Gene mutation analysis using molecular-barcoding next-generation sequencer

• Project/Area Number: 17K10784
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Respiratory surgery
• Research Institution: Okayama University
• Principal Investigator: Tomida Shuta 岡山大学, 大学病院, 准教授 (10372111)
• Co-Investigator(Kenkyū-buntansha): 豊岡 伸一 岡山大学, 医歯薬学総合研究科, 教授 (30397880) ; 宗 淳一 岡山大学, 大学病院, 講師 (90559890)
• Project Period (FY): 2017-04-01 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2019: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2017: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: 分子バーコード / 次世代シーケンサー / 遺伝子変異解析 / 非小細胞肺癌 / EGFR / ALK / 肺癌 / co-mutation / VUS / compound mutation / 次世代シークエンサー / がんゲノム医療 / ターゲットシークエンス / 生体生命情報学 / ゲノム

Outline of Final Research Achievements

In this research, we examined the clinical usefulness of the next-generation sequencer analysis method using molecular barcode technology (molecular-barcoding NGS). After confirming the technical reproducibility of molecular-barcoding NGS, we applied it for 64 cases of lung adenocarcinoma with epithelial growth factor receptor (EGFR) mutation, and found that in 7 cases, the minor EGFR gene mutations, such as E709G/K, D761Y, G598V, and R776H, were detected.
We also applied the molecular-barcoding NGS method for a lung adenocarcinoma case with ALK fusion gene mutation, who showed resistance to the ALK inhibitor treatment. The ALK fusion gene mutation was detected in the sample obtained before treatment, and the gene mutation causing resistance to the ALK inhibitor was also detected in the sample obtained after treatment. Altogether these results showed clearly the clinical beneficial for the diagnosis of lung adenocarcinoma cases with EGFR and/or ALK mutation.

Academic Significance and Societal Importance of the Research Achievements

EGFRのG719Xを有する症例で統計学的に有意に複合変異（compound mutation）が検出されることが分かった。またTCGAのPan-Lung cancerデータセットから660症例の肺腺癌症例を抽出・解析したところ、同様の傾向が確認されたことから、G719X遺伝子変異陽性の肺腺癌症例に対する診断への応用が期待される。
ALK阻害剤治療に耐性を示し、急激に増悪した症例のサンプルの解析を実施したところ、治療後のサンプルからはALK阻害剤への耐性を示すALK G1202R変異を引き起こす遺伝子変異が検出されており、ALK融合遺伝子陽性の肺腺癌症例に対する診断への応用が期待される。

Research Products

• [Journal Article] YES1 activation induces acquired resistance to neratinib in HER2 ‐amplified breast and lung cancers (2020)
  • Author(s): Takeda Tatsuaki、Yamamoto Hiromasa、Suzawa Ken、Tomida Shuta、Miyauchi Shunsaku、Araki Kota、Nakata Kentaro、Miura Akihiro、Namba Kei、Shien Kazuhiko、Soh Junichi、Shien Tadahiko、Kitamura Yoshihisa、Sendo Toshiaki、Toyooka Shinichi
  • Journal Title: Cancer Science Volume: 111 Issue: 3 Pages: 849-856
  • DOI: 10.1111/cas.14289
  • NAID: 120006839439
  • Peer Reviewed / Open Access
• [Journal Article] Rapid Acquisition of Alectinib Resistance in ALK-Positive Lung Cancer With High Tumor Mutation Burden. (2019)
  • Author(s): Makimoto G, Ohashi K, Tomida S, Nishii K, Matsubara T, Kayatani H, Higo H, Ninomiya K, Sato A, Watanabe H, Kano H, Ninomiya T, Kubo T, Rai K, Ichihara E, Hotta K, Tabata M, Toyooka S, Takata M, Maeda Y, Kiura K.
  • Journal Title: J Thorac Oncol. Volume: 11 Issue: 11 Pages: 2009-2018
  • DOI: 10.1016/j.jtho.2019.07.017
  • NAID: 120006871852
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Acquired resistance mechanisms to afatinib in HER2-amplified gastric cancer cells (2019)
  • Author(s): Yoshioka, T. Shien, K. Takeda, T. Takahashi, Y. Kurihara, E. Ogoshi, Y. Namba, K. Torigoe, H. Sato, H. Tomida, S. Yamamoto, H. Soh, J. Fujiwara, T. Toyooka, S.
  • Journal Title: Cancer Sci Volume: 110 Issue: 8 Pages: 2549-2557
  • DOI: 10.1111/cas.14089
  • NAID: 120006816640
  • Peer Reviewed / Open Access
• [Journal Article] Clinical and immune profiling for cancer of unknown primary site. (2019)
  • Author(s): Haratani K, Hayashi H, Takahama T, Nakamura Y, Tomida S, Yoshida T, Chiba Y, Sawada T, Sakai K, Fujita Y, Togashi Y, Tanizaki J, Kawakami H, Ito A, Nishio K, Nakagawa K
  • Journal Title: Journal for immunotherapy of cancer Volume: 7 Issue: 1 Pages: 251-251
  • DOI: 10.1186/s40425-019-0720-z
  • Peer Reviewed / Open Access
• [Journal Article] Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naive lung adenocarcinoma (2019)
  • Author(s): Namba Kei、Tomida Shuta、Matsubara Takehiro、Takahashi Yuta、Kurihara Eisuke、Ogoshi Yusuke、Yoshioka Takahiro、Takeda Tatsuaki、Torigoe Hidejiro、Sato Hiroki、Shien Kazuhiko、Yamamoto Hiromasa、Soh Junichi、Tsukuda Kazunori、Toyooka Shinichi
  • Journal Title: BMC Cancer Volume: 19 Issue: 1 Pages: 1-9
  • DOI: 10.1186/s12885-019-5374-1
  • Peer Reviewed / Open Access
• [Journal Article] Activation of AXL as a Preclinical Acquired Resistance Mechanism Against Osimertinib Treatment in EGFR-Mutant Non-Small Cell Lung Cancer Cells (2019)
  • Author(s): Namba Kei、Shien Kazuhiko、Takahashi Yuta、Torigoe Hidejiro、Sato Hiroki、Yoshioka Takahiro、Takeda Tatsuaki、Kurihara Eisuke、Ogoshi Yusuke、Yamamoto Hiromasa、Soh Junichi、Tomida Shuta、Toyooka Shinichi
  • Journal Title: Molecular Cancer Research Volume: 17 Issue: 2 Pages: 499-507
  • DOI: 10.1158/1541-7786.mcr-18-0628
  • Peer Reviewed
• [Journal Article] Transduced caudal-type homeobox (CDX) 2/CDX1 can induce growth inhibition on CDX-deficient gastric cancer by rapid intestinal differentiation (2018)
  • Author(s): Nakayama Chiemi、Yamamichi Nobutake、Tomida Shuta、Takahashi Yu、Kageyama-Yahara Natsuko、Sakurai Kouhei、Takeuchi Chihiro、Inada Ken-ichi、Shiogama Kazuya、Nagae Genta、Ono Satoshi、Tsuji Yosuke、Niimi Keiko、Fujishiro Mitsuhiro、Aburatani Hiroyuki、Tsutsumi Yutaka、Koike Kazuhiko
  • Journal Title: Cancer Science Volume: 109 Issue: 12 Pages: 3853-3864
  • DOI: 10.1111/cas.13821
  • Peer Reviewed / Open Access
• [Journal Article] Comparative mutational evaluation of multiple lung cancers by multiplex oncogene mutation analysis (2018)
  • Author(s): Takahashi Yuta、Shien Kazuhiko、Tomida Shuta、Oda Shinsuke、Matsubara Takehiro、Sato Hiroki、Suzawa Ken、Kurihara Eisuke、Ogoshi Yusuke、Namba Kei、Yoshioka Takahiro、Torigoe Hidejiro、Yamamoto Hiromasa、Soh Junichi、Toyooka Shinichi
  • Journal Title: Cancer Science Volume: 109 Issue: 11 Pages: 3634-3642
  • DOI: 10.1111/cas.13797
  • Peer Reviewed / Open Access
• [Journal Article] Combined effect of cabozantinib and gefitinib in crizotinib-resistant lung tumors harboring ROS1 fusions (2018)
  • Author(s): Kato Yuka、Ninomiya Kiichiro、Ohashi Kadoaki、Tomida Shuta、Makimoto Go、Watanabe Hiromi、Kudo Kenichiro、Matsumoto Shingo、Umemura Shigeki、Goto Koichi、Ichihara Eiki、Ninomiya Takashi、Kubo Toshio、Sato Akiko、Hotta Katsuyuki、Tabata Masahiro、Toyooka Shinichi、Maeda Yoshinobu、Kiura Katsuyuki
  • Journal Title: Cancer Science Volume: 109 Issue: 10 Pages: 3149-3158
  • DOI: 10.1111/cas.13752
  • Peer Reviewed / Open Access
• [Journal Article] MET or NRAS amplification is an acquired resistance mechanism to the third-generation EGFR inhibitor naquotinib (2018)
  • Author(s): Ninomiya Kiichiro、Ohashi Kadoaki、Makimoto Go、Tomida Shuta、Higo Hisao、Kayatani Hiroe、Ninomiya Takashi、Kubo Toshio、Ichihara Eiki、Hotta Katsuyuki、Tabata Masahiro、Maeda Yoshinobu、Kiura Katsuyuki
  • Journal Title: Scientific Reports Volume: 8 Issue: 1 Pages: 1955-1955
  • DOI: 10.1038/s41598-018-20326-z
  • Peer Reviewed / Open Access
• [Journal Article] Therapeutic potential of targeting S100A11 in malignant pleural mesothelioma (2018)
  • Author(s): Sato Hiroki、Sakaguchi Masakiyo、Yamamoto Hiromasa、Tomida Shuta、Aoe Keisuke、Shien Kazuhiko、Yoshioka Takahiro、Namba Kei、Torigoe Hidejiro、Soh Junichi、Tsukuda Kazunori、Tao Hiroyuki、Okabe Kazunori、Miyoshi Shinichiro、Pass Harvey I.、Toyooka Shinichi
  • Journal Title: Oncogenesis Volume: 7 Issue: 1 Pages: 11-11
  • DOI: 10.1038/s41389-017-0017-3
  • Peer Reviewed / Open Access
• [Journal Article] Distinct dependencies on receptor tyrosine kinases in the regulation of MAPK signaling between BRAF V600E and non-V600E mutant lung cancers (2018)
  • Author(s): Kotani Hiroshi、Adachi Yuta、Kitai Hidenori、Tomida Shuta、Bando Hideaki、Faber Anthony C.、Yoshino Takayuki、Voon Dominic C.、Yano Seiji、Ebi Hiromichi
  • Journal Title: Oncogene Volume: 37 Issue: 13 Pages: 1775-1787
  • DOI: 10.1038/s41388-017-0035-9
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Therapeutic Potential of Afatinib for Cancers with ERBB2 (HER2) Transmembrane Domain Mutations G660D and V659E. (2018)
  • Author(s): Yamamoto H, Toyooka S, Ninomiya T, Matsumoto S, Kanai M, Tomida S, Kiura K, Muto M, Suzawa K, Desmeules P, Kris MG, Li BT, Ladanyi M.
  • Journal Title: Oncologist Volume: 23 Issue: 2 Pages: 150-154
  • DOI: 10.1634/theoncologist.2017-0345
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] PIK3R1Met326Ile germline mutation correlates with cysteine-rich protein 61 expression and poor prognosis in glioblastoma (2017)
  • Author(s): Otani Yoshihiro、Ishida Joji、Kurozumi Kazuhiko、Oka Tetsuo、Shimizu Toshihiko、Tomita Yusuke、Hattori Yasuhiko、Uneda Atsuhito、Matsumoto Yuji、Michiue Hiroyuki、Tomida Shuta、Matsubara Takehiro、Ichikawa Tomotsugu、Date Isao
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 7391-7391
  • DOI: 10.1038/s41598-017-07745-0
  • Peer Reviewed / Open Access
• [Presentation] 非小細胞肺癌におけるモネンシン併用療法によるEMT関連薬剤耐性の克服 (2019)
  • Author(s): 大智宏佑、諏澤憲、冨田秀太、豊岡伸一
  • Organizer: 第78回 日本癌学会学術総会
• [Presentation] 分子バーコード技術を用いた低頻度多重変異の同定 (2017)
  • Author(s): 難波圭、冨田秀太、枝園和彦、山本寛斉、宗淳一、佃和憲、豊岡伸一
  • Organizer: 日本癌学会学術総会