GEO series

Epigenetic heterogeneity and state-specific transcriptional programs determine differential drug response in osteosarcoma [Cut&Run]

GSE270503 Homo sapiens Other 56 samples Submitted 2025/09/29 Platform GPL18573

Summary

Osteosarcoma is a genomically complex tumor with structural rearrangements, aneuploidy, and chromosomal alterations, resulting in significant intertumoral heterogeneity. This complexity hampers the identification of key oncogenic pathways and subtypes. We hypothesized that chromatin accessibility could uncover molecular features to clarify their transcriptional programs, suggesting new therapies. Using ATAC-seq, H3K27ac profiling, and single-cell multiome analysis, we identified two distinct cellular states in osteosarcoma driven by unique transcription factor networks linked to normal bone development. These subtypes can be detected in patient samples via a specific gene expression signature with prognostic value.

This dataset

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Direct links to NCBI, no account and no request form: the whole study as GSE270503_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 56 samples.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗

Also filed as BioProject PRJNA1126764. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

16 conditions, mostly in duplicate

OS742_IgG ×5 OS152_IgG ×3 OS152_H3K27Ac ×3 OS526_IgG ×3 OS526_H3K27Ac ×3 OS742_H3K27Ac ×3 OS052_IgG ×2 OS052_H3K27Ac ×2 +8 more

Supports a between-group comparison across 40 samples.

16 replicated groups read from the first 40 of 56 sample titles; they account for 40 of them. Check it against the sample list below before relying on it.

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