NBDC Research ID: hum0402.v1
SUMMARY
Aims: Recently, single cell RNA sequencing has been used to analyze cell-cell interactions between colon cancer cells and stromal cells. However, the important cancer microenvironment during early cancer development from adenomas, especially the mechanism of immune tolerance acquisition, is unclear. In this study, we investigated immune tolerance and the formation of the tumor microenvironment at the adenoma-cancer interface by integrating single-cell and spatial transcriptome analyses obtained from public databases. By integrating scRNA-seq of colorectal cancer and spatial transcriptome analysis in carcinoma in adenoma tissues, we investigated immune tolerance and tumor microenvironment formation at the adenoma-tumor interface thereby searching for new therapeutic target molecules.
Methods: Formalin-fixed paraffin-embedded (FFPE) samples were used to prepare for spatial transcriptomic construction and sequencing. 5μm thick sections were prepared from the FFPE samples and processed using Visium Spatial Gene Expression Slide Kit (10x Genomics) according to the Visium Spatial Gene Expression Reagent Kits for FFPE User Guide. First, sections were stained with H&E and imaged followed by probe hybridization and ligation. Then, the captured probe library was sequenced using an MGI DNBSEQ-G400 system for 28, 10, 10, and 50 cycles for Read 1, i7, i5, and Read2 sequences respectively.
Participants/Materials: Patients with colorectal cancer with a background of adenocarcinoma sequence (ACS)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| NGS (Visium Spatial Gene Expression), Histological image | Unrestricted-access | 2024/04/12 |
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials |
colorectal cancer with a background of ACS (ICD10: D01.0): 4 cases FFPE tumor tissue section: 4 samples |
| Targets | Visium Spatial Gene Expression |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400] |
| Library Source | RNAs extracted from FFPE tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Visium Spatial Gene Expression Reagent Kits for FFPE |
| Fragmentation Methods | Hybrid Selection |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp on average |
| Software | Space Ranger software v.1.3.1 |
| Reference | GRCh38 (build 2020-A, 10x Genomics) |
| Tissue Image | hematoxylin-eosin staining |
| DDBJ Sequence Read Archive ID | DRA016537 |
| Genomic Expression Archive ID | E-GEAD-622 |
| Total Data Volume |
DRA016537: 84 GB (fastq) E-GEAD-622: 73 MB (tif, png, json, csv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Koshi Mimori
Affiliation: Department of Surgery, Kyushu University Beppu Hospital
Project / Group Name: Elucidation of the mechanisms that give rise to driver mutations in colorectal carcinogenesis
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Clinical significance of evolutionary phylogenetic tree for colorectal cancer ctDNA for early postoperative recurrence diagnostic system development and recurrence | JP21K07179 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) | Diversity in colorectal cancer tumors by multi-domain sequencing and evolutionary simulation | JP20H05039 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Elucidation of the pattern of progression from early colorectal tumor lesions to advanced cancer and establishment of treatment methods | JP19H03715 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Aberrant regulation of protein translation start sites in colorectal cancer identified by genome evolution model | JP19K09176 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | New approach to implement ctDNA methylation detection for early diagnosis of colorectal cancer recurrence | JP20K08930 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Malignant transformation and immune tolerance in the cancer microenvironment by colocalization with colon cancer cells and other cells | JP22H02903 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Spatial single-cell analysis of the mechanism of immune tolerance in early colorectal carcinogenesis | JP23K08074 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Development of new therapies based on the elucidation of epigenetic diversity and environmental adaptive genesis mechanisms in refractory cancer | JP22ama221501 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Integrated analysis of large-scale Japanese cancer genome, omics, and clinical data for international collaborative research and construction of knowledge base for the promotion of genomic medicine | JP20ck0106547 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Novel preventive treatment strategies by understanding the mechanisms of micrometastasis formation in colorectal cancer | JP20ck0106541 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Establishment of a ctDNA detection method targeting intractable cancer-specific epigenomic mutations | JP20cm0106475 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Elucidation of molecular genetic diversity creation mechanism of intractable cancer linked to microenvironmental diversity and development of new cancer therapies and predictive medical technologies | JP19cm0106504 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis | doi: 10.1016/j.ebiom.2024.105102 | DRA016537 E-GEAD-622 |
| 2 |
