GEO series

Coupling of response biomarkers between tumour and peripheral blood in patients undergoing chemoimmunotherapy

GSE252990 Homo sapiens (human) Single-cell RNA-seq 120 samples Submitted 2024/10/31 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 120 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)
Topic: MesotheliomaThis series is part of our curated briefing on it.
Samples: 120 samples: 120 samples, each with a distinct title — no replicated groupsGroups 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: Coupling of response biomarkers between tumor and peripheral blood in patients undergoing chemoimmunotherapyCell reports. Medicine · 2025

Summary (written by the submitters)

Platinum-based chemotherapy in combination with anti-PD-L1 antibodies has shown promising results in mesothelioma. However, the immunological mechanisms underlying its efficacy are not well understood and there are no predictive biomarkers to guide treatment decisions. Here, we combine time-course RNA sequencing of peripheral blood mononuclear cells with pre-treatment tumour transcriptome data from the 54-patient single arm phase II DREAM study.

Read the full summary ↓

Single cell RNA-seq and TCR-seq reveal CD8+ T effector memory (TEM) cells with stem-like properties are more abundant in peripheral blood of responders and this population expands upon treatment. These peripheral blood changes are linked to the transcriptional state of the tumour microenvironment. Combining information from both compartments, rather than individually, is most predictive of response. Our study highlights the complex, but predictive interactions between the tumour and immune cells in peripheral blood during the response to chemoimmunotherapy.

Published in

Coupling of response biomarkers between tumor and peripheral blood in patients undergoing chemoimmunotherapy

Chin WL, Cook AM, Chee J et al. · Cell reports. Medicine 2025 · PMID 39731918 · doi:10.1016/j.xcrm.2024.101882

This dataset

Open GSE252990 in finder → Find more human RNA-seq datasets → Mesothelioma 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 GSE252990_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 PRJNA1063601. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39731918) ↗

Study design

120 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 120 sample titles: 120 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

GSM8011949 PT01, Baseline
GSM8011950 PT01, C2D1
GSM8011951 PT01, C3D1
GSM8011952 PT02, Baseline
GSM8011953 PT02, C2D1
GSM8011954 PT02, C3D1
GSM8011955 PT03, Baseline
GSM8011956 PT03, C2D1
GSM8011957 PT03, C3D1
GSM8011958 PT05, Baseline
GSM8011959 PT05, C2D1
GSM8011960 PT05, C3D1
GSM8011961 PT06, Baseline
GSM8011962 PT06, C2D1
GSM8011963 PT06, C3D1
GSM8011964 PT07, Baseline
GSM8011965 PT07, C2D1
GSM8011966 PT07, C3D1
GSM8011967 PT09, Baseline
GSM8011968 PT09, C2D1
GSM8011969 PT09, C3D1
GSM8011970 PT10, Baseline
GSM8011971 PT10, C2D1
GSM8011972 PT10, C3D1
GSM8011973 PT11, Baseline
GSM8011974 PT11, C2D1
GSM8011975 PT11, C3D1
GSM8011976 PT13, Baseline
GSM8011977 PT13, C2D1
GSM8011978 PT13, C3D1
GSM8011979 PT15, Baseline
GSM8011980 PT15, C2D1
GSM8011981 PT15, C3D1
GSM8011982 PT18, Baseline
GSM8011983 PT18, C2D1
GSM8011984 PT18, C3D1
GSM8011985 PT19, Baseline
GSM8011986 PT19, C2D1
GSM8011987 PT19, C3D1
GSM8011988 PT20, Baseline

+ 80 more — browse all 120 samples with per-sample file links →

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GSE249903 Activation of hepatocyte growth factor (HGF)/MET signaling as a mechanism of acquired resistance to a novel YAP1/TEAD small molecule inhibitor. 49 samples same disease briefing
GSE262853 Gene expression analysis in mesothelioma cell lines with and without K-975 treatment 36 samples same disease briefing
GSE250038 Gene expression data from precision cut tumor slices from head and neck or mesothelioma tumors 26 samples same disease briefing
GSE274983 Soluble Mesothelin-Related Peptide as a Prognosticator in Pleural Mesothelioma Patients Receiving Checkpoint Immunotherapy 18 samples same disease briefing
GSE282239 A new soluble CSF1R-dimeric mutein with enhanced trapping of both CSF-1 and IL-34 reduces suppressive tumor-associated macrophages in mesothelioma. 12 samples same disease briefing
GSE292620 Genome-wide CRISPR Screen Identifies BUB1 Kinase as a Druggable Vulnerability in Malignant Pleural Mesothelioma 12 samples same disease briefing

Search all human RNA-seq datasets in GEO →

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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.