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The paradoxical significance of CD39+CD8+ T cells in clear cell renal cell carcinoma [scRNA-seq]

GSE285701 Homo sapiens (human) Single-cell RNA-seq 13 samples Submitted 2025/07/23 Platform GPL20301
At a glance

Single-cell RNA-seq · human · 13 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Topic
Kidney cancerThis series is part of our curated briefing on it.
Samples
13 samples: 3 × CD8+ Tcells, RT183 vs 3 × CD8+ Tcells, RT199 vs 3 × CD8+ Tcells, RT208 vs 2 × CD8+ Tcells, RB183Groups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinomaCell reports. Medicine · 2025
Summary (written by the submitters)
CD39+CD8+ T cells are known as tumour antigen-specific cells among CD8+ tumour-infiltrating lymphocytes (TILs). However, CD39+CD8+ T cells also reportedly exhibit immunosuppressive activity in hypoxic tumour models. Here we investigated CD39+CD8+ TILs with regards to their molecular phenotypes, developmental mechanisms, functions, and prognostic significance in clear cell renal cell carcinoma (ccRCC), a VHL mutation-associated hypoxic tumour.
Read the full summary ↓
Single-cell RNA and TCR analyses confirmed that CD39+CD8+ cells are a terminally exhausted subset of tumour-specific CD8+ TILs. CD39+CD8+ T-cell development was highly correlated with cAMP signals, and was directly induced by cAMP and TCR signallings. Analysis of an RCC cohort revealed a markedly elevated proportion of CD39+ cells among CD8+ TILs in ccRCC, compared to non-ccRCC. Moreover, the proportion of CD39+CD8+ TILs was associated with high tumour mutational burden and hypoxic features. Ex vivo functional assays revealed that CD39+CD8+ TILs exerted immunosuppressive activity on neighbouring CD8+ T cells via ectonucleotidase activity- and adenosine-dependent mechanisms. CD39+CD8+ TIL enrichment predicted poor prognosis of ccRCC patients, yet also predicted favourable treatment responses to anti-PD-1 therapy. This paradoxical prognostic significance in ccRCC is explained by the dual properties of CD39+CD8+ TILs: tumour antigen specificity and immunosuppressive activity.
Published in
Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma
Lee YJ, Jeon SH, Yeo JH et al. · Cell reports. Medicine 2025 · PMID 40961944 · doi:10.1016/j.xcrm.2025.102360
This dataset
Open GSE285701 in finder → Find more human RNA-seq datasets → Kidney cancer landscape →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE285701_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1200786 and SRA study SRP552817. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40961944) ↗
Study design
3 × CD8+ Tcells, RT183 vs 3 × CD8+ Tcells, RT199 vs 3 × CD8+ Tcells, RT208 vs 2 × CD8+ Tcells, RB183

Supports a between-group comparison across 11 samples.

How we read this: 4 replicated groups read from 13 sample titles; they account for 11 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
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