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Interleukin-15-armored GPC3-CAR T cells for patients with solid cancers

GSE253352 Homo sapiens (human) Single-cell RNA-seq 83 samples Submitted 2024/05/01 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 83 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
83 samples: 13 conditions, mostly with about 9 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
Interleukin-15-armored GPC3-CAR T cells for patients with solid cancersResearch square · 2024
Summary (written by the submitters)
Interleukin-15 (IL15) enhances the antitumor properties of CAR T cells in preclinical solid tumor models but its effects on CAR T cells in humans are not known. Here, we report the first-in-human evaluation of IL15 co-expression in CAR T cells in two cohorts of a total of 24 patients with glypican-3 (GPC3) expressing solid neoplasms. In cohort 1, GPC3-CAR T cells were safe, no objective antitumor responses were detected.
Read the full summary ↓
In cohort 2, co-expression of IL15 in GPC3-CAR T cells was associated with increased peak expansion in blood and measurable antitumor responses. Cytokine release syndrome was controlled with immunomodulation or with the inducible caspase 9 safety switch. Single cell transcriptomic analyses identified gene expression of tumor infiltrating CAR T cells associated with antitumor responses.
Published in
Interleukin-15-armored GPC3-CAR T cells for patients with solid cancers
Steffin D, Ghatwai N, Montalbano A et al. · Research square 2024 · PMID 38645165 · doi:10.21203/rs.3.rs-4103623/v1
This dataset
Open GSE253352 in finder → Find more human 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 GSE253352_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 PRJNA1056257 and SRA study SRP480600. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38645165) ↗
Study design
13 conditions, mostly with about 9 replicates each
Product IL15.CAR 15.CAR mRNA Patient ×12 PBMCs IL15.CAR 15.CAR mRNA Patient ×9 PBMCs IL15.CAR 15.CAR CAR-PCR Patient ×9 Biopsy IL15.CAR 15.CAR mRNA Patient ×8 Biopsy IL15.CAR TCR Patient ×8 PBMCs IL15.CAR TCR Patient ×7 Product IL15.CAR TCR Patient ×7 Product CAR DL1.CAR mRNA Patient ×6 +6 more

Supports a between-group comparison across 82 samples.

How we read this: 13 replicated groups read from 83 sample titles; they account for 82 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

+ 43 more — browse all 83 samples with per-sample file links →

Datasets on a similar topic

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