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Gene expression data from precision cut tumor slices from head and neck or mesothelioma tumors

GSE250038 Homo sapiens (human) RNA-seq (gene expression) 26 samples Submitted 2024/05/22 Platform GPL21697
At a glance

RNA-seq (gene expression) · human · 26 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
MesotheliomaThis series is part of our curated briefing on it.
Samples
26 samples: 4 × HNC43 T vs 4 × Meso2 T vs 3 × Meso1 T vs 3 × Meso3 TGroups 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
Transcriptomic analysis-guided assessment of precision-cut tumor slices (PCTS) as an ex-vivo tool in cancer researchScientific reports · 2024
Summary (written by the submitters)
As cancer immunotherapy and precision medicine dynamically evolve, there is greater need for pre-clinical models that can better replicate the intact tumor and its complex tumor microenvironment (TME). Precision-cut tumor slices (PCTS) have recently emerged as an ex vivo human tumor model, offering the opportunity to study individual patient responses to targeted therapies, including immunotherapies.
Read the full summary ↓
However, little is known about the physiologic status of PCTS and how they can be utilized in view of the intra-tumoral heterogeneity. In this study, we generated PCTS from head and neck cancers (HNC) and mesotheliomas (Meso) and studied their viability in culture, the extent of variability in serial PCTS, and whether tumor immune response can be measured following PCTS T cell activation. We also undertook transcriptomic analyses to understand the changes that occur in the timeframe between PCTS generation and up to 72hr in culture. Our findings suggest that PCTS viability can be tumor-specific and culture conditions-dependent, but an overall viability of up to 72 hrs was observed. Tumor heterogeneity is present and can skew findings if appropriate experimental design and multiple control PCTS are not considered. Activation of endogenous T cells and measurement of immune responses is possible, however, our transcriptomic analyses showed major changes occurring during the first 24hr culture period of PCTS, involving genes related to wound healing, extracellular matrix, hypoxia, and IFNγ-dependent pathways. Our data suggest the PCTS model may be especially useful for studies involving exogenous immune therapies, such as adoptive cell therapy, rather than for the study of the effects of therapy on endogenous immune systems.
Published in
Transcriptomic analysis-guided assessment of precision-cut tumor slices (PCTS) as an ex-vivo tool in cancer research
Trivedi S, Tilsed C, Liousia M et al. · Scientific reports 2024 · PMID 38744944 · doi:10.1038/s41598-024-61684-1
This dataset
Open GSE250038 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 GSE250038_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 PRJNA1051641. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38744944) ↗
Study design
4 × HNC43 T vs 4 × Meso2 T vs 3 × Meso1 T vs 3 × Meso3 T

Supports a between-group comparison across 14 samples.

How we read this: 4 replicated groups read from 26 sample titles; they account for 14 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
More Mesothelioma datasets

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