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Gene expression profiles of stimulated CAR-T cells targeting TNF-NTF

GSE279778 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/07/23 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 12 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
Homo sapiens (human)
Topic
Acute myeloid leukemiaThis series is part of our curated briefing on it.
Samples
12 samples: 3 × TNF-NTF CART, +NALM6 TNF-NTF, dono vs 3 × G6/7R TNF-NTF CART, +NALM6 TNF-NTF, dono vs 3 × TNF-NTF CART, +THP1, dono vs 3 × G6/7R TNF-NTF CART, +THP1, donoGroups 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
JAK-STAT-activated, fratricide-resistant CAR-T cells targeting membrane-bound TNF effectively treat AML and solid tumorsJournal for immunotherapy of cancer · 2025
Summary (written by the submitters)
Chimeric antigen receptor (CAR)-T cell therapy is a promising therapeutic approach for relapsed or refractory acute myeloid leukemia (AML). However, optimal target antigens have yet to be established. A subset of AML cells express TNF, which is initially expressed on the cell surface and subsequently secreted by proteolytic cleavage of the extracellular portion.
Read the full summary ↓
We generated CAR-T cells targeting the N-terminal fragment of TNF (TNF-NTF) that remains on the cell surface after shedding. We ablated TNF gene to avoid fratricide and coexpressed chimeric cytokine receptor (G6/7R) that we had previously developed in CAR-T cells to provide constitutive IL-7 signaling. The G6/7R-expressing TNF-TNF CAR-T cells exhibited potent and durable therapeutic efficacy in vivo. Our data suggest that TNF-TNF may be a promising target antigen for CAR-T cells applicable to AML.
Published in
JAK-STAT-activated, fratricide-resistant CAR-T cells targeting membrane-bound TNF effectively treat AML and solid tumors
Nakashima T, Ouchida T, Ishikawa Y et al. · Journal for immunotherapy of cancer 2025 · PMID 40659447 · doi:10.1136/jitc-2024-011067
This dataset
Open GSE279778 in finder → Find more human RNA-seq datasets → Acute myeloid leukemia 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 GSE279778_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 PRJNA1174337 and SRA study SRP539256. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40659447) ↗
Study design
3 × TNF-NTF CART, +NALM6 TNF-NTF, dono vs 3 × G6/7R TNF-NTF CART, +NALM6 TNF-NTF, dono vs 3 × TNF-NTF CART, +THP1, dono vs 3 × G6/7R TNF-NTF CART, +THP1, dono

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
More Acute myeloid leukemia datasets

Search all human RNA-seq datasets in GEO →

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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.