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Sex-specific differences of amlexanox in a mouse model for atherosclerosis and MASLD

GSE338111 Mus musculus (mouse) RNA-seq (gene expression) 11 samples Submitted 2026/07/14 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 11 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
11 samples
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)
Inhibitor‑κB kinase epsilon (IKKε) is a non‑canonical IκB kinase involved in NF‑κB signaling and type I interferon responses. We recently demonstrated sex‑dependent effects of IKKε deletion on atherosclerosis and metabolic dysfunction‑associated steatotic liver disease (MASLD), with male knockout mice showing protection against both diseases, while female mice exhibited exacerbated inflammatory and metabolic disturbances.
Read the full summary ↓
These divergent outcomes were linked to differential effects on inflammatory pathways and lipid metabolism. To evaluate the therapeutic potential of pharmacological IKKε inhibition, we treated wild type mice with established atherosclerotic plaques and hepatic steatosis - induced by PCSK9 gain‑of‑function and Paigen diet - with the IKKε inhibitor amlexanox. Amlexanox modulated serum lipid levels and altered plaque composition but did not halt plaque progression. In the liver, treatment produced marked sex‑specific effects: male mice exhibited substantial improvement in steatosis, whereas female mice showed worsened lipid accumulation. These outcomes were reflected in pronounced sex‑dependent differences in serum and hepatic lipid and metabolite profiles, indicating regulation of fatty acid and bile-acid metabolism predominantly in males. Protein analyses in liver and adipose tissue further supported opposing metabolic and inflammatory responses between sexes after amlexanox treatment. Collectively, our findings indicate that therapeutic IKKε inhibition with amlexanox does not prevent progression of advanced atherosclerosis in this model but effectively ameliorates MASLD in male mice. In contrast, female mice experience aggravated hepatic lipid deposition. These results underscore the importance of incorporating sex‑specific analyses in metabolic and cardiovascular research and highlight the need to evaluate therapeutic strategies such as amlexanox in both sexes.
This dataset
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.

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 GSE338111_RAW.tar (it can run to tens of gigabytes).

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.

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 PRJNA1492523 and SRA study SRP716635. Searching any of these in the dataset finder brings you back here.

Samples in this study

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+ 11 more — browse all 11 samples with per-sample file links →

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