama Y, Tonooka A, Kitaura S, Minegishi R, Sano M, Amino S, Kosugi M, Furuya R, Tanaka N, Kaneyasu T, Kumegawa K, Abe A, Nomura H, Takazawa Y, Kanao H, Maruyama R, Noda T, Mori S.
  Genetic and epigenetic alterations in precursor lesions of endometrial endometrioid carcinoma.
  J Pathol. 2024;263:275-287.

• Maezawa M, Watanabe KI, Kobayashi Y, Yoshida K, Chambers JK, Uchida K, Maruyama R, Inokuma H.
  Diffuse large B-cell lymphoma with DNA copy number changes in a Japanese black calf.
  Vet Res Commun. 2024;48:2651-2656.

• Chuaychob S, Lyu R, Tanaka M, Haginiwa A, Kitada A, Nakamura T, Yokokawa R.
  Mimicking angiogenic microenvironment of alveolar soft-part sarcoma in a microfluidic coculture vasculature chip.
  Proc Natl Acad Sci U S A. 2024;121:e2312472121.

• Yang L*, Kumegawa K*¶, Sumito S, Nakadai T, Maruyama R¶.
  Identification of lineage-specific epigenetic regulators FOXA1 and GRHL2 through chromatin accessibility profiling in breast cancer cell lines.
  Cancer Gene Ther. 2024;31:736-745.(*co-first, ¶co-corresponding)

• Murayama T, Nakayama J, Jiang X, Miyata K, Morris AD, Cai KQ, Prasad RM, Ma X, Efimov A, Belani N, Gerstein ER, Tan Y, Zhou Y, Kim W, Maruyama R, Campbell KS, Chen L, Yang Y, Balachandran S, Cañadas I.
  Targeting DHX9 triggers tumor-intrinsic interferon response and replication stress in Small Cell Lung Cancer.
  Cancer Discov. 2024;14:468-491.

• Inoue F, Sone K, Kumegawa K, Toyohara Y, Tanimoto S, Natsumi T, Takahashi Y, Kusakabe M, Kukita A, Honjoh H, Nishijima A, Taguchi A, Miyamoto Y, Tanikawa M, Iriyama T, Uchino M, Wada-Hiraike O, Oda K, Suzuki H, Maruyama R, Osuga Y.
  Inhibition of protein arginine methyltransferase 6 activates interferon signaling and induces the apoptosis of endometrial cancer cells via histone modification.
  Int J Oncol. 2024;64:32.

• Iesato A, Fushimi A, Tahara R, Terada M, Iwase M, Kawamura C, Yamashita N.
  A novel system to provide information via online YouTube videos and an evaluation of current online information about hereditary breast cancer.
  Breast Cancer. 2024;31:63-74.

2023

• Chiba M, Miyata K, Okawa H, Tanaka Y, Ueda K, Seimiya H, Takahashi A.
  YBX1 Regulates Satellite II RNA Loading into Small Extracellular Vesicles and Promotes the Senescent Phenotype.
  Int J Mol Sci. 2023;24:16399.

• Mezawa Y, Wang T, Daigo Y, Atsushi T, Miyagi Y, Yokose T, Yamashita T, Yang L, Maruyama R, Seimiya H, Orimo A.
  Glutamine deficiency induces class I histone deacetylase activity that mediates TGF-β signaling activation and the myofibroblastic state in carcinoma-associated fibroblasts.
  Cancer Science. 2023;114:4376-4387.

• Koyama Y, Okazaki H, Yang S, Mezawa Y, Wang Z, Sakimoto M, Ishizuka A, Ito Y, Koyama T, Daigo Y, Takano A, Miyagi Y, Yokose T, Yamashita T, Sugahara K, Hino O, Yang L, Maruyama R, Katakura A, Yasukawa T, Orimo A.
  Increased RUNX3 expression mediates tumor-promoting ability of human breast cancer-associated fibroblasts.
  Cancer Medicine. 2023;12:18062-18077.

• Yi JM, Kang TH, Han YK, Park HY, Yang JH, Bae JH, Suh JS, Kim TJ, Kim JG, Cui YH, Suzuki H, Kumegawa K, Kim SJ, Zhao Y, Park IJ, Hong SM, Chung JY, Lee SJ.
  Human Neuralized is a novel tumour suppressor targeting Wnt/β-catenin signalling in colon cancer.
  EMBO Rep. 2023;24:e56335.

• Miyata K, Zhou X, Nishio M, Hanyu A, Chiba M, Kawasaki H, Osako T, Takeuchi K, Ohno S, Ueno T, Maruyama R, Takahashi A.
  Chromatin conformational changes at the human satellite II contribute to the senescence phenotype in the tumor microenvironment.
  Proc Natl Acad Sci USA. 2023;120:e2305046120.
  (pdf) (press_release)

• Kitajima H*, Maruyama R*, Niinuma T, Yamamoto E, Takasawa A, Takasawa K, Ishiguro K, Suzuki R, Tsuyada A, Idogawa M, Tange S, Toyota M, Yoshido A, Kumegawa K, Kai M, Tokino T, Osanai M, Nakase H, Suzuki H.
  TM4SF1-AS1 inhibits apoptosis through stress granule formation in cancer cells.
  Cell Death Dis. 2023;14:424.(*co-first)
  (pdf)

• Kumegawa K*¶, Yang L*, Miyata K, Maruyama R.
  FOXD1 is associated with poor outcome and maintains tumor-promoting enhancer-gene programs in basal-like breast cancer.
  Frontiers in Oncology. 2023;13:1156111.(*co-first)
  (github page) (pdf)

• Tanaka M¶, Homme M, Teramura Y, Kumegawa K, Yamazaki Y, Yamashita K, Osato M, Maruyama R, Nakamura T¶.
  HEY1-NCOA2 expression modulates chondrogenic differentiation and induces mesenchymal chondrosarcoma in mouse.
  JCI insight. 2023;8:e160279.(¶co-corresponding)
  (pdf) (summary) (press_release)

• Tanaka M, Nakamura T.
  Targeting epigenetic aberrations of sarcoma in CRISPR era.
  Genes Chromosomes Cancer. Online ahead of print.

• Tanaka M¶, Chuaychob S, Homme M, Yamazaki Y, Lyu R, Yamashita K, Ae K, Matsumoto S, Kumegawa K, Maruyama R, Qu W, Miyagi Y, Yokokawa R, Nakamura T¶.
  ASPSCR1–TFE3 orchestrates the angiogenic program of alveolar soft part sarcoma.
  Nature Communications. 2023;14:1957.(¶co-corresponding)
  (pdf) (press_release)

• Saeki S*, Kumegawa K*, Takahashi Y, Yang L, Osako T, Yasen M, Otsuji K, Miyata K, Yamakawa K, Suzuka J, Sakimoto Y, Ozaki Y, Takano T, Sano T, Noda T, Ohno S, Yao R, Ueno T, Maruyama R¶.
  Transcriptomic intratumor heterogeneity of breast cancer patient-derived organoids may reflect the unique biological features of the tumor of origin.
  Breast Cancer Research. 2023;25:21.(*co-first)
  (github page) (summary) (pdf)

• Kumegawa K*, Saeki S*, Takahashi Y*, Yang L, Osako T, Nakadai T, Mori S, Noda T, Ohno S, Ueno T, Maruyama R¶.
  Chromatin profiles identify a novel subgroup of ER-positive breast cancer with reduced accessibility of estrogen receptor responsive elements.
  British Journal of Cancer. 2023;128:1208-22. (*co-first)
  (github page) (summary) (pdf)

• Nakadai T, Shimada M, Ito K, Cevher MA, Chu CS, Kumegawa K, Maruyama R, Malik S, Roeder R.
  Two target gene activation pathways for orphan ERR nuclear receptors.
  Cell Research. 2023;33:165-83.

2022

• Nakadai T¶, Yang L, Kumegawa K, Maruyama R.
  ERα K303R mutation reorganizes its binding to FoxA1 regions and induces chromatin opening.
  Molecular Biology Reports. 2023;50:1209-20.

• Kumegawa K*, Takahashi Y*, Saeki S*, Yang L, Nakadai T, Osako T, Mori S, Noda T, Ohno S, Ueno T, Maruyama R¶.
  GRHL2 motif is associated with intratumor heterogeneity of cis-regulatory elements in luminal breast cancer.
  NPJ Breast Cancer. 2022;8:70.(*co-first)
  (github page)

• Ito K, Nagata K, Ohta S, Matsuda Y, Ukai T, Yasuda I, Ota A, Kobayashi R, Kabata M, Sankoda N, Maeda T, Woltjen K, Yang L, Maruyama R, Katayama R, Yamamoto T, Yamada Y.
  The oncogene-dependent resistance to reprogramming unveils cancer therapeutic targets.
  Cell Reports. 2022;39:110721.

2021

• Leonen CJA, Shimada M, Weller CE, Nakadai T, Hsu PL, Tyson EL, Mishra A, Shelton PMM, Sadilek M, Hawkins RD, Zheng N, Roeder RG, Chatterjee C.
  Sumoylation of the human histone H4 tail inhibits p300-mediated transcription by RNA polymerase II in cellular extracts.
  Elife. 2021;10:e67952.

• Hatanaka Y, Niinuma T, Kitajima H, Nishiyama K, Maruyama R, Ishiguro K, Toyota M, Yamamoto E, Kai M, Yorozu A, Sekiguchi S, Ogi K, Dehari H, Idogawa M, Sasaki Y, Tokino T, Miyazaki A, Suzuki H.
  DLEU1 promotes oral squamous cell carcinoma progression by activating interferon-stimulated genes.
  Sci Rep. 2021;11:20438.

• Miyata K, Imai Y, Hori S, Nishio M, Loo TM, Okada R, Yang L, Nakadai T, Maruyama R, Fujii R, Ueda K, Jiang L, Zheng H, Toyokuni S, Sakata T, Shirahige K, Kojima R, Nakayama M, Oshima M, Nagayama S, Seimiya H, Hirota T, Saya H, Hara E, Takahashi A.
  Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer.
  Proc Natl Acad Sci USA. 2021;118:e2025647118.

• Minegishi R, Gotoh O, Tanaka N, Maruyama R, Chang JT, Mori S.
  A method of sample-wise region-set enrichment analysis for DNA methylomics.
  Epigenomics. 2021;13:1081-1093.

• Niinuma T, Kitajima H, Yamamoto E, Maruyama R, Aoki H, Harada T, Ishiguro K, Sudo G, Toyota M, Yoshido A, Kai M, Nakase H, Sugai T, Suzuki H.
  An Integrated Epigenome and Transcriptome Analysis to Clarify the Effect of Epigenetic Inhibitors on GIST.
  Anticancer Res. 2021;41:2817-2828

• Horii R, Nitta H, Nojima M, Maruyama R, Ueno T, Ito Y, Ohno S, Banks B, Kanda H, Akiyama F.
  Predictive significance of HER2 intratumoral heterogeneity, determined by simultaneous gene and protein analysis, for resistance to trastuzumab-based treatments for HER2-positive breast cancer.
  Virchows Arch. 2021;479:13-21.

• Ishiguro K, Kitajima H, Niinuma T, Maruyama R, Nishiyama N, Sudo G, Toyota M, Yamamoto E, Kai M, Nakase H, Suzuki H.
  Dual EZH2 and G9a inhibition suppresses multiple myeloma cell proliferation by regulating the interferon signal and IRF4-MYC axis.
  Cell Death Discov. 2021;7:7.

• Seimiya T, Otsuka M, Iwata T, Tanaka E, Sekiba K, Shibata C, Moriyama M, Nakagawa R, Maruyama R, Koike K.
  Aberrant expression of a novel circular RNA in pancreatic cancer.
  J Human Genet. 2021;66:181-191.

2020

• Ochi M, Otsuka M, Maruyama R, Koike K.
  HBx increases EGFR expression by inhibiting miR129–5p function.
  Biochem Biophys Res Commun. 2020;529:198-203.

• Nozawa RS, Yamamoto T, Takahashi M, Tachiwana H, Maruyama R, Hirota T, Saitoh N.
  Nuclear Microenvironment in Cancer: Control Through Liquid-Liquid Phase Separation.
  Cancer Sci. 2020; 111:3155-3163
  

• Yorozu A, Yamamoto E, Niinuma T,Tsuyada A, Maruyama R, Kitajima H, Numata Y,Kai M, Sudo G, Kubo T, Nishidate T, Okita K, Takemasa I, Nakase H, Sugai T, Takano K, Suzuki H.
  Upregulation of AEBP1 in endothelial cells promotes tumor angiogenesis in colorectal cancer.
  Cancer Sci. 2020;111:1631-1644.

• Fujita R, Yamamoto T, Arimura Y, Fujiwara S, Tachiwana H, Ichikawa Y, Sakata Y, Yang L, Maruyama R, Hamada M, Nakao M, Saitoh N, Kurumizaka H.
  Nucleosome destabilization by nuclear non-coding RNAs.
  Commun Biol. 2020; 3:60.

2019

• Ohka F, Shinjo K, Deguchi S, Matsui Y, Okuno Y, Katsushima K, Suzuki M, Kato A, Ogiso N, Yamamichi A, Aoki K, Suzuki H, Sato S, Rayan NA, Prabhakar S, Göke J, Shimamura T, Maruyama R, Takahashi S, Suzumura A, Kimura H, Wakabayashi T, Zong H, Natsume A, Kondo Y. Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-wild-type Diffuse Astrocytic Gliomas. Cancer Res. 2019; 79:4814-4827.

• Niinuma T, Kitajima H, Kai M, Yamamoto E, Yorozu A, Ishiguro K, Sasaki H, Sudo G, Toyota M, Hatahira T, Maruyama R, Tokino T, Nakase H, Sugai T, Suzuki H. UHRF1 depletion and HDAC inhibition reactivate epigenetically silenced genes in colorectal cancer cells. Clin Epigenetics. 2019;11:70.

2018

• Johmura Y, Maeda I, Suzuki N, Wu W, Goda A, Morita M, Yamaguchi K, Yamamoto M, Nagasawa S, Kojima Y, Tsugawa K, Inoue N, Miyoshi Y, Osako T, Akiyama F, Maruyama R, Inoue J, Furukawa Y, Ohta T, Nakanishi M. Fbxo22-mediated KDM4B degradation determines selective estrogen receptor modulator activity in breast cancer. J Clin Invest. 2018;128:5603-5619.

• Wu W, Rokutanda N, Takeuchi J, Lai Y, Maruyama R, Togashi Y, Nishikawa H, Arai N, Miyoshi Y, Suzuki N, Saeki Y, Tanaka K, Ohta T. HERC2 promotes BLM and WRN to suppress G-quadruplex DNA. Cancer Res. 2018;78:6371-6385.

• Ishiguro K, Kitajima H, Niinuma T, Ishida T, Maruyama R, Ikeda H, Hayashi T, Sasaki H, Wakasugi H, Nishiyama K, Shindo T, Yamamoto E, Kai M, Sasaki Y, Tokino T, Nakase H, Suzuki H. DOT1L inhibition blocks multiple myeloma cell proliferation by suppressing IRF4-MYC signaling. Haematologica. 2018;191262.

• Nishiyama K, Maruyama R, Niinuma T, Kai M, Kitajima H, Toyota M, Hatanaka Y, Igarashi T, Kobayashi JI, Ogi K, Dehari H, Miyazaki A, Yorozu A, Yamamoto E, Idogawa M, Sasaki Y, Sugai T, Tokino T, Hiratsuka H, Suzuki H. Screening for long noncoding RNAs associated with oral squamous cell carcinoma reveals the potentially oncogenic actions of DLEU1. Cell Death Dis. 2018;9:826.

• Shindo T, Niinuma T, Nishiyama N, Shinkai N, Kitajima H, Kai M, Maruyama R, Tokino T, Masumori N, Suzuki H. Epigenetic silencing of miR-200b is associated with cisplatin resistance in bladder cancer. Oncotarget. 2018;9:24457-24469.

• Shindo T, Shimizu T, Nojima M, Niinuma T, Maruyama R, Kitajima H, Kai M, Itoh N, Suzuki H, Masumori N. Evaluation of Urinary DNA Methylation as a Marker for Recurrent Bladder Cancer: A 2-Center Prospective Study. Urology. 2018;113:71-78.

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