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 IDType of DataCriteriaRelease 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

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

Exome

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

JGAD000708

JGAD000713

Total Data Volume

JGAD000708: 76 GB (bam)

JGAD000713: 25.5 GB (fastq)

Comments (Policies) NBDC policy

 

RNA-seq

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

JGAD000708

JGAD000713

JGAD000770

Total Data Volume

JGAD000708: 76 GB (bam)

JGAD000713: 25.5 GB (fastq)

JGAD000770: 19.8 GB (fastq)

Comments (Policies) NBDC policy

 

scRNA-seq

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):

NameTitleProject 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

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