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Therapeutically targeting perivascular macrophage effector function improves CD8+ T-cell infiltration and response to chemotherapeutic drugs in cancer

GSE248272 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2025/08/06 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 30 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
30 samples: 6 conditions, mostly with about 5 replicates eachGroups 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
An oral heme oxygenase inhibitor targets immunosuppressive perivascular macrophages in preclinical models of cancerScience translational medicine · 2025
Summary (written by the submitters)
The tumor microenvironment (TME) plays a crucial role in cancer progression and represents an appealing target for cancer treatment. Tumor-associated macrophages (TAMs) are an abundant stromal cell type in the TME and, due to their plasticity, TAMs can be exploited to promote a pro-tumoral response. TAMs have been implicated in facilitating a variety of pro-tumoral pathways including resistance to anti-cancer therapeutics, immune suppression, angiogenesis, and metastasis.
Read the full summary ↓
However, pan-TAM depleting approaches have not delivered robust clinical outcomes as single agents. This might be explained due to their non-selective targeting of both pro- and anti-tumoral macrophage subsets. As such, therapeutically targeting key pro-tumoral TAM subsets may be a more desirable and efficacious strategy. Our group has recently characterised a subpopulation of pro-angiogenic and immune-suppressive TAMs which can be identified by their expression of the lymphatic vessel endothelial hyaluronan receptor-1 (LYVE-1). LYVE-1+ TAMs reside spatially proximal to blood vasculature and adopt a collaborative multi-cellular ‘nest’ arrangement which supports their biological activity. LYVE-1+ TAMs selectively express high levels of the immunomodulatory enzyme heme oxygenase-1 (HO-1), an enzyme which catabolizes heme to generate the biologically active catabolites carbon monoxide (CO), biliverdin and ferrous iron. Genetic inactivation of HO-1 in LYVE-1+ TAMs improve anti-tumor CD8+ T-cell infiltration into the TME and enhances the immune-stimulating effects of chemotherapy, resulting in sustain control of tumor growth in a spontaneous MMTV-PyMT murine model of breast cancer. This highlights that HO-1 represents a key effector pathway of these cells that prevents immune-elimination of tumors. Considering translation of these observations, unfortunately, current HO-1 inhibitors are not orally bioavailable, which limits their utility for chronic diseases, such as cancer, where daily administration would be required. In response to this hurdle, we developed a next generation HO-1 inhibitor called KCL-HO-1i. We demonstrate in pharmacokinetic studies that KCL-HO-1i is orally bioavailable in murine models with a serum half-life of around 3hours. Furthermore, oral delivery of KCL-HO-1i alongside standard of care chemotherapy delivers durable tumor control in MMTV-PyMT mice. We have characterised the response of the TME to KCL-HO-1i using flow cytometry, immunofluorescence and RNA sequencing approaches and demonstrate that KCL-HO-1i targeting perivascular LYVE-1+ TAM function supports a broader switch from an immunological ‘cold’ to ‘hot’ TME which provides a more favourable immune landscape for improving the response to chemotherapeutic drugs. Taken together, our data support the use of KCL-HO-1i as novel immunotherapeutic for targeting the function of perivascular TAMs in cancer.
Published in
An oral heme oxygenase inhibitor targets immunosuppressive perivascular macrophages in preclinical models of cancer
Bahri M, Al-Adhami T, Demirel E et al. · Science translational medicine 2025 · PMID 40768602 · doi:10.1126/scitranslmed.ads3085
This dataset
Open GSE248272 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 GSE248272_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 PRJNA1043144 and SRA study SRP473081. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40768602) ↗
Study design
6 conditions, mostly with about 5 replicates each
Control, ×5 5-FU treated, ×5 Gemcitabine treated, ×5 KCL-HO-1i treated, ×5 KCL-HO-1i/5-FU treated, ×5 KCL-HO-1i/Gemcitabine treated, ×5

Supports a case/control comparison: 25 samples read as cases, 5 as controls.

How we read this: 6 replicated groups read from 30 sample titles; they account for 30 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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