NBDC Research ID: hum0320.v1
SUMMARY
Aims: Various immunocompetent cells and factors in the peripheral blood cells and tumor tissues of patients with malignant tumors were analyzed. The immunological status of patients with malignant tumors will be clarified by analyzing various immune cells and factors in peripheral blood cells and tumor tissues. The relationship between immune status and clinicopathological characteristics, molecular biological characteristics, therapeutic effects, and prognosis will be evaluated as well.
Methods: Expressions of CD4, CD8, FoxP3, CD25, CD45RA, CTLA-4, PD-1, ICOS, BTLA, Tim-3, LAG3, CCR7, and other molecules on immunocompetent cells (CD4/CD8 T cells, antigen-presenting cells, regulatory T cells, MDSCs, spontaneous lymphocytes, etc.) were analyzed by single-cell sequencing technology. The T-cell receptor (TCR) of immune cells was also analyzed in the same technology.
Participants/Materials: pulmonary gland cancer: 2 cases, head and neck part cancer: 3 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000480 | NGS (scRNA-seq, TCR-seq) | Controlled-access (Type I) | 2022/01/25 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 2 cases head and neck cancer (ICD10: C760): 3 cases tumor tissue: 1 sample each lymph node: 1 sample each peripheral blood; 1 sample each (Total 15 samples) |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400] |
| Library Source | RNAs extracted from a single T cell isolated from tumor tissues, lymph node,s and peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' Reagent Kits v2 |
| Fragmentation Methods | Hybrid Selection |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | average 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000597 |
| Total Data Volume | 719.9 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 2 cases head and neck cancer (ICD10: C760): 3 cases tumor tissue: 1 sample, lymph node: 1 sample, peripheral blood; 1 sample, Total 15 samples |
| Targets | TCR-seq |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400] |
| Library Source | RNAs extracted from a single T cell isolated from tumor tissue, lymph node and peripheral blood |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' Reagent Kits v2 |
| Fragmentation Methods | Hybrid Selection |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | average 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000597 |
| Total Data Volume | 719.9 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yosuke Togashi
Affiliation: Chiba Cancer Center Research Institute
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (B) | Analysis of PD-1+ tumor-infiltrating T cells according to cancer antigen hierarchy | 20H03694 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Spatial and temporal analysis of neoantigen-specific T-cell clones as a therapeutic target and biomarker | JP19ck0106521 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Novel tumor-infiltrating T cell analysis according to antigen epitope | JP18cm0106340 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Development of a single-cell analysis method for tumor-infiltrating lymphocytes with genomic abnormalities and elucidation of its clinical significance | JP21cm0106383 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | PD-1 blockade therapy promotes infiltration of tumor-attacking exhausted T cell clonotypes | doi: 10.1016/j.celrep.2022.110331 | JGAD000597 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Ansuman Satpathy | Department of Pathology, Stanford University | United States of America | Epigenetics of Inflammatory Skin Disorders | JGAD000597 | 2022/07/04-2023/05/31 |
