GEO series

Bi-directional immunosuppressive interactions between astrocytes and glioblastoma cells identified by barcoded viral tracing [Human Single Cell Dataset]

GSE263612 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2025/04/28 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Topic: GlioblastomaThis series is part of our curated briefing on it.
Samples: 12 samples: 4 × 1 vs 2 × 2 vs 2 × 3_1 vs 2 × 3_2Groups 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: Barcoded viral tracing identifies immunosuppressive astrocyte-glioma interactionsNature · 2025

Summary (written by the submitters)

Glioblastoma (GBM) is the most lethal primary brain malignancy. Immunosuppression in the GBM tumor microenvironment (TME) presents a major barrier to immune-targeted therapies. However, our understanding of mechanisms of immunomodulation in the GBM TME is still limited.

Read the full summary ↓

To address this challenge, we developed a viral barcode interaction tracing approach for the analysis of cell-cell communication in the TME in GBM samples and preclinical models with single-cell resolution, which we combined with single-cell and bulk RNA-seq analyses of GBM clinical samples and pre-clinical models, human organotypic GBM slice cultures, in vivocell-specific CRISPR/Cas9-driven genetic perturbations and human and mousein vitroexperimental systems to identify a novel bi-directional communication pathway between ANXA1 expressed inastrocytes and its receptor FPR1 expressed by GBM cells that limits anti-tumor immune responses. ANXA1 expression in astrocytes and FPR1 expression in cancer cells are associated with shorter survival and earlier recurrence in GBM patients. The inactivation of astrocyte-glioma ANXA1/FPR1-signaling enhanced tumor specific CD4+ and CD8+ T-cell responses, increasing tumor infiltration by neoantigen-specific CD8+ T cells while limiting transcriptional modules linked to T-cell exhaustion; ANXA1/FPR1-signaling inactivation also boosted tumor-associated macrophage responses. Using pre-clinical models and human GBMin vitroexperimental systems, we established that FPR1 inhibits immunogenic necroptosis in tumor cells, while ANXA1 retrograde signaling suppresses NF-kB and inflammasome activation within astrocytes. In summary, we developed a new barcoding approach to analyze TME cell-cell interactions with single-cell resolution in clinical samples and pre-clinical models, and used it to identify a novel pathway of bidirectional ANXA1–FPR1 astrocyte-GBM communication which promotes immunoevasion and cancer progression.

Published in

Barcoded viral tracing identifies immunosuppressive astrocyte-glioma interactions

Andersen BM, Faust Akl C, Wheeler MA et al. · Nature 2025 · PMID 40562937 · doi:10.1038/s41586-025-09191-9

This dataset

Open GSE263612 in finder → Find more human RNA-seq datasets → Glioblastoma landscape →

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 GSE263612_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 PRJNA1098411 and SRA study SRP500633. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40562937) ↗

Study design

4 × 1 vs 2 × 2 vs 2 × 3_1 vs 2 × 3_2

Supports a between-group comparison across 10 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 10 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

GSM8195234 1_1 1
GSM8195235 1_2 1
GSM8195236 1_3 1
GSM8195237 1_4 1
GSM8195238 1_5_a
GSM8195239 1_5_b
GSM8195240 2_1 2
GSM8195241 2_2 2
GSM8195242 3_1_1 3_1
GSM8195243 3_1_2 3_1
GSM8195244 3_2_1 3_2
GSM8195245 3_2_2 3_2

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.