NBDC Research ID: hum0430.v1
SUMMARY
Aims: Colorectal cancer is the most common type of cancer in Japan. Although some colorectal cancers have a genetic background, most colorectal cancers are sporadic. Known risk factors for colorectal cancer include smoking, obesity, lack of exercise, and intake red or processed meat. Furthermore, although it has been suggested that changes in the intestinal environment due to changes in diet and lifestyle may be involved in the increased incidence of colorectal cancer in Japan, the molecular mechanism has not yet been fully elucidated. The main objective of this study is to elucidate the changes in the intestinal environment that cause colorectal tumors.
Methods: Research biopsies were obtained from the tumor, normal mucosa 1-2 cm away from the tumor, terminal ileum, cecum, ascending colon, descending colon, and sigmoid colon to rectum using a lower gastrointestinal endoscopy for participants. DNA/RNA was extracted from the samples and used for RNA-seq and whole exome sequencing analyses.
Participants/Materials:
RNA-seq: 14 patients with advanced colorectal cancer, 41 patients with early stage colorectal cancer, 6 patients with colorectal adenoma, and 17 healthy individuals
Exome: 24 patients with advanced colorectal cancer (including 14 same cases in RNA-seq), 23 patients with early stage colorectal cancer (including 20 same cases in RNA-seq)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000655 | NGS (RNA-seq, Exome) | Controlled-access (Type I) | 2025/12/02 |
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MOLECULAR DATA
| Participants/Materials |
advanced colorectal cancer (ICD10: C189): 14 cases colorectal cancer: 14 samples, colorectal adenoma: 1 sample, normal intestinal mucosa: 65 samples early stage colorectal cancer (ICD10: C189): 41 cases colorectal cancer: 38 samples, colorectal adenoma: 5 samples, normal intestinal mucosa: 160 samples colorectal adenoma (ICD10: D126): 6 cases colorectal adenoma: 11 samples, normal intestinal mucosa: 33 samples 17 healthy individuals normal intestinal mucosa: 61 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNA extracted from colorectal cancer, colorectal adenoma, and normal intestinal mucosa samples |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000785 |
| Total Data Volume | 1.1 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
advanced colorectal cancer (ICD10: C189): 24 cases colorectal cancer: 25 samples, colorectal adenoma: 1 sample, normal intestinal mucosa: 24 samples early stage colorectal cancer (ICD10: C189): 23 cases colorectal cancer: 23 samples, colorectal adenoma: 6 samples, normal intestinal mucosa: 23 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNA extracted from colorectal cancer, colorectal adenoma, and normal intestinal mucosa samples |
| Cell Lines | - |
| Library Construction (kit name) | Illumina DNA Prep with Enrichment, Twist Comprehensive Exome Panel |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000785 |
| Total Data Volume | 1.0 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shinichi Yachida
Affiliation: Division of Cancer Genomics, National Cancer Center Research Institute
Project / Group Name: Establishment of an Endoscopic Biopsy Repository for Comprehensive Characterization of the Gut Microenvironment in Colorectal Diseases and Its Application to Exploratory Translational Research
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| National Cancer Center Research and Development Fund | Establishment of a comprehensive metagenomic database of the gut microbiota in colorectal cancer patients and individuals at high risk for cancer development: A multi-institutional collaborative study | 2020-A-4 |
| National Cancer Center Research and Development Fund | Establishment of the infrastructure for a multicenter biobank of fecal and comprehensive gastrointestinal endoscopic biopsy specimens | 2023-A-6 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Development of target-selective mid-size drugs using cyclic peptide derivatives | 20H03362 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Studies on the elucidation of intestinal environmental changes in colorectal tumorigenesis via the serrated pathway | 23H02892 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Research aimed at elucidating alterations in the intestinal microenvironment associated with colorectal cancer development in high-risk individuals, and the development of personalized preventive strategies based on these findings | JP22ck0106546 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Development of personalized colorectal cancer prevention strategies through integrated profiling of the gut microbiome using stool and endoscopic biopsy specimens in ultra-high-risk populations | JP23ck0106799 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Research and development aimed at predicting the occurrence of adverse effects associated with anticancer drugs through comprehensive analysis of the gut microbiota | JP21cm0106477 |
| Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED) | Development of biomarkers for early detection and susceptibility assessment of young-onset colorectal cancer through comprehensive analysis of the intestinal microenvironment | JP23ama221404 |
| Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED) | Elucidation of the pathogenetic mechanisms underlying early-onset colorectal cancer through integrated analyses of diet, gut microbiota, and mucosal inflammation, and the development of novel susceptibility and early diagnostic strategies | JP24ama221430 |
| Research Program on the challenges of Global Health issues, Japan Agency for Medical Research and Development (AMED) | Investigation of infection-associated cancers conducted within the framework of the Japan–U.S. Medical Cooperation Program | JP23jk0210009 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Development of novel strategies for prevention, diagnosis, and treatment through comprehensive genomic analysis of rare cancers, including sarcomas and brain tumors | JP24ck0106877 |
| Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University | - | - |
| Joint Research Project of the Institute Medical Science, the University of Tokyo | Investigation of the role of the gut microbiota in the serrated pathway, a novel colorectal carcinogenesis mechanism | - |
| Takeda Science Foundation | Elucidation of colorectal carcinogenesis mechanisms and development of preventive strategies based on gut microbiome dynamics toward the implementation of microbiome-driven precision medicine | - |
| Yasuda Medical Foundation | Elucidation of the mechanisms underlying colorectal carcinogenesis based on gut microbiome dynamics | - |
| The Mitsubishi Foundation | Identification of gut microbial agents involved in colorectal tumorigenesis and elucidation of their underlying mechanistic pathways | - |
| Princess Takamatsu Cancer Research Fund | Investigation of the impact of gut microorganisms on the pathogenesis of colorectal cancer | - |
| Yakult Bio-Science Foundation | Investigation of intestinal microenvironment modulation for the prevention of colorectal cancer | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Variability in non-tumor areas of colorectal cancer patients as revealed by endoscopic intestinal step biopsies | doi: 10.1186/s12943-024-02159-9 | JGAD000785 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
