NBDC Research ID: hum0358.v2
SUMMARY
Aims: To identify molecular markers involved in the development and prognosis of cervical adenocarcinoma, we would like to elucidate the molecular biological characteristics of cervical adenocarcinoma in relation to the carcinogenesis of other cervical cancers (squamous cell carcinoma), vaginal and vulvar cancers. In addition, some squamous cell carcinomas of the cervix develop at a young age and have a poor prognosis. Furthermore, small cell carcinoma of the uterine cervix also progresses rapidly and has a poor prognosis, making the establishment of diagnostic and therapeutic methods an urgent task.
Methods: Whole exome sequencing, RNA-seq, single-cell RNA sequencing
Participants/Materials: cervical cancer total of 19 + 4 cases, NIKS18 cell line
[Whole exome sequencing] 1 case: 3 samples of tumor/tumor-derived organoids/peripheral blood cell, 4 cases: 8 tumor samples, 2 peripheral blood samples, 2 normal areas near the tumors
[RNA-seq] 1 case: 2 samples of tumor/tumor-derived organoids, 13 cases: 13 tumor samples, 5 cases: multiple sampling from within the same tumor for a total of 77 samples, 3 cases: 3 samples from normal cervical tissue-derived organoids, 1 case: 4 samples from normal cervical tissue, siRNA-mediated knockdown samples of NIKS18 cell line (siNPM3: 2 samples、siNC: 3 samples)
[single-cell RNA-seq] 1 case: 50cells of normal cervical tissue-derived organoids
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
|
JGAS000582 JGAS000586 |
NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2022/12/20 |
| JGAS000640 | NGS (RNA-seq, scRNA-seq) | Controlled-access (Type I) | 2023/10/19 |
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MOLECULAR DATA
| Participants/Materials |
cervical cancer (ICD10: C539) [JGAS000582] 4 cases: 8 tumor samples, 2 peripheral blood samples, 2 normal areas near the tumor [JGAS000586] 1 case: 3 samples of tumor/tumor-derived organoids/peripheral blood |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumors, tumor-derived organoids, peripheral blood cells, or normal areas near the tumor |
| Cell Lines | - |
| Library Construction (kit name) | Twist Comprehenive exome |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | bwa, bowtie2 |
| Mapping Quality | ≧30 |
| Reference Genome Sequence | hg38 |
| Coverage (Depth) | 168x (39x-318x) |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000708: 76 GB (bam) JGAD000713: 25.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
cervical cancer (ICD10: C539) [JGAS000582] 5 cases: multiple sampling each from within the same tumor for a total of 77 samples [JGAS000586] 1 case: 2 samples of tumor/tumor-derived organoids [JGAS000586] 13 cases: 13 samples of tumors [JGAS000640] 3 cases: 3 samples of normal cervical tissue-derived organoids [JGAS000640] 1 case: 4 samples of normal cervical tissue
siRNA-mediated knockdown samples of NIKS18 cell line [JGAS000640] siNPM3: 2 samples, siNC: 3 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [MiSeq] |
| Library Source | RNAs extracted from tumor tissues, non-tumor tissues, patient-derived organoids, or siRNA-mediated knockdown samples of NIKS18 |
| Cell Lines | NIKS18 is NIKS, which is a human keratinocyte cell line (ATCC CRL-12191), contain HPV18 genome as episomes |
| Library Construction (kit name) | Nextera XT DNA Library Preparation Kit |
| Fragmentation Methods | Nextera XT transposome |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000708: 76 GB (bam) JGAD000713: 25.5 GB (fastq) JGAD000770: 19.8 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
cervical cancer (ICD10: C539) 1 case: 50 cells of normal cervical tissue-derived organoids |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [MiSeq] |
| Library Source | RNAs extracted from cells of normal cervical tissue-derived organoids |
| Cell Lines | - |
| Library Construction (kit name) | Nextera XT DNA Library Preparation Kit |
| Fragmentation Methods | Nextera XT transposome |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000770 |
| Total Data Volume | 19.8 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Kenbun Sone
Affiliation: Department of obstetrics and gynecology, The university of Tokyo Hospital
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Japan Program for Infectious Diseases Research and Infrastructure, Japan Agency for Medical Research and Development (AMED) | Study of HPV-18 persistent infection and carcinogenesis in the squamocolumnar junction cells using novel culture technologies | JP22wm0325014 |
| Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS), Japan Agency for Medical Research and Development (AMED) | Transcriptome analysis of single cell and micro tissue sections for supporting of drug discovery | JP21am0101104 |
| Japan Program for Infectious Diseases Research and Infrastructure, Japan Agency for Medical Research and Development (AMED) | Elucidation of stem cell carcinogenesis mechanism of HPV18-associated cervical cancer by integration of single-cell analysis technologies Japan Agency for Medical Research and Development | JP23wm0325057 |
| KAKENHI Grant-in-Aid for Early-Career Scientists | Identification of the cell of origin of uterine cervical cancer and elucidation of the regulatory mechanism for carcinogenesis and differentiation | 22K16853 |
| Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS), Japan Agency for Medical Research and Development (AMED) | Support of life science studies by all-in-one single cell/micro tissue multi-omics analysis | JP22ama121055 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Cells with stem-like properties are associated with the development of HPV18-positive cervical cancer | doi: 10.1111/cas.15664 | JGAD000708 |
| 2 | Application of organoid culture from HPV18-positive small cell carcinoma of the uterine cervix for precision medicine | doi: 10.1002/cam4.5588 | JGAD000713 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
