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Dominant interfering CARD11 variants disrupt JNK signaling to promote GATA3 expression in T cells

GSE288360 Homo sapiens (human) RNA-seq (gene expression) 60 samples Submitted 2025/02/28 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 60 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)
Samples
60 samples: 12 conditions, mostly with about 5 replicates eachGroups 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
Dominant interfering CARD11 variants disrupt JNK signaling to promote GATA3 expression in T cellsThe Journal of experimental medicine · 2025
Summary (written by the submitters)
Several “primary atopic disorders” are linked to monogenic defects that attenuate TCR signaling, favoring T helper 2 (TH2) cell differentiation. Patients with CARD11-associated atopy with dominant interference of NF-κB signaling (CADINS) disease suffer from severe atopy, caused by germline loss-of-function/dominant interfering (LOF/DI) CARD11 variants.
Read the full summary ↓
The CARD11 scaffold enables TCR-induced activation of NF-κB, mTORC1, and JNK signaling, yet the function of CARD11-dependent JNK signaling in T cells remains nebulous. Here we show that CARD11 is critical for TCR-induced activation of JNK1 and JNK2, as well as canonical JUN/FOS AP-1 family members. Patient-derived CARD11 DI variants attenuated wild-type CARD11 JNK signaling, mirroring effects on NF-κB. Transcriptome profiling revealed JNK inhibition upregulated TCR-induced expression of GATA3 and NFATC1, key transcription factors for TH2 cell development. Further, impaired CARD11-JNK signaling was linked to enhanced GATA3 expression in CADINS patient T cells. Our findings reveal a novel intrinsic mechanism connecting impaired CARD11-dependent JNK signaling to enhanced GATA3/NFAT2 induction and TH2 cell differentiation in CADINS patients.
Published in
Dominant interfering CARD11 variants disrupt JNK signaling to promote GATA3 expression in T cells
Bauman BM, Stinson JR, Kallarakal MA et al. · The Journal of experimental medicine 2025 · PMID 40111223 · doi:10.1084/jem.20240272
This dataset
Open GSE288360 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 GSE288360_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 PRJNA1217020 and SRA study SRP560627. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40111223) ↗
Study design
12 conditions, mostly with about 5 replicates each
WT Jurkat, Unstimulated, No inhibitor, ×5 WT Jurkat, Unstimulated, JNK inhibitor IX, ×5 WT Jurkat , Unstimulated, JNK-IN-8, ×5 WT Jurkat, Stimulated, No inhibitor, ×5 WT Jurkat, Stimulated, JNK inhibitor IX, ×5 WT Jurkat , Stimulated, JNK-IN-8, ×5 CARD11 KO Jurkat, Unstimulated, No inhibitor, ×5 CARD11 KO Jurkat, Unstimulated, JNK inhibitor… ×5 +4 more

Supports a between-group comparison across 60 samples.

How we read this: 12 replicated groups read from 60 sample titles; they account for 60 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

+ 20 more — browse all 60 samples with per-sample file links →

Datasets on a similar topic

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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.