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X-ray-induced more serious damage to CD8+ T cells in patients with hypopharyngeal squamous cell carcinoma (HPSCC) than those in healthy individuals

GSE274788 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/10/26 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 12 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
Head and neck cancerThis series is part of our curated briefing on it.
Samples
12 samples: 3 × CD8+ T cells from healthy individuals, untreated, 24h, vs 3 × CD8+ T cells from healthy individuals, irradiated (2Gy), 24h, vs 3 × CD8+ T cells from patients with HPSCC, untreated, 24h, vs 3 × CD8+ T cells from patients with HPSCC, irradiated (2Gy), 24h,Groups 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.
Summary (written by the submitters)
Radiotherapy (RT) is a commonly used clinical management for hypopharyngeal squamous cell carcinoma (HPSCC), which represents the most unfavorable prognosis among all subtypes of head and neck squamous cell carcinoma. However, radiation may cause lymphopenia, a significantly adverse event with detrimental prognostic implications for patients.
Read the full summary ↓
While CD8+ T cells are vital in tumor immunity, the specific effects of RT on CD8+ T cells as well as the underlying mechanisms have not been clearly elucidated. Here we found that subpopulations of peripheral T lymphocytes exhibited differential profiles in patients with HPSCC compared to healthy individuals both pre- and post-irradiation. Importantly, CD8+ T cells from HPSCC patients showed greater reduction of cytokine production, more severe proliferation defect, and increased apoptosis compared to those of healthy individuals after in vitro irradiation. Mechanistically, ATM-Chk2 pathway mediated the attenuated radiation-induced apoptosis of CD8+ T lymphocytes from HPSCC patients. Our study demonstrated that CD8+ T cells in patients with HPSCC are more sensitive to the radiation-induced damage than those in healthy individuals. Therefore, our findings present a potential immunotherapeutic target for safeguarding CD8+ T cells against radiation-induced damage.
This dataset
Open GSE274788 in finder → Find more human RNA-seq datasets → Head and neck cancer 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 GSE274788_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 PRJNA1148058 and SRA study SRP526504. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × CD8+ T cells from healthy individuals, untreated, 24h, vs 3 × CD8+ T cells from healthy individuals, irradiated (2Gy), 24h, vs 3 × CD8+ T cells from patients with HPSCC, untreated, 24h, vs 3 × CD8+ T cells from patients with HPSCC, irradiated (2Gy), 24h,

Supports a case/control comparison: 3 samples read as cases, 3 as controls.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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 Head and neck cancer datasets

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