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The Cd4+ T cell population Partners with Tpex CD8 T cells to mediate Antitumor Immunity in the Tumor Microenvironment.[PB cohort2]

GSE308745 Homo sapiens (human) Single-cell RNA-seq 87 samples Submitted 2026/02/05 Platform GPL16791Platform GPL28038Platform GPL24676
At a glance

Single-cell RNA-seq · human · 87 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
87 samples: 87 samples, each with a distinct title — no replicated groupsGroups 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
The CD4(+) T cell population partners with Tpex CD8(+) T cells to mediate antitumor immunity in the tumor microenvironmentNature communications · 2026
Summary (written by the submitters)
The priming, expansion, and function of CD8⁺ T cells are helped by CD4⁺ T cells via dendritic cells. Precursor exhausted T cells (Tpex) maintain self-renewal and supply cytotoxic CD8⁺ T cells in the tumor microenvironment (TME), but the identity of their CD4⁺ T-cell partners remains unclear. Here, we perform scRNA-seq, scTCR-seq, and mass cytometry analysis on peripheral blood, tumor, and lymph nodes derived from lung cancer patients and identify a population of IL-7Rhigh CCR6⁺ Th1-like CD4⁺ T cells, namedTh7R, that is numerically and spatially partnered with Tpex cells.
Read the full summary ↓
Th7R cells express lymphotoxin-β and CXCL13, correlate with high endothelial venules, and co-localize with Tpex in tertiary lymphoid structures. Furthermore, Th7R cell abundance correlates with Tpex numbers in the TME and lymph nodes, and adoptive transfer of Th7R increases Tpex in a preclinical mouse model of skin cancer. In lung cancer patients, Th7R and Tpex in TME are associated with better response to neoadjuvant PD-1 blockade therapy. Thus, these results suggest that Th7R cells act as partners of Tpex CD8 T cells to sustain antitumor T-cell immunity.
Published in
The CD4(+) T cell population partners with Tpex CD8(+) T cells to mediate antitumor immunity in the tumor microenvironment
Takei S, Yamasaki S, Yamaguchi O et al. · Nature communications 2026 · PMID 41904165 · doi:10.1038/s41467-026-71161-0
This dataset
Open GSE308745 in finder → Find more human RNA-seq datasets →
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 GSE308745_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 PRJNA1332649 and SRA study SRP624803. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41904165) ↗
Study design
87 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 87 sample titles: 87 distinct titles with little repetition. 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

+ 47 more — browse all 87 samples with per-sample file links →

Datasets on a similar topic

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