GEO series

NF-κB transcription factors RelA and c-Rel selectively control CD4+ T-cell function in multiple sclerosis and cancer [bulk_mouse]

GSE239700 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/03/28 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 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: Mus musculus (mouse)
Samples: 12 samples: 4 × Rela-KO mouse Tconv cells, vs 4 × Rel-KO mouse Tconv cells, vs 4 × Ctrl mouse Tconv cells,Groups 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: NF-κB subunits RelA and c-Rel selectively control CD4+ T cell function in multiple sclerosis and cancerThe Journal of experimental medicine · 2024

Summary (written by the submitters)

The outcome of cancer and autoimmunity is dictated by the recruitment and effector functions of CD4+ conventional T cells (Tconv cells). The NF-kappaB (NF-κB) family of transcription factors is implicated in different aspects of Tconv cell biology, but the cell-autonomous roles of NF-κB subunits are elusive. Here, we explored the contributions of canonical RelA and c-Rel subunits to Tconv function in health and disease.

Read the full summary ↓

We found that RelA, rather than c-Rel, shaped the transcriptome of mouse and human Tconv cells at steady-state and was required for Tconv polarization toward the TH17 lineage in vitro. RelA-deficient mice were fully protected against neuro-inflammation in a mouse model of multiple sclerosis (MS), because of defective transition to a pathogenic TH17 gene expression program. In contrast, Tconv-restricted ablation of c-Rel, but not RelA, impaired their function in the microenvironment of transplanted tumors, resulting in enhanced cancer burden. c-Rel in Tconv cells was required for the response to PD-1-blockade therapy, and a c-Rel-dependent gene signature was correlated with better response and prognosis in anti-PD-1-treated patients. Our data demonstrate a division of labor between different subunits of the NF-κB pathway, paving the way for subunit-targeted immunotherapies.

Published in

NF-κB subunits RelA and c-Rel selectively control CD4+ T cell function in multiple sclerosis and cancer

Lalle G, Lautraite R, Bouherrou K et al. · The Journal of experimental medicine 2024 · PMID 38563819 · doi:10.1084/jem.20231348

This dataset

Open GSE239700 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 GSE239700_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 PRJNA1000591 and SRA study SRP452420. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38563819) ↗

Study design

4 × Rela-KO mouse Tconv cells, vs 4 × Rel-KO mouse Tconv cells, vs 4 × Ctrl mouse Tconv cells,

Supports a between-group comparison across 12 samples.

How we read this: 3 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

GSM7670193 Rela-KO mouse Tconv cells, rep. 1 Rela-KO mouse Tconv cel…
GSM7670194 Rela-KO mouse Tconv cells, rep. 2 Rela-KO mouse Tconv cel…
GSM7670195 Rela-KO mouse Tconv cells, rep. 3 Rela-KO mouse Tconv cel…
GSM7670196 Rela-KO mouse Tconv cells, rep. 4 Rela-KO mouse Tconv cel…
GSM7670197 Rel-KO mouse Tconv cells, rep. 1 Rel-KO mouse Tconv cell…
GSM7670198 Rel-KO mouse Tconv cells, rep. 2 Rel-KO mouse Tconv cell…
GSM7670199 Rel-KO mouse Tconv cells, rep. 3 Rel-KO mouse Tconv cell…
GSM7670200 Rel-KO mouse Tconv cells, rep. 4 Rel-KO mouse Tconv cell…
GSM7670201 Ctrl mouse Tconv cells, rep. 1 Ctrl mouse Tconv cells,
GSM7670202 Ctrl mouse Tconv cells, rep. 2 Ctrl mouse Tconv cells,
GSM7670203 Ctrl mouse Tconv cells, rep. 3 Ctrl mouse Tconv cells,
GSM7670204 Ctrl mouse Tconv cells, rep. 4 Ctrl mouse Tconv cells,

Datasets on a similar topic

GSE255887 HDAC1 controls the generation and maintenance of effector-like CD8+ T cells during chronic viral infection 76 samples shares nf, control
GSE261250 Gfi1 controls the formation of effector CD8+ T cells during chronic infection and cancer 47 samples shares nf, control
GSE301327 RiboTag and bulk RNA sequencing using AAV-Control and AAV-shLarp1 infected sensory neurons. 12 samples shares nf, control
GSE301320 RiboTag and bulk RNA sequencing using AAV-Control and AAV-shCsde1 infected sensory neurons. 12 samples shares nf, control
GSE283382 N6-methyladenosine modulate second cell fate decision by enhancing mRNA stability of pivotal transcription factors during primitive endoderm development [TBLC_RNAseq] 98 samples shares transcription, factors
GSE243165 Signal-responsive transcription factors cooperate to establish alveolar macrophage identity 42 samples shares transcription, factors
GSE283392 Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function 25 samples shares transcription, control
GSE294832 Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part10] 1000 samples shares nf

Search all mouse 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.