GEO series

Dissecting cellular state alterations critical for the synergistic response and therapy resistance of the combined Abemaciclib, Temozolomide, and Radiation in DIPG PDOX models

GSE301111 Homo sapiens (human) Single-cell RNA-seq 14 samples Submitted 2026/08/07 Platform GPL34284Platform GPL34290

At a glance

Single-cell RNA-seq · human · 14 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: Homo sapiens (human)
Samples: 14 samples: 13 distinct titles, 1 of them repeatedGroups 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: Therapy-associated lineage plasticity in DIPG following combined CDK4/6 inhibitor, temozolomide, and radiationCancer letters · 2026

Summary (written by the submitters)

Diffuse intrinsic pontine glioma (DIPG) is a lethal pediatric brain cancer. Here, we demonstrated that combining the CDK4/6 inhibitor abemaciclib with temozolomide and radiation (the triple therapy) yields synergistic anti-tumor effects in DIPG organoids and significantly extends survival times in patient-derived orthotopic (intra-brain stem) xenograft (PDOX) models.

Read the full summary ↓

Mechanistically, we performed scRNA-seq and identified dynamic reprogramming of tumor cell states, including the expansion of NPC-like, depletion of OPC- and AC-like subpopulations, and persistence of MES-like and mitotic-like cells, that contributed to therapeutic resistance. Pseudotime trajectory analysis further revealed therapy-induced cell fate transitions within NPC- and OPC-like compartments, including the enrichment of stem-like cells. More importantly, we discovered that an alternative trajectory—exit from stemness toward more differentiated states—may also contribute to therapeutic failure. Additionally, we identified a novel radiation-resistant subpopulation and found a new set of transcriptional targets indicative of therapeutic vulnerability. This study demonstrated the triple therapy as a promising DIPG regimen that can be rapidly translated into clinical trials and nominated new cellular and molecular targets to overcome residual disease.

Published in

Therapy-associated lineage plasticity in DIPG following combined CDK4/6 inhibitor, temozolomide, and radiation

Huang ZL, Jiang T, Suarez Palacios MM et al. · Cancer letters 2026 · PMID 42532370 · doi:10.1016/j.canlet.2026.218771

This dataset

Open GSE301111 in finder → Find more 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 GSE301111_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 PRJNA1283950 and SRA study SRP597919. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42532370) ↗

Study design

13 distinct titles, 1 of them repeated

IBs-A0317DIPG PDOX model treated with temozol… ×2

Supports a case/control comparison: 11 samples read as cases, 2 as controls.

How we read this: Read from 14 sample titles: 13 distinct titles with little repetition. 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

GSM9075542 IBs-A0317DIPG PDOX model under control group
GSM9075543 IBs-A0317DIPG PDOX model treated with abemaciclib
GSM9075544 IBs-A0317DIPG PDOX model treated with radiation
GSM9075545 IBs-A0317DIPG PDOX model treated with temozolomide and radiation_biol rep 1
GSM9075546 IBs-A0317DIPG PDOX model treated with temozolomide and radiation_biol rep 2
GSM9075547 IBs-A0317DIPG PDOX model treated with abemaciclib and radiation
GSM9075548 IBs-A0317DIPG PDOX model treated with abemaciclib, temozolomide, and radiation
GSM9075549 IBs-9119DIPG PDOX model under control group
GSM9075550 IBs-9119DIPG PDOX model treated with abemaciclib
GSM9075551 IBs-9119DIPG PDOX model treated with radiation
GSM9075552 IBs-9119DIPG PDOX model treated with temozolomide and radiation
GSM9075553 IBs-9119DIPG PDOX model treated with abemaciclib and radiation
GSM9075554 IBs-9119DIPG PDOX model treated with abemaciclib, temozolomide, and radiation
GSM9075555 Primary DIPG biopsy sample

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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.