NBDC Research ID: hum0461.v2

 

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

                 【Multiplex fluorescence immunostaining】Multiplex fluorescence immunostaining by CODEX (Akoya Biosciences)

Participants/Materials: 【scRNA-seq】esophageal squamous cell carcinoma: 5 cases

                                       【Spatial transcriptome seq】esophageal squamous cell carcinoma: 2 cases

                                       【Multiplex fluorescence immunostaining】esophageal squamous cell carcinoma: 2 cases

 

Dataset IDType of DataCriteriaRelease Date
JGAS000712

NGS (scRNA-seq)

NGS (Visium Spatial Gene Expression), Histological image

Controlled-access (Type I) 2024/05/31
JGAS000712 (Data addition) Multiplex fluorescence immunostaining Controlled-access (Type I) 2024/11/22

*Release Note

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MOLECULAR DATA

scRNA-seq

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

 

Multiplex Fluorescence Immunostaining

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 Multiplex Fluorescence Immunostaining
Target Loci for Capture Methods -
Platform Akoya Biosciences [CODEX]
Library Source surgically resected tissues
Cell Lines -
Cell Treatment Method (kit name) CODEX Staining Kit
Japanese Genotype-phenotype Archive Dataset ID JGAD000845
Total Data Volume 12.6 GB (qptiff: fluorescent images of tissues and immunostaining, txt: fluorescence and gene correspondence table)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Shun-Ichiro Kageyama

Affiliation: Department of Radiation Oncology, National Cancer Center Hospital East

Project / Group Name: -

NameTitleProject 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

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use