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Clonally expanded effector CD4+ cytotoxic T lymphocytes are associated with severe neurological adverse events after immune checkpoint inhibitor therapy

GSE278119 Homo sapiens (human) Single-cell RNA-seq 44 samples Submitted 2025/12/03 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 44 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
44 samples: 44 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
Clonally expanded effector CD4(+) cytotoxic T lymphocytes are associated with severe neurological adverse events after immune checkpoint inhibitor therapyJournal for immunotherapy of cancer · 2025
Summary (written by the submitters)
Immune checkpoint inhibitor (ICI) therapies present a pillar of modern cancer therapy but can cause severe and potentially fatal neurological immune-related adverse events (n-irAEs). Here, we performed single-cell RNA sequencing and T cell receptor profiling of PBMCs of a cohort of 17 cancer patients receiving ICI therapy. Our data suggest alterations in regulatory T cell frequencies and B cell states, and a significant enrichment of clonally expanded CD4+ cytotoxic T lymphocytes (CD4+ CTLs) with an effector gene expression profile in n-irAE patients.
Published in
Clonally expanded effector CD4(+) cytotoxic T lymphocytes are associated with severe neurological adverse events after immune checkpoint inhibitor therapy
Giguelay AM, Maschmeyer P, Müller-Jensen L et al. · Journal for immunotherapy of cancer 2025 · PMID 41167637 · doi:10.1136/jitc-2025-012350
This dataset
Open GSE278119 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 GSE278119_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 PRJNA1165731. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41167637) ↗
Study design
44 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 44 sample titles: 44 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

+ 4 more — browse all 44 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.