GEO series

MOF-mediated PRDX1 acetylation regulates LPS-induced macrophage activation.

GSE231941 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/12/31 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: 3 × shCTRL_LPS0 vs 3 × shMOF_LPS0 vs 3 × shCTRL_LPS3 vs 3 × shMOF_LPS3Groups 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.

Summary (written by the submitters)

Macrophages respond to environmental cues in a plastic manner and play a crucial role in host defense, inﬂammation, and tissue homeostasis. Macrophage activation undergoes metabolic and transcriptomic reprogramming to adapt and tailor an appropriate response, regulating inﬂammation. Reactive oxygen species (ROS) have been shown to play a pivotal role in macrophage activation.

Read the full summary ↓

Nevertheless, the detailed molecular mechanism of how initial redox signals direct macrophage activation is not fully elucidated. Here, we uncover an unconventional role for histone acetyltransferase MOF (also known as KAT8) in regulating LPS-induced macrophage activation via modulating the acetylation of peroxiredoxin 1 (PRDX1), an H2O2 scavenger. We demonstrate that PRDX1 is a novel substrate of MOF and identify the major MOF-mediated acetylation site at lysine 197. K197 acetylation of PRDX1 (K197ac PRDX1) is dynamic and reversely regulated by HDAC6 or SIRT2. We observe that this acetylation is readily diminished in the immediate response to LPS. We demonstrate that K197ac PRDX1 fine-tunes its peroxidase activity, leading to the modulation of intracellular ROS levels in early response to LPS stimulation. Moreover, K197ac PRDX1 specifically regulates ERK1/2 phosphorylation, thereby modulating glycolytic metabolism in inflammatory macrophages. Consequently, K197ac PRDX1 tunes the expression and production of the proinflammatory cytokine, IL-6. Taken together, our findings describe a novel signaling module, MOF-PRDX1-ERK, which regulates LPS-induced macrophage activation at the metabolic and transcriptional levels.

This dataset

Open GSE231941 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 GSE231941_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 PRJNA970276 and SRA study SRP436454. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × shCTRL_LPS0 vs 3 × shMOF_LPS0 vs 3 × shCTRL_LPS3 vs 3 × shMOF_LPS3

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

GSM7306335 shCTRL_LPS0_Rep1 shCTRL_LPS0
GSM7306336 shCTRL_LPS0_Rep2 shCTRL_LPS0
GSM7306337 shCTRL_LPS0_Rep3 shCTRL_LPS0
GSM7306338 shMOF_LPS0_Rep1 shMOF_LPS0
GSM7306339 shMOF_LPS0_Rep2 shMOF_LPS0
GSM7306340 shMOF_LPS0_Rep3 shMOF_LPS0
GSM7306341 shCTRL_LPS3_Rep1 shCTRL_LPS3
GSM7306342 shCTRL_LPS3_Rep2 shCTRL_LPS3
GSM7306343 shCTRL_LPS3_Rep3 shCTRL_LPS3
GSM7306344 shMOF_LPS3_Rep1 shMOF_LPS3
GSM7306345 shMOF_LPS3_Rep2 shMOF_LPS3
GSM7306346 shMOF_LPS3_Rep3 shMOF_LPS3

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