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AMPK suppresses multiple cell death pathways to sustain tumor-associated macrophage proportion and promotes tumor progression

GSE291140 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/07/13 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 × TAMs from AMPKfl/fl mice vs 3 × TAMs from AMPKfl/flLyz2cre/cre mice vs 3 × TAMs from early stage tumor (8day) vs 3 × TAMs from Late stage tumor (15day)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.
Summary (written by the submitters)
Tumor-associated macrophages (TAMs) are a major immune cell population in the tumor microenvironment (TME). This part depends on their capacity to resist cell death by adapting to the harsh tumor microenvironment, characterized by nutrient deprivation and the accumulation of metabolic waste, through metabolic reprogramming.
Read the full summary ↓
This enables TAMs to not only utilize excess metabolites and metabolic waste in the tumor microenvironment as energy sources, but also to cope with metabolic stress by upregulating cysteine uptake and activating hypoxia-inducible factors, thereby maintaining their survival and function. However, the core genes that suppress TAM death in response to the metabolic dynamics of the tumor microenvironment during tumor progression remain unknown. In this study, we used proteomics analysis combined with experimental validation found that the degree of TAM apoptosis decreased while the level of AMPK activation increased during tumor progression. Notably, myeloid-specific knockout of AMPK significantly inhibits tumor growth, reduces TAM proportion in the tumor, and weakens its pro-tumor phenotype. Bulk RNA sequencing data analysis further revealed that specific knockout of AMPK in TAMs triggers multiple forms of cell death, including apoptosis, ferroptosis, and necroptosis. Further experimental validation confirmed that AMPK knockout not only induces apoptosis and ferroptosis in TAMs but may also trigger disulfidptosis. Mechanistic research suggested that AMPK might regulate cysteine uptake and the pentose phosphate pathway to inhibit ferroptosis and disulfidptosis in TAMs. In conclusion, this study identifies AMPK as a key regulator that responds to the metabolic dynamics of the TME and inhibits various forms of cell death in TAMs, providing new theoretical insights for TAM-targeted metabolic therapies.
This dataset
Open GSE291140 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 GSE291140_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 PRJNA1232078 and SRA study SRP568075. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × TAMs from AMPKfl/fl mice vs 3 × TAMs from AMPKfl/flLyz2cre/cre mice vs 3 × TAMs from early stage tumor (8day) vs 3 × TAMs from Late stage tumor (15day)

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
Datasets on a similar topic

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