Annual Report 2023

Division of Cellular Signaling

Shinji Kohsaka, Toshihide Ueno, Yosuke Tanaka, Hiroyuki Mano

Introduction

 Through an approach combining high-sensitivity functional screening with next-generation sequencing analysis, we aim to elucidate the development mechanism of human tumors and develop novel molecular targeted therapies.

The Team and What We Do

• Identification of tumorigenesis and development of new drugs through comprehensive genome analysis.
• Establishment of functional assay to evaluate gene alterations.
• Development of new computational pipelines for cancer research.

Research Activities

 Comprehensive analysis of malignant tumor specimens was performed using next-generation sequencing technology in collaboration with clinical practice to study the nature of the tumors. Some of the findings could be translated into clinical practice. The main results were as follows.

1) Comprehensive molecular profiling of gliomas

 To classify gliomas and identify their molecular targets using TOP2-RNA, a custom-targeted RNA sequencing (RNA-seq), a total of 124 frozen samples of malignant gliomas were subjected to TOP2-RNA for classification based on molecular profiles and identification of molecular targets. of the 55 glioblastoma cases, gene fusions were detected in 11 cases (20%), including novel MET fusions. Astrocytomas and oligodendrogliomas showed little fusion or gene overexpression; molecular profiling with TOP2-RNA may provide predictive, prognostic, and diagnostic biomarkers for drug response and increase treatment options for individual glioma patients, as reported in a research article (Shirai Y. et al, 167, 1, 75-88, J Neurooncol. 2024).

2) Functional analysis of sarcoma fusion genes

 Sarcomas are malignant mesenchymal tumors and are extremely rare and diverse. Fusion genes are involved as driver oncogenes in approximately 30% of sarcomas, but their detailed functions are not fully understood. In this study, we have clarified the functional significance of 59 sarcoma-associated fusion genes. The transformation ability and drug sensitivity of these fusion genes were evaluated using the Focus formation assay (FFA) and Mixed-all-nominated-in-one (MANO) methods, respectively, and reported in a research article (Hirose T, et al. 114, 10, 4089- 4100, Cancer Sci. 2023).

3) Biomarker search for MDM2 inhibitors in endometrial sarcoma

 Intimal sarcoma is an extremely rare, malignant neoplasm in which amplification of Murine double minute 2 (MDM2) is observed in over 70% of patients, and the MDM2 inhibitor mirademetan may provide clinical benefit to this patient population. We conducted a phase Ib/II study in patients with MDM2-amplified, wild-type TP53 intimal sarcoma as a substudy of a large national registry of rare cancers in Japan. of the 11 patients enrolled, 10 were included in the efficacy analysis; 2 (20%) had durable responses of 15 months or longer. Acquired TP53 mutations were detected by serial liquid biopsies as a novel exploratory resistance mechanism to mirademetan. Mirademetan was shown to be a potential therapeutic strategy for intimal sarcoma and is reported in a research article (Koyama T, et al. 13, 8, 1814-1825. Cancer Discov. 2023).

4) Functional analysis of BRCA2 variants of unknown significance

 Ten Japanese patients from seven families with breast or ovarian cancer carrying the BRCA2 p.Ser2616Phe variant interpreted as VUS were reported. The MANO-B (mixed-all-nominated-in-one-BRCA) method and a validated functional assay, called the Accurate BRCA Companion Diagnostic (ABCD) test, demonstrated the detrimental effects of this variant. The authors concluded that BRCA2 p.Ser2616Phe variant is a likely oncogenic variant observed specifically in the Japanese population, leading to predisposition to breast and ovarian cancer, and reported the results in a research article (Yamazawa K, et al. 114, 7, 2993-3002 Cancer Sci. 2023).

Education

 One trainee from The University of Tokyo, two from Juntendo University, and one from Yokohama City University.

Future Prospects

 Genomic medicine is now being implemented in actual clinical practice, and analysis technologies such as whole genome analysis, long read sequencing, and single cell analysis are further advancing day by day. We aim to contribute to the development of genomic medicine through research and development of sequencing and screening technologies, development of algorithms for detection of ultra-low frequency mutations, and identification of useful biomarkers.

List of papers published in 2023

Journal

1. Takei S, Tanaka Y, Lin YT, Koyama S, Fukuoka S, Hara H, Nakamura Y, Kuboki Y, Kotani D, Kojima T, Bando H, Mishima S, Ueno T, Kojima S, Wakabayashi M, Sakamoto N, Kojima M, Kuwata T, Yoshino T, Nishikawa H, Mano H, Endo I, Shitara K, Kawazoe A. Multiomic molecular characterization of the response to combination immunotherapy in MSS/pMMR metastatic colorectal cancer. Journal for immunotherapy of cancer, 12:e008210, 2024

2. Sunami K, Naito Y, Saigusa Y, Amano T, Ennishi D, Imai M, Kage H, Kanai M, Kenmotsu H, Komine K, Koyama T, Maeda T, Morita S, Sakai D, Hirata M, Ito M, Kozuki T, Sakashita H, Horinouchi H, Okuma Y, Takashima A, Kubo T, Hironaka S, Segawa Y, Yakushijin Y, Bando H, Makiyama A, Suzuki T, Kinoshita I, Kohsaka S, Ohe Y, Ishioka C, Yamamoto K, Tsuchihara K, Yoshino T. A Learning Program for Treatment Recommendations by Molecular Tumor Boards and Artificial Intelligence. JAMA oncology, 10:95-102, 2024

3. Odate T, Satomi K, Kubo T, Matsushita Y, Ueno T, Kurose A, Shomori K, Nakai T, Watanabe R, Segawa K, Ohshika S, Miyake N, Kudo S, Shimoi T, Kobayashi E, Komiyama M, Yoshimoto S, Nakatani F, Kawai A, Yatabe Y, Kohsaka S, Ichimura K, Ichikawa H, Yoshida A. Inflammatory Rhabdomyoblastic Tumor: Clinicopathologic and Molecular Analysis of 13 Cases. Modern pathology, 37:100359, 2024

4. Shirai Y, Ueno T, Kojima S, Ikeuchi H, Kitada R, Koyama T, Takahashi F, Takahashi K, Ichimura K, Yoshida A, Sugino H, Mano H, Narita Y, Takahashi M, Kohsaka S. The development of a custom RNA-sequencing panel for the identification of predictive and diagnostic biomarkers in glioma. Journal of neuro-oncology, 167:75-88, 2024

5. Hasegawa N, Hayashi T, Niizuma H, Kikuta K, Imanishi J, Endo M, Ikeuchi H, Sasa K, Sano K, Hirabayashi K, Takagi T, Ishijima M, Kato S, Kohsaka S, Saito T, Suehara Y. Detection of Novel Tyrosine Kinase Fusion Genes as Potential Therapeutic Targets in Bone and Soft Tissue Sarcomas Using DNA/RNA-based Clinical Sequencing. Clinical orthopaedics and related research, 482:549-563, 2024

6. Watanabe K, Kohsaka S, Tatsuno K, Shinozaki-Ushiku A, Isago H, Kage H, Ushiku T, Aburatani H, Mano H, Oda K. Analysis of quality metrics in comprehensive cancer genomic profiling using a dual DNA-RNA panel. Practical laboratory medicine, 39:e00368, 2024

7. Okuma HS, Watanabe K, Tsuchihashi K, Machida R, Sadachi R, Hirakawa A, Ariyama H, Kanai M, Kamikura M, Anjo K, Hiramitsu A, Sekine S, Okita N, Mano H, Nishikawa H, Nakamura K, Yonemori K. Phase II Trial of Nivolumab in Metastatic Rare Cancer with dMMR or MSI-H and Relation with Immune Phenotypic Analysis (the ROCK Trial). Clinical cancer research, 29:5079-5086, 2023

8. Hirose T, Ikegami M, Kojima S, Yoshida A, Endo M, Shimada E, Kanahori M, Oyama R, Matsumoto Y, Nakashima Y, Kawai A, Mano H, Kohsaka S. Extensive analysis of 59 sarcoma-related fusion genes identified pazopanib as a potential inhibitor to COL1A1-PDGFB fusion gene. Cancer science, 114:4089-4100, 2023

9. Nishimura Y, Ryo E, Inoue S, Kawazu M, Ueno T, Namikawa K, Takahashi A, Ogata D, Yoshida A, Yamazaki N, Mano H, Yatabe Y, Mori T. Strategic Approach to Heterogeneity Analysis of Cutaneous Adnexal Carcinomas Using Computational Pathology and Genomics. JID innovations, 3:100229, 2023

10. Miyazaki B, Ueno T, Sugiyama M, Kojima S, Arakawa A, Tao K, Tanimura K, Shiraishi K, Yagishita S, Kohsaka S, Kato M, Kiyokawa N, Goto Y, Yatabe Y, Hamada A, Mano H, Ogawa C, Tanaka Y. Promoter swapping of truncated PDGFRB drives Ph-like acute lymphoblastic leukemia. NPJ precision oncology, 7:132, 2023

11. Terada M, Nakamura K, Matsuda T, Okuma HS, Sudo K, Yusof A, Imasa M, Sirachainan E, Anh PT, Fujiwara Y, Yamamoto N, Voon PJ, Chokephaibulkit K, Shibata T, Inoue M, Mano H, Shimoi T, Sriuranpong V, Yonemori K, Shimada K. A new era of the Asian clinical research network: a report from the ATLAS international symposium. Japanese journal of clinical oncology, 53:619-628, 2023

12. Yoshida T, Yatabe Y, Kato K, Ishii G, Hamada A, Mano H, Sunami K, Yamamoto N, Kohno T. The evolution of cancer genomic medicine in Japan and the role of the National Cancer Center Japan. Cancer biology & medicine, 21:29-44, 2023

13. Koyama T, Shimizu T, Kojima Y, Sudo K, Okuma HS, Shimoi T, Ichikawa H, Kohsaka S, Sadachi R, Hirakawa A, Yoshida A, Ando RM, Ueno T, Yanagaki M, Matsui N, Nakamura K, Yamamoto N, Yonemori K. Clinical Activity and Exploratory Resistance Mechanism of Milademetan, an MDM2 Inhibitor, in Intimal Sarcoma with MDM2 Amplification: An Open-Label Phase Ib/II Study. Cancer discovery, 13:1814-1825, 2023

14. Kobayashi H, Makise N, Shinozaki-Ushiku A, Zhang L, Ishibashi Y, Ikegami M, Tsuda Y, Kohsaka S, Ushiku T, Oda K, Miyagawa K, Aburatani H, Mano H, Tanaka S. Dramatic response to entrectinib in a patient with malignant peripheral nerve sheath tumor harboring novel SNRNP70-NTRK3 fusion gene. Genes, chromosomes & cancer, 62:47-51, 2023

15. Kusakabe M, Taguchi A, Tanikawa M, Wagatsuma R, Yamazaki M, Tsuchimochi S, Toyohara Y, Kawata A, Baba S, Ueno T, Sone K, Mori-Uchino M, Ikemura M, Matsunaga H, Nagamatsu T, Wada-Hiraike O, Kawazu M, Ushiku T, Takeyama H, Oda K, Kawana K, Mano H, Osuga Y. Cells with stem-like properties are associated with the development of HPV18-positive cervical cancer. Cancer science, 114:885-895, 2023

16. Kage H, Shinozaki-Ushiku A, Ishigaki K, Sato Y, Tanabe M, Tanaka S, Tanikawa M, Watanabe K, Kato S, Akagi K, Uchino K, Mitani K, Takahashi S, Miura Y, Ikeda S, Kojima Y, Watanabe K, Mochizuki H, Yamaguchi H, Kawazoe Y, Kashiwabara K, Kohsaka S, Tatsuno K, Ushiku T, Ohe K, Yatomi Y, Seto Y, Aburatani H, Mano H, Miyagawa K, Oda K. Clinical utility of Todai OncoPanel in the setting of approved comprehensive cancer genomic profiling tests in Japan. Cancer science, 114:1710-1717, 2023

17. Ishino T, Kawashima S, Tanji E, Ueno T, Ueda Y, Ogasawara S, Sato K, Mano H, Ishihara S, Kato N, Kawazu M, Togashi Y. Somatic mutations can induce a noninflamed tumour microenvironment via their original gene functions, despite deriving neoantigens. British journal of cancer, 128:1166-1175, 2023

18. Yamazawa K, Sugano K, Tanakaya K, Inoue S, Murakami H, Nakashima M, Adachi M, Oki S, Makabe T, Yamashita H, Ueki A, Sasaoka A, Nakashoji A, Kinoshita T, Matsunaga T, Arai M, Nakamura S, Miyata H, Ikegami M, Mano H, Kohsaka S, Matsui A. The pathogenic role of the BRCA2 c.7847C>T (p.Ser2616Phe) variant in breast and ovarian cancer predisposition. Cancer science, 114:2993-3002, 2023

19. Kobayashi K, Kawazu M, Yoshimoto S, Ueno T, Omura G, Saito Y, Ando M, Ryo E, Sakyo A, Yoshida A, Yatabe Y, Mano H, Mori T. Genome Doubling Shapes High-Grade Transformation and Novel EWSR1::LARP4 Fusion Shows SOX10 Immunostaining in Hyalinizing Clear Cell Carcinoma of Salivary Gland. Laboratory investigation; a journal of technical methods and pathology, 103:100213, 2023

20. Kobayashi Y, Niida A, Nagayama S, Saeki K, Haeno H, Takahashi KK, Hayashi S, Ozato Y, Saito H, Hasegawa T, Nakamura H, Tobo T, Kitagawa A, Sato K, Shimizu D, Hirata H, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Mizuno S, Kawazu M, Kohsaka S, Ueno T, Mano H, Ishihara S, Uemura M, Mori M, Doki Y, Eguchi H, Oshima M, Suzuki Y, Shibata T, Mimori K. Subclonal accumulation of immune escape mechanisms in microsatellite instability-high colorectal cancers. British journal of cancer, 129:1105-1118, 2023

21. Ohara K, Miyawaki S, Nakatomi H, Okano A, Teranishi Y, Shinya Y, Ishigami D, Hongo H, Takayanagi S, Tanaka S, Shinozaki-Ushiku A, Kohsaka S, Kage H, Oda K, Miyagawa K, Aburatani H, Mano H, Tatsuno K, Saito N. Case report and literature review: exploration of molecular therapeutic targets in recurrent malignant meningioma through comprehensive genetic analysis with Todai OncoPanel. Frontiers in neurology, 14:1270046, 2023