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Spatial transcriptomic analysis of head and neck squamous cell carcinoma reveals novel regulators of hybrid epithelial-to-mesenchymal transition

GSE279017 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2026/06/21 Platform GPL34295
At a glance

RNA-seq (gene expression) · human · 20 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
20 samples: 9 conditions, mostly in duplicateGroups 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)
Head and neck squamous cell carcinoma (HNSCC) is characterized by a high degree of intra- and inter-tumoral heterogeneity. Here we use spatial transcriptomics (ST) to profile both HPV-positive and HPV-negative HNSCC, uncovering distinct patterns of spatial organization of malignant cells and the surrounding tumor microenvironment across groups of tumors.
Read the full summary ↓
First, we find that HPV-positive HNSCC is characterized by high cellular density in all cellular compartments with distinct expression of hypoxia, senescence, and cell cycle-associated genes in the malignant compartment. In HPV-negative HNSCC, we find two distinct spatial patterns of a partial epithelial-to-mesenchymal transition (p-EMT) program. One pattern is spatially associated with fibroblasts, characterized by p-EMT at the leading edge of tumor nests (“p-EMT edge”), and mediated by TGFB-signaling. The other pattern features high p-EMT expression in the core of tumor nests (“p-EMT core”). In p-EMT core tumors, we observe high co-localization of p-EMT cells with an inflammatory response program including neutrophils and macrophages, as well as differential expression of distinct ligands, including OSM. In vitro experiments demonstrate that OSM can induce the p-EMT state in multiple HNSCC models. Together these findings suggest that multiple p-EMT phenotypes exist across HPV-unrelated HNSCC and are mediated by distinct cell-to-cell signaling mechanisms, highlighting potential novel therapeutic vulnerabilities.
This dataset
Open GSE279017 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 GSE279017_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 PRJNA1169917 and SRA study SRP537043. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 conditions, mostly in duplicate
JHU-06, PBS vehicle control 72hr, ×2 JHU-06, 50 ng/mL OSM 72hr, ×2 JHU-06, 100 ng/mL SPP1 72hr, ×2 JHU-06, 50 ng/mL IL-1B 72hr, ×2 93VU147T, PBS vehicle control 72hr, ×2 93VU147T, 10 ng/mL TGFB1 + 10 ng/mL TGFB3 72h… ×2 93VU147T, 50 ng/mL OSM 72hr, ×2 93VU147T, 100 ng/mL SPP1 72hr, ×2 +3 more

Supports a between-group comparison across 18 samples.

How we read this: 9 replicated groups read from 20 sample titles; they account for 18 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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