Annual Report 2021
Division of Biomarker Discovery (Tsukiji Campus)
Fumitaka Takeshita, Hiroki Sasaki, Fumiko Chiwaki, Masayuki Komatsu, Megumi Miyagi, Serina Chinen
The Team and What We Do
The three major research areas of the Department of Translational Oncology were 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 and 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) we supported microarray analysis and gene selection for inside and outside researchers as work 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 in about 1,500 cancer cell lines is available on CCLE (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 desired for functional selection of driver gene mutations. The wait is on for 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 2010-2021, we successfully established over 100 diffuse-type GC cell lines (National Cancer Center Stomach Cancer (NSC) series) from 76 patients, and also established 77 pancreatic and 25 ovarian cancer cell lines, and more. We are conducting omics analyses for gene expression and copy number variation, and hot spot- and genome wide-gene alteration in these cell lines. Moreover, for in vivo preclinical study, their tumorigenicity and histopathological characteristics in the xenograft, such as fibroblast rich-, hypovascular-, and dormant-state, were evaluated. Through collaboration with five pharmaceutical companies, in vitro and in vivo preclinical studies were conducted to derivate clinical trials in our hospitals. A highlight of this year was the signing of licensing agreements for two therapeutic patents.
2. Basic Research and Development of Personalized Diagnosis and Treatment for GC and ESCC
Research for GC: Scirrhous gastric cancer is included in diffuse-type gastric cancer, but many cases have already undergone peritoneal dissemination by the time they are diagnosed and are often not curatively resectable. Even if resected specimens are obtained, the tumor cell content is low due to fibrosis and stromal hyperplasia, resulting in low detection sensitivity in genome analysis. In collaboration with Dr. Mano, director of our Research Institute, we performed a multi-omics analysis including whole genome analysis of 59 cell lines established from ascites fluid of 98 gastric cancer patients with peritoneal dissemination and 76 cancer cell samples purified from the above. We found that high gene amplification and gene fusion of receptor-type tyrosine kinase and RAS pathway genes occurred in more than 50% of scirrhous gastric cancer patients. In vitro and in vivo experiments successfully showed that at least 50% of them could be treated with existing molecular targeted drugs. On the other hand, RNA sequencing, chromatin analysis, and methylation analysis revealed two subtypes (EMT and non-EMT types), and found that the expression of TEAD1, a transcription factor of the Hippo pathway that regulates organ size and cell proliferation, is markedly elevated in EMT types. Furthermore, the effectiveness of treatment with TEAD1 inhibitors was confirmed in a mouse model. These results were published in Nature Cancer, an American international journal (Tanaka Y, Chiwaki F., et.al., 2021).
Research for ESCC: Definitive chemoradiotherapy (CRT) is a less invasive therapy for ESCC; however, the five-year survival rate of locally advanced ESCC patients was only 37%. Therefore, the predicted CRT-responder is awaited. We have successfully identified two intrinsic subtypes (M2 and E) of ESCCs 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% in subtype M2, whereas it was 74% in subtype E. Furthermore, we found transcriptional pathways activated characteristically in each subtype; subtype E showed a differentiation phenotype, while 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 2021, we supported requests from inside researchers for comprehensive gene expression analysis using Affymetrix Genechip U133 v2 by performing principal component analysis, cluster analysis, and gene selection. For example, we contributed to the discovery of a new synthetic lethality by providing our established ovarian cancer cell lines, which was highly appreciated (Ogiwara H, et al., Cancer Cell, 2019). We also showed that this synthetic lethality occurs in a subset of the aforementioned undifferentiated gastric cancers (Sasaki M, et al., BBRC, 2020). In addition, requests for the use of autologous strains from domestic researchers in academia and from inside researchers are increasing, and we are providing them as part of collaborative research. In addition, we have been providing this service to domestic pharmaceutical companies for a fee under the terms of an MTA.
Education
We supported a postdoctoral fellow with their research design, writing a paper, and grant applications, and nurtured three trainees including an undergraduate school student through experiments, discussions, and writing reports or papers.
Future Prospects
Co-development of new drugs with companies using novel gastric and pancreatic cancer cell lines, etc. will continue. Development of in vitro diagnostics for predicting esophageal cancer subtypes will be promoted. We will also promote the acquisition of research funds and intellectual property for researchers at NCC and innovative basic research by providing core facility services and our established cell lines.
List of papers published in 2021
Journal
1. Kobayashi Y, Takeda T, Kunitomi H, Chiwaki F, Komatsu M, Nagai S, Nogami Y, Tsuji K, Masuda K, Ogiwara H, Sasaki H, Banno K, Aoki D. Response Predictive Markers and Synergistic Agents for Drug Repositioning of Statins in Ovarian Cancer. Pharmaceuticals (Basel, Switzerland), 15:2022
2. Komatsu M, Nakamura K, Takeda T, Chiwaki F, Banno K, Aoki D, Takeshita F, Sasaki H. Aurora kinase blockade drives de novo addiction of cervical squamous cell carcinoma to druggable EGFR signalling. Oncogene, 41:2326-2339, 2022
3. Tsuchiya R, Yoshimatsu Y, Noguchi R, Sin Y, Ono T, Sei A, Takeshita F, Sugaya J, Nakatani F, Yoshida A, Ohtori S, Kawai A, Kondo T. Establishment and characterization of NCC-ssRMS2-C1: a novel patient-derived cell line of spindle cell/sclerosing rhabdomyosarcoma. Human cell, 34:1569-1578, 2021
4. Tanaka Y, Chiwaki F, Kojima S, Kawazu M, Komatsu M, Ueno T, Inoue S, Sekine S, Matsusaki K, Matsushita H, Boku N, Kanai Y, Yatabe Y, Sasaki H, Mano H. Multi-omic profiling of peritoneal metastases in gastric cancer identifies molecular subtypes and therapeutic vulnerabilities. Nature cancer, 2:962-977, 2021
5. Tanabe S, Perkins EJ, Ono R, Sasaki H. Artificial intelligence in gastrointestinal diseases. Aritif. Intell, Gastroenterol, 2:69-76, 2021
6. Tanabe S, Quader S, Ono R, Cabral H, Aoyagi K, Hirose A, Yokozaki H, Sasaki H. Cell Cycle Regulation and DNA Damage Response Networks in Diffuse- and Intestinal-Type Gastric Cancer. Cancers, 13:2021
7. Abe S, Matsuzaki J, Sudo K, Oda I, Katai H, Kato K, Takizawa S, Sakamoto H, Takeshita F, Niida S, Saito Y, Ochiya T. A novel combination of serum microRNAs for the detection of early gastric cancer. Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association, 24:835-843, 2021
8. Tsuchiya R, Yoshimatsu Y, Noguchi R, Sei A, Takeshita F, Sugaya J, Fukushima S, Yoshida A, Ohtori S, Kawai A, Kondo T. Establishment and characterization of NCC-DDLPS1-C1: a novel patient-derived cell line of dedifferentiated liposarcoma. Human cell, 34:260-270, 2021
9. Tsuchiya R, Yoshimatsu Y, Noguchi R, Ono T, Sei A, Takeshita F, Sugaya J, Fukushima S, Yoshida A, Ohtori S, Kawai A, Kondo T. Establishment and characterization of NCC-DDLPS3-C1: a novel patient-derived cell line of dedifferentiated liposarcoma. Human cell, 34:1008-1018, 2021
10. Tsuchiya R, Yoshimatsu Y, Noguchi R, Ono T, Sei A, Takeshita F, Sugaya J, Iwata S, Yoshida A, Ohtori S, Kawai A, Kondo T. Establishment and characterization of NCC-SS4-C1: a novel patient-derived cell line of synovial sarcoma. Human cell, 34:998-1007, 2021