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The Small Extracellular Vesicle-Mediated Intercellular Transformation of CXCR1Low to CXCR1High Tumor Cells Promotes the Progression of Head and Neck Squamous Cell Carcinoma

GSE253091 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2024/04/03 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 36 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
36 samples: 12 conditions, mostly in triplicateGroups 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
The small extracellular vesicle-mediated intercellular transformation of CXCR1(Low) to CXCR1(High) tumour cells promotes the progression of head and neck squamous cell carcinomaJournal of extracellular vesicles · 2024
Summary (written by the submitters)
The heterogeneity of tumor cells enables cancers to dynamically adapt to microenvironmental stresses during progression. However, the mechanism underlying the transformation and intercellular communication between heterogeneous tumor cells has remained elusive. Here, we report a “contagion model” that mediates intercellular transformation between heterogeneous tumor cells which facilitates tumor progression.
Read the full summary ↓
Initially identifying heterogeneous expression of CXCR1, a receptor for interleukin-8, in head and neck squamous cell carcinoma (HNSCC) tumor cells. Following interleukin-8-mediated activation, CXCR1High cells transformed CXCR1Low cells into CXCR1High cells through the secretion of small extracellular vesicles (sEVs), which increased the proportion of CXCR1High cells and facilitated tumor progression. Mechanistically, we demonstrate that sEVs derived from interleukin-8-activated CXCR1High cells contain high levels of ATP citrate lyase (ACLY), which acetylates NF-κB p65 and facilitates its nuclear translocation to transcribe CXCR1 in CXCR1Low cells. That process could be inhibited by Bempedoic acid, an FDA-approved ACLY-targeted drug. Taken together, our study reveals an sEV-mediated transformation of CXCR1Low to CXCR1High cells that promotes HNSCC progression. This provides a new paradigm to explain the dynamic changes of heterogeneous tumor cells, and identifies Bempedoic acid as a potential drug for HNSCC treatment.
Published in
The small extracellular vesicle-mediated intercellular transformation of CXCR1(Low) to CXCR1(High) tumour cells promotes the progression of head and neck squamous cell carcinoma
Xu Q, Cheng A, Li B et al. · Journal of extracellular vesicles 2024 · PMID 38545803 · doi:10.1002/jev2.12427
This dataset
Open GSE253091 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 GSE253091_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 PRJNA1064027 and SRA study SRP483359. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38545803) ↗
Study design
12 conditions, mostly in triplicate
HN4 cells, without treatment ×3 HN4 cells treated with IL-8 ×3 HN6 cells, without treatment ×3 HN6 cells treated with IL-8 ×3 Cal27 cells, without treatment ×3 Cal27 cells treated with IL-8 ×3 HN4 cells transfected with vector plasmids ×3 HN4 cells transfected with plasmids contained… ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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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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.