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Research ID

hum0277-v1Release info

This page is a past version (v1). The latest version is v4.
Latest version (v4)

Research title

Analysis of genes related to the oncogenesis, progression or effectiveness of drug therapies of urological tumors

Research overview

Aims
To clarify the oncogenesis and the progression mechanism of urological tumors, we continuously collect tumor samples of our patients with high quality. Then we used them to comprehensive analyses such as genome sequencing or epi-genome sequencing. Through these analyses, we aim for elucidating the oncogenesis or for developing newly treatment strategies of each cancer.
Methods
single-cell RNA sequencing (scRNA-seq), whole exome sequencing (WES), RNA-seq, and Whole genome sequencing (WGS)
- scRNA-seq: We sliced surgically resected specimens and minced and digested into the single cell level. Libraries were prepared using Chromium single cell 3' kit (10X Genomics) according to the manufacturer's protocol. Paired-end sequencing was conducted on the NextSeq 500 platform (Illumina).
- WES: Libraries were prepared using SureSelect Human All Exon V6 (Agilent Technologies) and sequenced by using of NovaSeq 6000/PE150 (Illumina).
- RNA-seq: Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA CD Index Kit (Dual Index) and sequenced by using of HiSeq 2500 (Illumina).
- WGS: Genomic DNAs were extracted from frozen tissues. The library construction was done using the TruSeq Nano DNA Library Prep Kit and sequenced by using of NovaSeq 6000 (Illumina).
Participants/materials
19 patients with Birt-Hogg-Dubé (BHD) associated renal cell carcinoma (RCC), 1 patient with hereditary leiomyomatosis and renal cell cancer (HLRCC) associated RCC, 2 patients with Von Hippel-Lindau (VHL) associated RCC, 2 patients with sporadic clear cell RCC (ccRCC), 21 patients with sporadic chromophobe RCC (chRCC), 7 patients with sporadic oncocytoma, and 167 patients with RCC
- scRNA-seq: 2 BHD-associated RCC, 1 HLRCC-associated RCC, 2 VHL-associated RCC, and 2 ccRCC
- WES: 2 BHD-associated RCC, 1 HLRCC-associated RCC, 2 VHL-associated RCC, and 2 ccRCC
- RNA-seq: 10 BHD-associated RCC, 21 chRCC, 7 sporadic oncocytoma, and 167 RCC
- WGS: 9 BHD-associated RCC, and 69 RCC
URL
N/A

Datasets

The list is the one this version published; each dataset's content is shown as it is now.

CartDataset IDType of dataAnalysis methodAccess criteriaDate published
JGAD000414NGS (scRNA-seq, Exome, RNA-seq)
  • RNA-seq
  • scRNA-seq
  • WES
Controlled-access (Type I)2022-08-25

Data provider

Principal investigator
Hisashi Hasumi
Affiliation
Department of Urology, Yokohama City University

Research projects

No research projects.

Grants

NameTitleProject number
KAKENHI Grant-in-Aid for Scientific Research (C)
Analysis on the mechanism of renal tumorigenesis focusing on the metabolic and membrane transport regulation of FLCN
  • 19K09694
the MEXT Joint Usage/Research Center Program
The Advanced Medical Research Center of Yokohama City University "Center for Advanced Medical Research Collaboration in Multi-omics Gene Expression Regulation"
N/A

Related publications

TitleDOIDataset ID
Single-cell transcriptomes underscore genetically distinct tumor characteristics and microenvironment for hereditary kidney cancers
https://doi.org/10.1016/j.isci.2022.104463 (opens in a new tab)
Comparative analyses define differences between BHD-associated renal tumour and sporadic chromophobe renal cell carcinoma
https://doi.org/10.1016/j.ebiom.2023.104596 (opens in a new tab)
Comparative transcriptome atlas as an assistive modality for complex classification of rare kidney cancers
https://doi.org/10.1038/s41467-025-65303-z (opens in a new tab)

Controlled access users

Principal investigatorAffiliationCountry/RegionResearch titlePeriod of data useDataset ID
Antonio FinelliDepartment of Surgical Oncology, University Health Network/Princess Margaret Cancer CenterCanadaIdentifying novel immune evasion tumor immune networks as targets for ccRCC immunotherapy2023-11-16 – 2024-11-13
Soki KashimaUrology, Akita UniversityJapanA study to identify biomarkers for predicting treatment response and adverse events in immunotherapy for urological cancers (renal cell carcinoma and urothelial carcinoma)2026-06-18 – 2034-05-31