GEO series

Xenoline-polarized macrophages as a physiologically relevant in vitro model of tumor-associated macrophages in glioblastoma

GSE296472 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2025/07/02 Platform GPL34284

At a glance

RNA-seq (gene expression) · human · 20 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: Homo sapiens (human)
Topic: GlioblastomaThis series is part of our curated briefing on it.
Samples: 20 samples: 5 conditions, mostly with about 4 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: Xenoline-polarized macrophages as an alternative in vitro model of tumor-associated macrophages in glioblastomaActa neuropathologica communications · 2025

Summary (written by the submitters)

Tumor-associated macrophages (TAMs) are the most abundant non-cancerous cell type in glioblastoma (GBM) and heavily influence GBM biology, contributing to tumor progression, therapeutic resistance, immune evasion, and neovascularization. Current in vitro models that utilize IL-4/IL-13 stimulation fail to capture the transcriptional and functional heterogeneity of TAMs observed in vivo.

Read the full summary ↓

In this study, we utilize a serum-free indirect co-culture model with patient-derived xenolines to polarize primary human macrophages and characterize their molecular and functional phenotypes. We demonstrate that xenoline-polarized macrophages diverge from classical M1/M2 states and instead adopt transcriptional signatures reflective of TAM subsets identified from patients. Notably, macrophages polarized with the radiation-therapy selected xenoline, JX14P-RT, exhibited gene expression patterns enriched for interferon response and hypoxia, mirroring recurrent GBM samples. In contrast, JX14P TAMs showed enrichment in phagocytic gene sets. Functional validation of these phenotypes revealed discrepancies between the transcriptionally predicted and observed phenotypes, emphasizing the importance of integrating phenotypic validation in sequencing studies. Altogether, our findings establish xenoline-polarized macrophages as a more physiologically relevant alternative to traditional models, offering a useful model for studying tumor-immune interaction in vitro.

Published in

Xenoline-polarized macrophages as an alternative in vitro model of tumor-associated macrophages in glioblastoma

Alrefai H, Lin B, Elkholy A et al. · Acta neuropathologica communications 2025 · PMID 40581639 · doi:10.1186/s40478-025-02057-1

This dataset

Open GSE296472 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 GSE296472_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 PRJNA1259443 and SRA study SRP583353. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40581639) ↗

Study design

5 conditions, mostly with about 4 replicates each

Macrophage, M0, ×4 Macrophage, M1, ×4 Macrophage, M2, ×4 Macrophage, 14P TAM, ×4 Macrophage, 14P-RT TAM, ×4

Supports a between-group comparison across 20 samples.

How we read this: 5 replicated groups read from 20 sample titles; they account for 20 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

GSM8970959 Macrophage, M0, rep 1 Macrophage, M0,
GSM8970960 Macrophage, M1, rep 1 Macrophage, M1,
GSM8970961 Macrophage, M2, rep 1 Macrophage, M2,
GSM8970962 Macrophage, 14P TAM, rep 1 Macrophage, 14P TAM,
GSM8970963 Macrophage, 14P-RT TAM, rep 1 Macrophage, 14P-RT TAM,
GSM8970964 Macrophage, M0, rep 2 Macrophage, M0,
GSM8970965 Macrophage, M1, rep 2 Macrophage, M1,
GSM8970966 Macrophage, M2, rep 2 Macrophage, M2,
GSM8970967 Macrophage, 14P TAM, rep 2 Macrophage, 14P TAM,
GSM8970968 Macrophage, 14P-RT TAM, rep 2 Macrophage, 14P-RT TAM,
GSM8970969 Macrophage, M0, rep 3 Macrophage, M0,
GSM8970970 Macrophage, M1, rep 3 Macrophage, M1,
GSM8970971 Macrophage, M2, rep 3 Macrophage, M2,
GSM8970972 Macrophage, 14P TAM, rep 3 Macrophage, 14P TAM,
GSM8970973 Macrophage, 14P-RT TAM, rep 3 Macrophage, 14P-RT TAM,
GSM8970974 Macrophage, M0, rep 4 Macrophage, M0,
GSM8970975 Macrophage, M1, rep 4 Macrophage, M1,
GSM8970976 Macrophage, M2, rep 4 Macrophage, M2,
GSM8970977 Macrophage, 14P TAM, rep 4 Macrophage, 14P TAM,
GSM8970978 Macrophage, 14P-RT TAM, rep 4 Macrophage, 14P-RT TAM,

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