NBDC Research ID: hum0356.v2
SUMMARY
Aims: Recently, single-cell RNA sequencing analysis has been used to analyze cell-cell interactions between colorectal cancer cells and stromal cells in colorectal cancer patients with an adenocarcinoma sequence background. 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, and thereby searching for new therapeutic target molecules.
Methods: Surgical specimens were frozen in liquid nitrogen. Specimens were cut according to the capture area and sectioned into 10-μm sections using a cryostat. The specimens were placed on Visium Spatial slides and stored at -80 °C until use. Tissues were permeabilized with permeabilization enzyme (10x Genomics: 2000214) for 50 min, washed with 0.1 x SSC buffer (Sigma-Aldrich), and imaged. All steps were performed according to the manufacturer's protocol (CG000240 Rev D, CG000160 Rev A).
Participants/Materials: A patient with colorectal cancer with a background of adenocarcinoma sequence
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| NGS (Visium Spatial Gene Expression), histological image | Unrestricted-access | 2022/12/20 | |
| NGS (Visium Spatial Gene Expression), histological image | Unrestricted-access | 2024/05/31 |
*When the research results including the data which were downloaded from DRA/GEA, 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 |
[DRA015288 / E-GEAD-579] colon cancer (ICD10: D01.0): 1 case fragment tumor tissue section: 4 samples [DRA016520 / E-GEAD-619] colon cancer (ICD10: D01.0): 2 cases (early colorectal cancer: 1 case, advanced colorectal cancer: 1 case) fragment tumor tissue section: 2 samples |
| Targets | Visium Spatial Gene Expression, histological image |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from sample tissues |
| Cell Lines | - |
| Library Construction (kit name) | Visium Spatial Gene Expression Reagent Kits |
| Fragmentation Methods | included in the above library construction kit (enzymatic fragmentation) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 118 bp |
| Software | spaceranger-1.2.1 |
| Reference | GRCh38 |
| Tissue Image | hematoxylin-eosin staining |
| DDBJ Sequence Read Archive ID | |
| Genomic Expression Archive ID | |
| Total Data Volume |
DRA015288 / E-GEAD-579: 142.6 GB (fastq, tif, png, json, csv) DRA016520 / E-GEAD-619: 67.3 GB (fastq, png, json, csv, tsv, mtx, html, cloupe, xlx) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Koshi Mimori
Affiliation: Department of Surgery, Kyushu University Beppu Hospital
Project / Group Name: Elucidation of genetic alterations in colorectal carcinogenesis and establishment of clinical significance of interstitial
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 | 21K07179 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) | Understanding Diversity within Colorectal Cancer Tumors by Multi-Domain Sequencing and Evolutionary Simulation | 20H05039 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Elucidation of the true evolutionary pattern from early colorectal lesions to advanced cancer and establishment of treatment methods | 19H03715 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Aberrant Regulation of Protein Translation Start Sites in Colorectal Cancer Identified by Genome Evolution Models | 19K09176 |
| 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 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Elucidation of the true evolutionary pattern from early colorectal lesions to advanced cancer and establishment of treatment methods | 19H03715 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Aberrant Regulation of Protein Translation Start Sites in Colorectal Cancer Identified by Genome Evolution Models | 19K09176 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) | Understanding Diversity within Colorectal Cancer Tumors by Multi-Domain Sequencing and Evolutionary Simulation | 20H05039 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Establishment of early diagnosis of colorectal cancer recurrence by a new approach implementing ctDNA methylation detection | 20K08930 |
| 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 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Elucidation of microenvironmental network mechanisms regulating multistep malignant transformation of colorectal cancer cells and establishment of novel preventive therapeutic strategies | JP19ck0106259 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | spatial and single-cell transcriptomics to decipher the cellular society containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer | doi: 10.1016/j.celrep.2022.111929 | DRA015288 E-GEAD-579 |
| 2 | 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 | DRA016520 E-GEAD-619 |
