GEO series

Stem cell-like CD8+ T cells lacking PD-1 adapt to chronic stimulation by reducing TCR signaling and self-renewal capacity [RNA-seq]

GSE277648 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2026/01/16 Platform GPL21103

At a glance

RNA-seq (gene expression) · mouse · 16 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 16 samples: 8 conditions, mostly in duplicateGroups 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: Memory-like CD8(+) T cells lacking PD-1 adapt to persistent stimulation by reducing TCR signal transduction rather than increasing exhaustionFrontiers in immunology · 2026

Summary (written by the submitters)

CD8+ T cells responding to chronic viral infection adapt to continuous antigenic stimulation by the upregulation of inhibitory receptors. Here we addressed how memory-like CD8+ T cells (TML), which sustain the immune response in chronic infection due to their stem cell-like properties, adapt to chronic stimulation when they cannot express the co-inhibitory receptor PD-1.

Read the full summary ↓

We found that PD-1 deficient TML cells did not show evidence of a compensatory increases in the expression of other inhibitory receptors or exhaustion-related genes. Rather, these cells displayed a reduced ability to activate multiple signaling pathways downstream of the TCR. By-passing proximal TCR signaling events restored the activation of PD-1-deficient TML cells. Consistent with reduced TCR signaling, PD-1-deficient TML cells had a reduced ability to expand and self-renew in response to recall stimulation. Transient blockade of PD-1/PD-L1 interaction similarly reduced the stemness of TML cells. Thus, in the absence of PD-1, stem-like CD8+ T cells adapt to chronic stimulation by reducing the capacity of the TCR to transmit activating signals, which limits the stemness of these cells. Thus, PD-1 preserves the stemness of TML cells ensuring the long-term maintenance of the immune response to chronic infection.

Published in

Memory-like CD8(+) T cells lacking PD-1 adapt to persistent stimulation by reducing TCR signal transduction rather than increasing exhaustion

Charmoy M, Maier JM, Wyss T et al. · Frontiers in immunology 2026 · PMID 41727489 · doi:10.3389/fimmu.2026.1743170

This dataset

Open GSE277648 in finder → Find more mouse 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 GSE277648_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1163280 and SRA study SRP533820. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41727489) ↗

Study design

8 conditions, mostly in duplicate

WT naive, Tcf7+, S ×2 WT TEX, Tcf7-, S ×2 WT TML, Tcf7+, S ×2 PD-1 KO TML, Tcf7+, S ×2 PD-1 KO TEX, Tcf7-, S ×2 PD-1 KO naive, Tcf7+, S ×2 aPD-L1 TML, Tcf7+, S ×2 aPD-L1 TEX, Tcf7-, S ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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

GSM8526922 WT naive, Tcf7+, S1 WT naive, Tcf7+, S
GSM8526923 WT TEX, Tcf7-, S10 WT TEX, Tcf7-, S
GSM8526924 WT TML, Tcf7+, S11 WT TML, Tcf7+, S
GSM8526925 WT TEX, Tcf7-, S12 WT TEX, Tcf7-, S
GSM8526926 PD-1 KO TML, Tcf7+, S13 PD-1 KO TML, Tcf7+, S
GSM8526927 PD-1 KO TEX, Tcf7-, S14 PD-1 KO TEX, Tcf7-, S
GSM8526928 PD-1 KO TML, Tcf7+, S15 PD-1 KO TML, Tcf7+, S
GSM8526929 PD-1 KO TEX, Tcf7-, S16 PD-1 KO TEX, Tcf7-, S
GSM8526930 WT naive, Tcf7+, S2 WT naive, Tcf7+, S
GSM8526931 PD-1 KO naive, Tcf7+, S3 PD-1 KO naive, Tcf7+, S
GSM8526932 PD-1 KO naive, Tcf7+, S4 PD-1 KO naive, Tcf7+, S
GSM8526933 aPD-L1 TML, Tcf7+, S5 aPD-L1 TML, Tcf7+, S
GSM8526934 aPD-L1 TEX, Tcf7-, S6 aPD-L1 TEX, Tcf7-, S
GSM8526935 aPD-L1 TML, Tcf7+, S7 aPD-L1 TML, Tcf7+, S
GSM8526936 aPD-L1 TEX, Tcf7-, S8 aPD-L1 TEX, Tcf7-, S
GSM8526937 WT TML, Tcf7+, S9 WT TML, Tcf7+, S

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