Annual Report 2020
Division of Biomarker Discovery (Tsukiji Campus)
Fumitaka Takeshita, Hiroki Sasaki, Fumiko Chiwaki, Masayuki Komatsu, Moeko Inoue, Megumi Miyagi
The Team and What We Do
The three major research areas of the Division of Biomarker Discovery are: 1) preclinical studies using newly established gastric, esophageal, pancreatic, and ovarian cancer cell lines for derivation of industrial and academia seeds/drugs to the Exploratory Oncology Research & Clinical Trial Center (EPOC), 2) basic research and development of personalized cancer diagnosis and treatment for gastric cancer (GC) and esophageal squamous cell carcinoma (ESCC), and 3) microarray analysis and gene selection for internal and external researchers as a task of the core facility in the Fundamental Innovative Oncology Core Center (FIOC).
Research activities
1. Preclinical Studies Using Newly Established Cell Lines from Common Cancers in Asia
Genome-wide genetic information for approximately 1,500 cancer cell lines is available on CCLE (the Cancer Cell Line Encyclopedia, The Broad Institute of MIT & Harvard); however, among them, only 11 cell lines are derived from diffuse-type GC. Since driver gene mutation frequency in a certain cancer is often less than 5%, the establishment of cell lines from each patient to be analyzed is desirable for the functional selection of driver gene mutations. We expect the establishment of new GC cell lines, especially from metastatic sites after therapy. Peritoneal metastasis is most frequent in GCs, especially diffuse-type GCs. In 2010-2019, we successfully established over 100 diffuse-type GC cell lines (National Cancer Center Stomach Cancer (NSC) series) from 72 patients, and also established 68 pancreatic and 22 ovarian cancer cell lines, and more. We are conducting omics analyses for gene expression and copy number variation, as well as hotspot and genome-wide gene alteration in these cell lines. Moreover, for in vivo preclinical studies, their tumorigenicity and histopathological characteristics in the xenograft were evaluated, such as their fibroblast rich, hypovascular, and dormant states. Through collaboration with five pharmaceutical industries, we conducted in vitro and in vivo preclinical studies to derivate clinical trials in our hospitals.
2. Basic Research and Development of Personalized Diagnoses and Treatment for GC and ESCC
The study for GC: GC is one of the leading causes of cancer-related death worldwide.
Histopathologically, GCs can be divided into two major categories: intestinal-type and diffuse-type. Unlike the decreasing incidence of intestinal type, the prevalence of the diffuse type is reportedly increasing worldwide. Although therapeutic results for GC have recently improved, the prognosis for advanced diffuse-type GC still remains poor. Peritoneal dissemination is a frequent form of metastasis in diffuse-type GC. The survival rates of patients with peritoneal metastasis (P1) at 3 and 5 years are only 9.8% and 0%, respectively. To improve immunotherapy, we performed cell surface marker analyses by multicolor FCM (flow cytometry) and gene expression analysis using cells derived from the ascites of gastric and ovarian cancer patients. We also developed an ex vivo immune-response evaluation system based on fresh clinical samples and performed prospective omics analyses of patients treated with nivolumab. As a result, we successfully demonstrated that patients with high levels of IFNγ-responsive gene expression were likely sensitive to nivolumab, and we determined the importance of combination therapy of anti-PD-1, -TIGIT, and -TIM-3 antibodies. We prepared figures and tables for publication in scientific journals.
The study for ESCC: Definitive chemoradiotherapy (CRT) is a less invasive therapy for ESCC; however, the five-year survival rate of locally advanced ESCC patients is only 37%. Therefore, the prediction of the CRT responders is awaited. We have successfully identified 2 intrinsic subtypes (M2 and E) of ESCC by gene expression, profile-based unsupervised clustering of 274 biopsy samples obtained before treatment. For cases treated with CRT, the 5-year survival rate was 24% for subtype M2 and 74% for subtype E. Furthermore, we found transcriptional pathways activated characteristically in each subtype; subtype E showed a differentiation phenotype, whereas M2 showed an epithelial-mesenchymal transition phenotype (Tamaoki M, et al., Cancer Sci, 2018, Takashima K, et al, Int. J. Oncology, 2019). To develop an IVD for predicting subtype E with high SIM2 expression, we are collaborating with a pharmaceutical company and ten medical institutes for clinical investigation of 225 ESCC patients with the support of the Japan Agency for Medical Research and Development. We performed integrative clinical data analyses in these two cohort studies.
3. Support of Microarray Analysis and Animal Studies in the FIOC
In 2020, we supported gene expression and subtyping analyses for internal and external researchers and provided originally established cancer cell lines to internal and external researchers and industries under the Material Transfer Agreement.
We have also provided training and counseling for techniques of developing animal models of cancer, as well as in vivo imaging to internal and external research groups.
Education
We supported a postdoctoral fellow in their research design, writing of a paper, and grant applications, and nurtured four assisting scientists, and three undergraduates through experiments, discussion, and writing of a study or paper.
Future Prospects
To develop IVD and to derivate new drugs to the EPOC, collaboration with pharmaceutical industries will be continued. To facilitate innovative basic research and to create intellectual properties, we will make continuous efforts to support internal researchers by providing established cell lines with omics information and microarray analysis.
List of papers published in 2020
Journal
1. Sugano T, Masuda M, Takeshita F, Motoi N, Hirozane T, Goto N, Kashimoto S, Uno Y, Moriyama H, Sawa M, Nagakawa Y, Tsuchida A, Seike M, Gemma A, Yamada T. Pharmacological blockage of transforming growth factor-β signalling by a Traf2- and Nck-interacting kinase inhibitor, NCB-0846. Br J Cancer, 124:228-236, 2021
2. Zhou Y, Yamamoto Y, Takeshita F, Yamamoto T, Xiao Z, Ochiya T. Delivery of miR-424-5p via Extracellular Vesicles Promotes the Apoptosis of MDA-MB-231 TNBC Cells in the Tumor Microenvironment. Int J Mol Sci, 22:2021
3. Liew LC, Gailhouste L, Tan GC, Yamamoto Y, Takeshita F, Nakagama H, Ochiya T. MicroRNA-124a inhibits endoderm lineage commitment by targeting Sox17 and Gata6 in mouse embryonic stem cells. Stem Cells, 38:504-515, 2020
4. Sanchez Calle A, Yamamoto T, Kawamura Y, Hironaka-Mitsuhashi A, Ono M, Tsuda H, Shimomura A, Tamura K, Takeshita F, Ochiya T, Yamamoto Y. Long non-coding NR2F1-AS1 is associated with tumor recurrence in estrogen receptor-positive breast cancers. Mol Oncol, 14:2271-2287, 2020
5. Kurashima K, Kashiwagi H, Shimomura I, Suzuki A, Takeshita F, Mazevet M, Harata M, Yamashita T, Yamamoto Y, Kohno T, Shiotani B. SMARCA4 deficiency-associated heterochromatin induces intrinsic DNA replication stress and susceptibility to ATR inhibition in lung adenocarcinoma. NAR Cancer, 2:zcaa005, 2020
6. Tsumura R, Koga Y, Hamada A, Kuwata T, Sasaki H, Doi T, Aikawa K, Ohashi A, Katano I, Ikarashi Y, Ito M, Ochiai A. Report of the use of patient-derived xenograft models in the development of anticancer drugs in Japan. Cancer Sci, 111:3386-3394, 2020
7. Tanooka H, Inoue A, Takahashi RU, Tatsumi K, Fujikawa K, Nagao T, Ishiai M, Chiwaki F, Aoyagi K, Sasaki H, Ochiya T. Bacterial SOS Genes mucAB/umuDC Promote Mouse Tumors by Activating Oncogenes Nedd9/Aurkb via a miR-145 Sponge. Mol Cancer Res, 18:1271-1277, 2020
8. Sasaki M, Chiwaki F, Kuroda T, Komatsu M, Matsusaki K, Kohno T, Sasaki H, Ogiwara H. Efficacy of glutathione inhibitors for the treatment of ARID1A-deficient diffuse-type gastric cancers. Biochem Biophys Res Commun, 522:342-347, 2020
9. Takashima K, Fujii S, Komatsuzaki R, Komatsu M, Takahashi M, Kojima T, Daiko H, Minashi K, Chiwaki F, Muto M, Sasaki H, Yano T. CD24 and CK4 are upregulated by SIM2, and are predictive biomarkers for chemoradiotherapy and surgery in esophageal cancer. Int J Oncol, 56:835-847, 2020
10. Tanabe S, Quader S, Ono R, Cabral H, Aoyagi K, Hirose A, Yokozaki H, Sasaki H. Molecular Network Profiling in Intestinal- and Diffuse-Type Gastric Cancer. Cancers (Basel), 12:2020