GEO series

Interferon subverts an AHR-JUN axis to promote CXCL13+ T cell in lupus [Time_coure_RNAseq]

GSE277730 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/09/22 Platform GPL16791

At a glance

RNA-seq (gene expression) · human · 24 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: 24 samples: 24 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: Interferon subverts an AHR-JUN axis to promote CXCL13(+) T cells in lupusNature · 2024

Summary (written by the submitters)

Expansion of B cell-helper T cells including T follicular helper (Tfh) and T peripheral helper (Tph) cells is a prominent feature of systemic lupus erythematosus (SLE), a prototypical autoimmune disease with broad autoantibody production. Human Tfh and Tph cells are marked by high production of the B cell chemoattractant CXCL13, yet regulation of T cell CXCL13 production and the relationship between a CXCL13+ state and other differentiated T cell states remains largely undefined.

Read the full summary ↓

Here, we identify a dramatic imbalance in CD4 T cell phenotypes in SLE patients, with expansion of PD-1+/ICOS+ CXCL13+ T cells and reduction of CD96hi IL-22+ T cells. Using CRISPR screens, we identify the aryl hydrocarbon receptor (AHR) as a potent negative regulator of CXCL13 production by human CD4 T cells. Transcriptomic, epigenetic, and functional studies demonstrate that AHR coordinates with AP-1 family member JUN to prevent CXCL13+ Tph/Tfh cell differentiation and promote an IL-22+ phenotype. Type I interferon (IFN), a pathogenic driver of SLE, opposes AHR and JUN to promote T cell production of CXCL13. These results place CXCL13+ Tph/Tfh cells on a polarization axis opposite from Th22 cells and reveal AHR, JUN, and IFN as key regulators of these divergent T cell states.

Published in

Interferon subverts an AHR-JUN axis to promote CXCL13(+) T cells in lupus

Law C, Wacleche VS, Cao Y et al. · Nature 2024 · PMID 38987586 · doi:10.1038/s41586-024-07627-2

This dataset

Open GSE277730 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 GSE277730_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 PRJNA1163685 and SRA study SRP533994. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38987586) ↗

Study design

24 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 24 sample titles: 24 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

GSM8528581 L29 AHRinh 12h RNA
GSM8528582 L29 TCDD 12h RNA
GSM8528583 L30 AHRinh 12h RNA
GSM8528584 L30 TCDD 12h RNA
GSM8528585 L31 AHRinh 12h RNA
GSM8528586 L31 TCDD 12h RNA
GSM8528587 L29 AHRinh 24h RNA
GSM8528588 L29 TCDD 24h RNA
GSM8528589 L30 AHRinh 24h RNA
GSM8528590 L30 TCDD 24h RNA
GSM8528591 L31 AHRinh 24h RNA
GSM8528592 L31 TCDD 24h RNA
GSM8528593 L29 AHRinh 48h RNA
GSM8528594 L29 TCDD 48h RNA
GSM8528595 L30 AHRinh 48h RNA
GSM8528596 L30 TCDD 48h RNA
GSM8528597 L31 AHRinh 48h RNA
GSM8528598 L31 TCDD 48h RNA
GSM8528599 L29 AHRinh 72h RNA
GSM8528600 L29 TCDD 72h RNA
GSM8528601 L30 AHRinh 72h RNA
GSM8528602 L30 TCDD 72h RNA
GSM8528603 L31 AHRinh 72h RNA
GSM8528604 L31 TCDD 72h RNA

Datasets on a similar topic

GSE233050 Interferon subverts an AHR-JUN axis to promote CXCL13+ T cells in lupus 76 samples shares ahr-jun, cxcl13, interferon, subverts, promote, lupus, axis
GSE252917 Interferon subverts an AHR-JUN axis to promote CXCL13+ T cells in lupus [JUN IFN] 12 samples shares ahr-jun, cxcl13, interferon, subverts, promote, lupus, axis
GSE302359 Interferons promote autophagy via the STAT1/STAT5B-SOCS1 axis 12 samples shares interferon, promote, axis
GSE277909 Epigenetic attenuation of interferon signaling drives aging-related improvements in systemic lupus 271 samples shares interferon, lupus
GSE298908 Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet's syndrome [RNA-seq] 113 samples shares interferon, promote
GSE278120 Interferon activation in bone marrow long-lived plasma cells in systemic lupus erythematosus 48 samples shares interferon, lupus
GSE299256 Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet's syndrome. 116 samples shares interferon, promote
GSE317789 Single-cell and spatial profiling reveal cDC2A-CXCL13+ CD8+ T-epithelial cell crosstalk and cytotoxicity through TNFRSF9 in cutaneous and mucosal lichen planus 42 samples shares cxcl13

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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.