NBDC Research ID: hum0268.v2
SUMMARY
Aims: Proteogenomic discovery of a novel class of cancer antigens by HLA ligandome analysis of colon cancer tissues
Methods:
[Human colon cancer cell line, colon cancer] RNA-seq, CAGE-seq and Iso-seq data were used to analyze the transcript variants coding an identified non-coding RNA-derived antigen.
[Endometrial cancer] Bulk RNA-seq of tumor tissues was used to comprehensively analyze the set of genes expressed in each tissue sample. WES of tumor tissue and peripheral blood detected somatic mutations in each case and was combined with HLA ligandome analysis using mass spectrometry to identify neoantigens. Single-cell RNA-seq/TCR-seq of tumor-infiltrating T cells was used to identify tumor-reactive cytotoxic CD4+ T cells and marker genes.
Participants/Materials: Human colon cancer cell line: 1, colon cancer: 6 cases, endometrial cancer: 5 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000280 | NGS (Iso-seq, CAGE-seq, RNA-seq) | Controlled-access (Type I) | 2021/04/09 |
| JGAS000766 | NGS (RNA-seq, scRNA-seq, scTCR-seq, Exome) | Controlled-access (Type I) | 2025/08/29 |
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MOLECULAR DATA
| Participants/Materials | Human colon cancer cell line (ICD10: C18): 1 sample |
| Targets | Iso-seq |
| Target Loci for Capture Methods | - |
| Platform | PacBio [Sequel] |
| Library Source | RNAs extracted from cells |
| Cell Lines | ATCC (CCL-220) |
| Library Construction (kit name) | SMRTbell Template Prep Kit 2.0 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000386 |
| Total Data Volume | 16.1 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | Human colon cancer cell line (ICD10: C18): 1 sample |
| Targets | CAGE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq] |
| Library Source | RNAs extracted from cells |
| Cell Lines | ATCC (CCL-220) |
| Library Construction (kit name) | - |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000386 |
| Total Data Volume | 16.1 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Human colon cancer cell line (ICD10: C18): 1 sample Colon cancer: 6 patients (6 tumor tissues and 5 non-tumor tissues) Endometrial cancer (ICD10: C54.9): 5 patients (5 tumor tissues） |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from cells |
| Cell Lines | ATCC (CCL-220) |
| Library Construction (kit name) | TruSeq Stranded mRNA LT Sample Prep Kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
Human colon cancer cell line + Colon cancer: JGAD000386 Endometrial cancer: JGAD000907 |
| Total Data Volume |
Human colon cancer cell line + Colon cancer: 153.2 GB (fastq) Endometrial cancer: 217.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | Endometrial cancer (ICD10: C54.9): 1 patient (tumor-infiltrating T cells from 1 tumor tissue: 1 sample） |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ] |
| Library Source | RNAs extracted from tumor-infiltrating T cells |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 91 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000907 |
| Total Data Volume | 217.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | Endometrial cancer (ICD10: C54.9): 1 patient (tumor-infiltrating T cells from 1 tumor tissue: 1 sample） |
| Targets | scTCR-seq |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ] |
| Library Source | RNAs extracted from tumor-infiltrating T cells |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 91 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000907 |
| Total Data Volume | 217.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | Endometrial cancer (ICD10: C54.9): 5 patients (5 tumor tissues, 5 peripheral blood cells） |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor tissues and peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000907 |
| Total Data Volume | 217.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takayuki Kanaseki
Affiliation: Department of Pathology, Sapporo Medical University/Division of Molecular Pathology, Niigata University School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Proteogenomic discovery of HLA presented tumor antigens that arise from non-coding RNAs | JP20cm0106352 |
| Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED) | Multiomics study of tumor-specific antigens and reactive T cells based on NAP proteogenomics | JP24ama221315 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Functional Analysis of Tumor-Specific CD4+ T Cells Using a Novel Neoantigen Detection Technology | 24K02252 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | CD8+ T-cell Immune Surveillance against a Tumor Antigen Encoded by the Oncogenic Long Noncoding RNA PVT1 | doi: 10.1158/2326-6066.CIR-20-0964 | JGAD000386 |
| 2 | Identification and Phenotypic Characterization of Neoantigen-Specific Cytotoxic CD4+ T Cells in Endometrial Cancer | doi: 10.1158/2326-6066.CIR-24-0514 | JGAD000907 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000386 | 2022/12/26-2025/03/31 |
