GEO series

Trained immunity is facilitated by T cell-induced CD40-TRAF6 signaling [ChIP-seq]

GSE228182 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2024/08/26 Platform GPL18573

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Homo sapiens (human)
Samples: 18 samples: 18 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: Trained immunity is regulated by T cell-induced CD40-TRAF6 signalingCell reports · 2024

Summary (written by the submitters)

Trained immunity refers to epigenetic and metabolic changes in innate immune cells following exposure to inflammatory signals, leading to a heightened response to secondary stimuli. Although this innate immune memory contributes to host defense against infections, it can also have maladaptive consequences in a broad range of immune-driven conditions.

Read the full summary ↓

During the past decade, we have gained an increasingly better understanding of the molecular regulation of trained immunity, but the role of adaptive immune cells in modulation of trained immunity remains largely unknown. Here, we show that T cell interactions contribute to the induction of trained immunity in monocytes and that this mediated by CD40-TRAF6 signaling. Specifically, we found that inhibiting CD40-TRAF6 signaling prevents the induction of functional, transcriptomic, metabolic and epigenetic changes associated with trained immunity. Apart from detailed in vitro studies, we inhibited CD40-TRAF6 signaling in vivo in myeloid cells in a murine heart transplantation model which resulted in prolonged allograft survival. When the animals were additionally treated with costimulatory blockade by CTLA4-Ig, we observed immunological tolerance to the graft. Combined, our study reveals that trained immunity induction is regulated by CD40-TRAF6 signaling between myeloid and adaptive immune cells, and that this signaling can be efficiently leveraged for therapeutic purposes.

Published in

Trained immunity is regulated by T cell-induced CD40-TRAF6 signaling

Jacobs MME, Maas RJF, Jonkman I et al. · Cell reports 2024 · PMID 39178113 · doi:10.1016/j.celrep.2024.114664

This dataset

Open GSE228182 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE228182_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA948446 and SRA study SRP429158. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39178113) ↗

Study design

18 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 18 sample titles: 18 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

GSM7116191 BC2118 RPMI H3K4me3
GSM7116192 BC2118 HKCA H3K4me3
GSM7116193 BC2118 HKCA+CD40i H3K4me3
GSM7116194 BC2119 RPMI H3K4me3
GSM7116195 BC2119 HKCA H3K4me3
GSM7116196 BC2119 HKCA + CD40i H3K4me3
GSM7116197 BC2121 RPMI H3K4me3
GSM7116198 BC2121 HKCA H3K4me3
GSM7116199 BC2121 HKCA + CD40i H3K4me3
GSM7116200 BC2118 RPMI H3K27Ac
GSM7116201 BC2118 HKCA H3K27Ac
GSM7116202 BC2118 HKCA+CD40i H3K27Ac
GSM7116203 BC2119 RPMI H3K27Ac
GSM7116204 BC2119 HKCA H3K27Ac
GSM7116205 BC2119 HKCA + CD40i H3K27Ac
GSM7116206 BC2121 RPMI H3K27Ac
GSM7116207 BC2121 HKCA H3K27Ac
GSM7116208 BC2121 HKCA + CD40i H3K27Ac

Datasets on a similar topic

GSE228184 Trained immunity is facilitated by T cell-induced CD40-TRAF6 signaling 27 samples shares cd40-traf6, cell-induced, facilitated, immunity, trained
GSE323311 Human Macrophages Encode Stimulus-Specific Information of Prior Exposures Through Trained Immunity 48 samples shares immunity, trained
GSE262097 Remodeling of Histone 3 Lysine 18 lactylation (H3K18lac) in monocytes-to-macrophage differentiation and induction of Trained Immunity by BCG in vitro 37 samples shares immunity, trained
GSE280903 Trained immunity suppression determines kidney allograft survival [ChIP] 24 samples shares immunity, trained
GSE246075 Anchored screening identifies transcription factor blueprints underlying dendritic cell diversity and subset-specific anti-tumor immunity [human ChIP-seq] 13 samples shares immunity, chip-seq
GSE328649 Lineage 2-Beijing Mycobacterium tuberculosis strains suppress BCG-trained innate immunity early after infection 39 samples shares immunity, trained
GSE262099 Effect of Lactate dehydrogenase inhibitor (LDHi; GSK2837808A) on BCG vaccine induced trained immunity in vitro 28 samples shares immunity, trained
GSE262098 Transcriptomes during monocyte-to-macrophage differentiation and BCG induced trained immunity in vitro 21 samples shares immunity, trained

Search all human ChIP / ATAC / CUT&Tag 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.