NBDC Research ID: hum0461.v1
SUMMARY
Aims: Radiotherapy (RT) is pivotal in cancer care, with 50 to 60% of patients receiving it. Traditionally, RT's primary mechanism was deemed to induce lethal DNA damage. However, recent findings unveil contributions from immune responses and immunological cell death to its anti-tumor efficacy. Since RT alone has limitations in maximizing these effects, novel strategies to activate immune responses are sought. Despite trials combining RT with immune checkpoint inhibitors (ICIs), optimal combinations remain elusive. This study aims to elucidate post-RT dynamics of cancer immune responses and gene expression profiles, aiming to optimize both immunotherapy and radiotherapy.
Methods: 【scRNA-seq】single cell sequencing by illumima
【Spatial transcriptome seq】Spatial transcriptome sequencing Visium
Participants/Materials: 【scRNA-seq】esophageal squamous cell carcinoma: 5 cases
【Spatial transcriptome seq】esophageal squamous cell carcinoma: 2 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000712 | Controlled-access (Type I) | 2024/05/31 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
esophageal squamous cell carcinoma (ICD10: C153, C154, C155): 5 cases, 11 samples pre-RT: 4 samples during RT: 3 samples just after-RT: 2 samples after RT: 2 samples |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 3000, NovaSeq 6000] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Single Cell 3ʹ Reagent Kits v3, Chromium Single Cell 5' Reagent Kits v1 |
| Fragmentation Methods | enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 126bp, 116bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000845 |
| Total Data Volume | 436.8 GB (fastq) |
| Comments (Policies) | NBDC policy |
Visium Spatial Gene Expression, Histological image
| Participants/Materials |
esophageal squamous cell carcinoma (ICD10: C153, C154, C155): 2 cases, 2 samples resected tissue from a patient who underwent surgery only (non-RT) resected tissue from a patient who received preoperative RT |
| Targets | Visium Spatial Gene Expression, Histological image |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | FFPE tumor samples from surgically resected tissues |
| Cell Lines | - |
| Library Construction (kit name) | Visium Spatial Gene Expression Slide & Reagent Kit |
| Fragmentation Methods | enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 78 bp |
| Software | spaceranger-1.3.1 |
| Reference | hg38 |
| Tissue Image | hematoxylin-eosin staining |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000845 |
| Total Data Volume | 436.8 GB (fastq, png, json, mtx, csv, xlsx, tsv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shun-Ichiro Kageyama
Affiliation: Department of Radiation Oncology, National Cancer Center Hospital East
Project / Group Name: -
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Analysis of the Non-coding RNA Pathway in Radiation-induced Immune Responses | 21K07582 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Platform for Advanced Genome Sciences | 16H06279 |
| KAKENHI Grant-in-Aid for Transformative Research Areas | Platform for Advanced Genome Sciences | 22H04925 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Comprehensive single-cell analysis demonstrates radiotherapy-induced infiltration of macrophages expressing immunosuppressive genes into tumor in esophageal squamous cell carcinoma | doi: 10.1126/sciadv.adh9069 | JGAD000845 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
