動的なゲノムシステムとしてのがん病態における分子ネットワーク異常の解明

2011 Fiscal Year Annual Research Report

• Project Area: Integrative Systems Understanding of Cancer for Advanced Diagnosis, Therapy and Prevention
• Project/Area Number: 23134508
• Research Institution: National Cancer Center Japan
• Principal Investigator: 柴田 龍弘 独立行政法人国立がん研究センター, 研究所, 分野長 (90311414)
• Keywords: がん / ゲノム / エピゲノム / 統合解析 / 転移

Research Abstract

本研究は、がんの悪性度に関連するゲノム変化を時系列の視点から包括的に解析することを目的としている。今年度は以下の2つの研究を遂行した。
1.進行乳がんの原発巣並びにリンパ節転移病変における全エクソン解読
3症例トリオ(進行乳がん原発腫瘍、リンパ節転移腫瘍、非腫瘍部)から顕微鏡下に腫瘍細胞を単離し、DNA抽出後、全エクソンを濃縮し、高速シークエンサーによる解読を行った。原発腫瘍3検体においてアミノ酸置換を生じる遺伝子塩基置換(nonsynonymous変異)またはスプライシング部位における塩基置換を56遺伝子に、リンパ節転移腫瘍3検体においては107遺伝子に予測した。3検体のうち1検体を除いてリンパ節転移腫瘍の方が原発腫瘍よりも2倍近い数の遺伝子変異が予測された。
2.ChIPシークエンス解析を用いた乳がん細胞株におけるポリコーム複合体標的探索
EZH2はポリコーム複合体を形成し、ヒストン3の27番目のリジン残基(H3K27)をトリメチル化してエピジェネテックな転写抑制を行う。乳がん細胞株HCC1143の細胞抽出液からEZH2抗体とH3K27トリメチル化抗体による免疫沈降を行い、濃縮された結合DNA断片を解読した。ゲノム配列上へマッピングされたDNA断片からEZH2とH3K27トリメチル化の結合ピークをFDR(False Discovery Rate)値0.05未満の条件でそれぞれ検出し、両者に共通する1414個の近傍遺伝子を同定した。

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

当初計画をほぼ予定通り進めている。乳がんにおけるゲノム・エピゲノムデータを先行して集計する目的で、平成24年度に行う予定であった乳がん細胞株のChIPシークエンス解析を前倒しで行った。平成23年度計画にあった膵がん検体の解析についても、すでに着手している。

Strategy for Future Research Activity

1.乳がんのリンパ節転移に関わる遺伝子変異の特異性や共通性をより明確に分類する目的で、追加症例トリオのエクソンシークエンス解析を実施する。更に膵がん検体の解析を進める。また、同定した遺伝子変異について、多数検体を用いて候補遺伝子変異の出現頻度を測定する。
2.ChIPシークエンスに加えて発現解析や上記変異解析データを統合して、乳がんの進行に関連する新たな分子パスウエイ解析を進める。

Research Products

• [Journal Article] Induction of ZEB by inactivation of RB is a key determinant of the mesenchymal phenotype of breast cancer (2012)
  • Author(s): Arima Y, Hayashi H, Sasaki M, Hosonaga M, Goto TM, Chiyoda T, Kuninaka S, Shibata T, Ohata H, Nakagama H, Taya Y, Sata H
  • Journal Title: J.Bio Chem. Volume: 287 Pages: 7896-7906
  • Peer Reviewed
• [Journal Article] KIF5B-RET fusions in lung adenocarcinoma (2012)
  • Author(s): Kohno T, Ichikawa H, Totoki Y, Yasuda K, Hiramoto M, Nammo T, Sakamoto H, Tsuta K, Furuta K, Shimada Y, Iwakawa R, Ogiwara H, Oike T, Enari M, Schetter AJ, Okayama H, Haugen A, Skaug V, Chiku S, Yamanaka I, Watanabe S, Sekine I, Ogawa S, Harris CC, Tsuda H, Yoshida T, Yokota J, Shibata T
  • Journal Title: Nature Med Volume: 18 Pages: 375-377
  • Peer Reviewed
• [Journal Article] Identification of Genes Up-regulated in ALK-positive and EGFR/KRAS/ALK-negat ive Lung Adenocarcinomas (2012)
  • Author(s): Okayama H, Kohno T, Ishii Y, Shimada Y, Shiraishi K, Iwakawa R, Furuta K, Tsuta K, Shibata T, Yamamoto S, Watanabe S, Sakamoto H, Kumamoto K, Takenoshita S, Gotoh N, Mizuno H, Sarai A, Kawano S, Yamaguchi R, Miyano S, Yokota J
  • Journal Title: Cancer Res Volume: 72 Pages: 100-111
  • Peer Reviewed
• [Journal Article] MDM2 and CDK4 Immunohistochemical Coexpress ion in High-Grade Osteosarcoma : Correlation with a Dedifferentiated Subtype (2012)
  • Author(s): Yoshida A, Ushiku T, Motoi T, Beppu Y, Fukayama M, Tsuda H, Shibata T
  • Journal Title: Am J Surg Pathol Volume: 36 Pages: 423-431
  • Peer Reviewed
• [Journal Article] Important histologic outcome predictors for patients with invasive ductal carcinoma of the breast (2011)
  • Author(s): Hasebe T, Iwasaki M, Akashi-Tanaka S, Hojo T, Shibata T, Kinoshita T, Tsuda H
  • Journal Title: Am J Surg Pathol Volume: 35 Pages: 1484-1497
  • Peer Reviewed
• [Journal Article] Pfetin as a prognostic biomarker for gastrointestinal stromal tumor : Validation study in multiple clinical facilities (2011)
  • Author(s): Kubota D, Orita H, Yoshida A, Gotoh M, Kanda T, Tsuda H, Hasegawa T,Katai H, Shimada Y, Kaneko K,Kawai A, Suehara Y, Kikuta K, Sato K, Tochigi N, Seki K, Shibata T, Toyama Y, Beppu Y, Kondo T
  • Journal Title: Jpn J Clin Oncol Volume: 41 Pages: 1194-1202
  • Peer Reviewed
• [Journal Article] Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency (2011)
  • Author(s): Wang L, Tsutsumi S, Kawaguchi T, Nagasaki K, Tatsuno K, Yamamoto S, Sang F, Sonoda K, Sugawara M, Hirono S, Yamaue H, Miki Y, Isomura M, Totoki Y, Nagae G, Isagawa T, Hiroki U, Murayama-Hosokawa S, Shibata T, Sakamoto H, Kanai Y, Kaneda A, Noda T, Aburatani H
  • Journal Title: Genome Res Volume: 22 Pages: 208-219
  • Peer Reviewed
• [Journal Article] Modified primary tumour/vessel tumour/nodal tumour classification for patients with invasive ductal carcinoma of the breast (2011)
  • Author(s): Hasebe T, Iwasaki M, Akashi-Tanaka S, Hojo T, Shibata T, Sasajima Y, Kinoshita T, Tsuda H
  • Journal Title: Br J Cancer Volume: 105 Pages: 698-708
  • Peer Reviewed
• [Journal Article] Prognostic significance of mitotic figures in metastatic mammary ductal carcinoma to the lymph nodes (2011)
  • Author(s): Hasebe T, Iwasaki M, Akashi-Tanaka S, Hojo T, Shibata T, Sasajima Y, Kinoshita T, Tsuda H
  • Journal Title: Hum Pathol Volume: 42 Pages: 1823-1832
  • Peer Reviewed
• [Journal Article] NRF2 mutation confers malignant potential and resistance to chemoradiation therapy in advanced esophageal squamous cancer (2011)
  • Author(s): Shibata T, Kokubu A, Saito S, Narisawa-Saito N, Sasaki H, Aoyagi K, Yoshimatsu Y, Tachimori Y, Kushima R, Kiyono T, Yamamoto M
  • Journal Title: Neoplasia Volume: 13 Pages: 864-873
  • Peer Reviewed
• [Journal Article] Maintenance of tumor initiating cells of defined genetic composition by a complex composed of nucleostemin, hTERT and BRG1 (2011)
  • Author(s): Okamoto N, Yasukawa M, Nguyen C, Kasim V, Maida Y, Possemato R, Shibata T, Ligon K, Fukami K, Hahn W, Masutomi K
  • Journal Title: Proc Natl Acad Sci USA Volume: 108 Pages: 20388-20393
  • Peer Reviewed
• [Journal Article] Bright-field dual-color chromogenic in situ hybridization for diagnosing echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase-positive lung adenocarcinomas (2011)
  • Author(s): Yoshida A, Tsuta K, Nitta H, Hatanaka Y, Asamura H, Sekine I, Grogan TM, Fukayama M, Shibata T, Furuta K, Kohno T, Tsuda H
  • Journal Title: Journal of Thoracic Oncology Volume: 6 Pages: 1677-1686
  • Peer Reviewed
• [Journal Article] Comprehensive histological analysis of ALK-rearranged lung carcinomas (2011)
  • Author(s): Yoshida A, Tsuta K, Nakamura H, Kohno T, Takahashi F, Asamura H, Sekine I, Fukayama M, Shibata T, Furuta K, Tsuda H
  • Journal Title: Am J Surg Pathol Volume: 35 Pages: 1226-1234
  • Peer Reviewed
• [Journal Article] Genome-wide DNA methylation profiles in renal tumors of various histological subtypes and non-tumorous renal tissues (2011)
  • Author(s): Arai E, Wakai-Ushijima S, Fujimoto H, Hosoda F, Shibata T, Kondo T, Yokoi S, Imoto I, Inazawa J, Hirohashi S, Kanai Y
  • Journal Title: Pathobiology Volume: 78 Pages: 1-9
  • Peer Reviewed
• [Journal Article] Role for piRNAs and a novel non-coding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus (2011)
  • Author(s): Watanabe T, Tomizawa S, Mitsuya K, Totoki Y, Yamamoto Y, Kuramochi-Miyagawa S, Iida N, Hoki Y, Murphy PJ, Toyoda A, Gotoh K, Hiura H, Arima T, Fujiyama A, Sado T, Shibata T, Nakano T, Lin H, Ichiyanagi K, Soloway PD, Sasaki H
  • Journal Title: Science Volume: 332 Pages: 848-852
  • Peer Reviewed
• [Journal Article] High-resolution characterization of a hepatocellular carcinoma genome (2011)
  • Author(s): Totoki Y, Tatsuno K, Yamamoto S, Arai Y, Hosoda F, Ishikawa S, Tsustumi S, Sonoda K, Totsuka H, Shirakihara T, Sakamoto H, Wang L, Ojima H, Shimada K, Kosuge T, Okusaka T, Kato K, Kusuda J, Yoshida T, Aburatani H, Shibata T
  • Journal Title: Nat Genet Volume: 43 Pages: 464-469
  • Peer Reviewed
• [Journal Article] Cancer susceptibility polymorphism of p53 at codon 72 affects phopshorylation and degradation of p53 protein (2011)
  • Author(s): Ozeki C, Sawai Y, Shibata T, Kohno T, Okamoto K, Yokota J, Tashiro F, Tanuma S, Sakai R, Kawase T, Kitabayashi I, Taya Y, Ohki R
  • Journal Title: J.Bio Chem. Volume: 286 Pages: 18251-18260
  • Peer Reviewed
• [Journal Article] Prognostic significance of overexpression of c-Met oncoprotein in cholangiocarcinoma (2011)
  • Author(s): Miyamoto M, Ojima H, Iwasaki M, Shimizu H, Kokubu A, Hiraoka N, Kosuge T, Yoshikawa D, Kono T, Furukawa H, Shibata T
  • Journal Title: Br J Cancer Volume: 105 Pages: 131-138
  • Peer Reviewed
• [Journal Article] Atypical tumor-stroma fibroblasts in the invasive ductal carcinomas of the breast (2011)
  • Author(s): Hasebe T, Iwasaki M, Akashi-Tanaka S, Hojo T, Shimizu S, Andoh M, Shibata T, Sasajima Y, Kinoshita T, Tsuda H
  • Journal Title: Am J Surg Pathol Volume: 35 Pages: 325-336
  • Peer Reviewed
• [Journal Article] MotoPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline (2011)
  • Author(s): Watanabe T, Chuma S, Yamamoto Y, Kuramochi-Miyagawa S, Totoki Y, Toyoda A, Hoki Y, Fujiyama A, Shibata T, Sado T, Noce T, Nakatsuji N, Lin H, Sasaki H
  • Journal Title: Dev Cell Volume: 20 Pages: 364-375
  • Peer Reviewed
• [Journal Article] Copy number alterations in urothelial carcinomas : Their clinicopathological significance and correlation with DNA methylation alterations (2011)
  • Author(s): Nishiyama N, Arai E, Nagashio R, Fujimoto H, Hosoda F, Shibata T, Tsukamoto T, Yokoi Y, Imoto I, Inazawa J, Kanai Y
  • Journal Title: Carcinogenesis Volume: 32 Pages: 462-469
  • Peer Reviewed
• [Journal Article] Mutant IDH1 confers an in vivo growth in a melanoma cell line with BRAF mutation (2011)
  • Author(s): Shibata T, Kokubu A, Miyamoto M, Sasajima Y, Yamazaki Y
  • Journal Title: Am J Pathol Volume: 178 Pages: 1395-1402
  • Peer Reviewed
• [Journal Article] TGF-b regulates isoform switching of FGF receptors and epithelial-mesenchymal transition (2011)
  • Author(s): Shirakihara T, Horiguchi K, Miyazawa K, Ehata S, Shibata T, Morita I, Miyazono K, Saitoh M
  • Journal Title: EMBO J Volume: 30 Pages: 783-795
  • Peer Reviewed
• [Journal Article] Atypical tumor-stromal fibroblasts in invasive ductal carcinomas of the breast treated with neoadjuvant therapy (2011)
  • Author(s): Hasebe T, Iwasaki M, Akashi-Tanaka S, Hojo T, Shimizu S, Andoh M, Fujiwara Y, Shibata T, Sasajima Y, Kinoshita T, Tsuda H
  • Journal Title: Human.Pathol. Volume: 42 Pages: 998-1006
  • Peer Reviewed
• [Journal Article] A histopathological study for evaluation of therapeutic effects of radiofrequency ablation in patients with breast cancer (2011)
  • Author(s): Tsuda H, Seki K, Hasebe T, Sasajima Y, Shibata T, Iwamoto E, Kinoshita T
  • Journal Title: Breast Cancer Volume: 18 Pages: 24-32
  • Peer Reviewed
• [Presentation] Discovering the cancer genome signatures by whole genome sequencing (2012)
  • Author(s): 柴田龍弘
  • Organizer: Next-generation sequencing application Asia
  • Place of Presentation: シンガポール(招待講演)
  • Year and Date: 2012-03-29
• [Presentation] Multiple epigenetic remodeling in hepatocellular carcinoma (2012)
  • Author(s): 柴田龍弘
  • Organizer: The 15^<th> US-Japan Cellular and Gene Therapy Conference on Epigenetics in cancer
  • Place of Presentation: 米国(ワシントン)
  • Year and Date: 2012-02-23
• [Presentation] Whole genome and transcriptome sequencing shapes the picture of cancer genome towards the personalized medicine (2012)
  • Author(s): 柴田龍弘
  • Organizer: 駐日英国大使館セミナー
  • Place of Presentation: 東京(招待講演)
  • Year and Date: 2012-02-13
• [Presentation] 全ゲノム解読から見える新たながんゲノム像 (2012)
  • Author(s): 柴田龍弘
  • Organizer: 第3次対がん10カ年総合戦略・文科省がん支援活動合同公開シンポジウム
  • Place of Presentation: 東京(招待講演)
  • Year and Date: 2012-01-31
• [Presentation] Whole genome sequencing analysis of virus-associated hapatocellular carcinoma (2011)
  • Author(s): 柴田龍弘
  • Organizer: 9^<th> China-Japan joint conference of cancer
  • Place of Presentation: 中国(上海)(招待講演)
  • Year and Date: 2011-12-23
• [Presentation] Whole genome sequencing analysis of virus-associated hepatocellular carcinoma (2011)
  • Author(s): 柴田龍弘
  • Organizer: 第3回グローバルCOE国際シンポジウム
  • Place of Presentation: 名古屋(招待講演)
  • Year and Date: 2011-12-08
• [Presentation] Genome Sequencing Analysis of Virus-associated Hepatocellular carcinoma (2011)
  • Author(s): 柴田龍弘
  • Organizer: デンマーク大使館主催ライフサイエンスセミナー
  • Place of Presentation: 東京(招待講演)
  • Year and Date: 2011-10-26
• [Presentation] Whole genome sequencing of virus-associated hepatocellular carcinoma (2011)
  • Author(s): 柴田龍弘
  • Organizer: The U.S.-Japan Cooperative Cancer Research Program Workshop
  • Place of Presentation: 京都(招待講演)
  • Year and Date: 2011-10-25
• [Presentation] Integrated genome and transcriptome sequencing analyses of virus-associated hepatocellular carcinoma (2011)
  • Author(s): 柴田龍弘
  • Organizer: EMBO/EMBL Symposium
  • Place of Presentation: ドイツ(ハイデルベルグ)(招待講演)
  • Year and Date: 2011-10-19
• [Presentation] Whole genome sequencing analysis of virus-associated hepatocellular carcinoma (2011)
  • Author(s): 柴田龍弘
  • Organizer: 第70回日本癌学会
  • Place of Presentation: 名古屋
  • Year and Date: 2011-10-04
• [Presentation] Integrated genome and transcriptome sequencing analyses of virus-associated hepatocellular carcinoma (2011)
  • Author(s): 柴田龍弘
  • Organizer: The 9^<th> International Workshop on Advanced Genomics
  • Place of Presentation: 東京(招待講演)
  • Year and Date: 2011-07-13
• [Presentation] 肝がんにおけるmicroRNA生合成経路因子の発現異常とその制御 (2011)
  • Author(s): 柴田龍弘
  • Organizer: 第100回日本病理学会総会
  • Place of Presentation: 横浜
  • Year and Date: 2011-04-28