scRNAseq analysis of CD8 T cells infiltrating the bladder and tumor of 4 non-muscle-invasive bladder cancer patients, before and after BCG treatment.

We performed scRNAseq analysis of CD8 T cells infiltrating the bladder and tumor of 4 non-muscle-invasive bladder cancer patients, before and after BCG treatment. In order to identify tumor-specific T cells, we selected CD8 T cells that were enriched in the tumor of the patient. We also selected CD8 T cells appearing in the bladder after BCG treatment, with the hypothesis that BCG treatment stimulates tumor-specific CD8 T cells. Next, we cloned the TCR of these T cells in a Jurkat cell line and tested these TCR for recognition of tumor-specific antigens.

Type: Transcriptome Sequencing
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000002007	FASTQ files from scRNAseq (smartseq2 protocol) from 2485 CD8 T cells from 4 non-muscle-invasive bladder cancer patients who received BCG treatment (induction treatment of 6 weekly instillations). Concerning the 'phenotype' column in metadata : pre-treatment samples include tumor samples ('Tumor') and normal adjacent bladder tissue ('Extratumor'). For post-treatment samples : no residual tumor was found in the bladder of the 4 patients after the BCG treatment . The post-treatment samples with 'Tumor' as phenotype denote samples from macroscopically suspect zones, but with microscopically no tumor detected.	Illumina HiSeq X	2485

Publications	Citations
Detection of spontaneous anti-neoepitope T-cell responses in non-metastatic bladder cancer patients. Brochier W, Nguyen S, Cesson V, Bricard O, van Baren N, Hames G, Dauguet N, Dano H, Tombal B, Rodrigues-Dias SC, Masnada A, Genolet R, Harari A, Roth B, Lucca I, Nardelli-Haefliger D, Coulie PG, Derré L. Front Immunol 16: 2025 1627914	0