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IFN-γ-STAT1 Axis Drives MHC-II Antigen Presentation Potentiation in Tumor Associated Macrophages

GSE293728 Mus musculus (mouse) Single-cell RNA-seq 18 samples Submitted 2026/02/22 Platform GPL28330
At a glance

Single-cell RNA-seq · mouse · 18 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
18 samples: 6 conditions, mostly in triplicateGroups 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
Pan-cancer macrophage atlas uncovers that MHC-II(high) TAMs induce Treg activation through physical interactionsCell reports · 2026
Summary (written by the submitters)
While the IFN-γ-STAT1 signaling pathway is well-characterized in promoting MHC class II (MHC-II)-dependent antigen presentation within pro-inflammatory macrophages during acute infections, its functional dynamics in tumor-associated macrophages (TAMs) remain poorly understood. Here, we systematically investigated the immunomodulatory role of IFN-γ-STAT1 axis in TAMs through integrative bioinformatics and experimental validation.
Read the full summary ↓
Transcriptomic analysis of tumor-infiltrating myeloid cells across multiple cancer cohorts revealed a strong correlation between STAT1 activation and MHC-II pathway enrichment, particularly in IFN-γ-high TAM subsets. To mechanistically dissect this relationship, we employed bone marrow-derived macrophages (BMDMs) polarized under tumor-conditioned media and subjected them to IFN-γ stimulation. Single-cell RNA sequencing demonstrated that IFN-γ triggered STAT1 nuclear translocation, upregulating MHC-II genes. Our findings establish IFN-γ-STAT1 as a master regulator of TAM immunogenicity, proposing targeted STAT1 activation as a strategy to overcome myeloid-driven immunosuppression in cancer.
Published in
Pan-cancer macrophage atlas uncovers that MHC-II(high) TAMs induce Treg activation through physical interactions
Yang N, Yuan H, Wang W et al. · Cell reports 2026 · PMID 41966824 · doi:10.1016/j.celrep.2026.117230
This dataset
Open GSE293728 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 GSE293728_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1246119 and SRA study SRP576266. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41966824) ↗
Study design
6 conditions, mostly in triplicate
control ×3 bone marrow-derived macrophages stimulated th… ×3 bone marrow-derived macrophages stimulated wi… ×3 bone marrow-derived macrophages stimulated wi… ×3 bone marrow-derived macrophages stimulated wi… ×3 bone marrow-derived macrophages stimulated wi… ×3

Supports a case/control comparison: 15 samples read as cases, 3 as controls.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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
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