GEO series

3D genome of CD8+ T cells reveals IRF8-mediated exhaustion in cancer

GSE269676 Mus musculus (mouse) Other 18 samples Submitted 2025/10/01 Platform GPL21273

At a glance

mouse · 18 samples

Organism: Mus musculus (mouse)
Samples: 18 samples: 9 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.

Summary (written by the submitters)

CD8+ T cell responses are essential for anti-tumor immunity, but chronic antigen exposure in cancer can lead to T cell exhaustion, marked by high PD-1 expression. Recent studies have identified progenitor-like CD8+ T cells (Tprog cells) within tumor-infiltrating lymphocytes (TILs) that sustain antitumor responses. These cells can differentiate into terminally exhausted cells (Tterm cells), losing their proliferative and effector functions.

Read the full summary ↓

Immunotherapy aims to enhance CD8+ TILs functionality, promoting their transition from Tprog to Tterm cells. However, the mechanisms behind this exhaustion remain unclear. Single-cell RNA sequencing and ATAC-seq have revealed distinct profiles and chromatin accessibility between progenitor and terminally exhausted states. Histone modifications predict a loss of enhancer-promoter contacts during this transition. Chromatin structure plays a crucial role in T cell differentiation. We constructed a high-resolution 3D genome map of CD8+ T cell subsets and, through multi-omics integration, identified chromatin structure changes linked to T cell exhaustion, including alterations in topologically associating domains (TADs) and chromatin loops, providing new insights into the genetic basis of CD8+ T cell exhaustion in cancer.

This dataset

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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE269676_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA1123215. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

9 conditions, mostly in duplicate

naive ×2 effector ×2 memory ×2 pro_tumor ×2 ter_tumor ×2 pro_cl13 ×2 ter_cl13 ×2 WT ×2 +1 more

Supports a case/control comparison: 4 samples read as cases, 4 as controls.

How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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

GSM8324483 naive_rep1 naive
GSM8324484 naive_rep2 naive
GSM8324485 effector_rep1 effector
GSM8324486 effector_rep2 effector
GSM8324487 memory_rep1 memory
GSM8324488 memory_rep2 memory
GSM8324489 pro_tumor_rep1 pro_tumor
GSM8324490 pro_tumor_rep2 pro_tumor
GSM8324491 ter_tumor_rep1 ter_tumor
GSM8324492 ter_tumor_rep2 ter_tumor
GSM8324493 pro_cl13_rep1 pro_cl13
GSM8324494 pro_cl13_rep2 pro_cl13
GSM8324495 ter_cl13_rep1 ter_cl13
GSM8324496 ter_cl13_rep2 ter_cl13
GSM8324497 WT_rep1 WT
GSM8324498 WT_rep2 WT
GSM8324499 Irf8_KO_rep1 Irf8_KO
GSM8324500 Irf8_KO_rep2 Irf8_KO

Datasets on a similar topic

GSE299305 3D genome of CD8+ T cells reveals IRF8-mediated exhaustion in cancer [Hi-C] 4 samples shares cd8, irf8-mediated, exhaustion
GSE277610 Endothelial PD-L1 brakes CD8+ T cell exhaustion, empowering anti-tumor immunity in non-small cell lung cancer 17 samples shares cd8, exhaustion
GSE333230 The Transcription Factor IRF8 drives tumor-specific exhaustion in CD8 T cells 12 samples shares cd8, exhaustion
GSE223164 Osr2 functions as a biomechanical checkpoint to aggravate CD8+ T cell exhaustion in tumor 49 samples shares cd8, exhaustion
GSE310452 Sustained A2AR expression and loss paradoxically promote CD8+ T cell exhaustion 12 samples shares cd8, exhaustion
GSE320177 All -trans retinoic acid suppresses CD8+ T cell terminal exhaustion which enhances anti–PD-1 efficacy against glioblastoma [RNA-Seq] 12 samples shares cd8, exhaustion
GSE223157 Osr2 functions as a mechanical checkpoint to augment CD8+ T cell exhaustion [YODA1_vs_DMSO_ATAC_CD8] 12 samples shares cd8, exhaustion
GSE307051 Active aldehydes accelerate CD8+ T cell exhaustion by metabolic alteration in the tumor microenvironment 3 samples shares cd8, exhaustion

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