GEO series
Expression profiling of primary and metastatic oral squamous cell carcinoma identifies progression-associated transcriptome changes and therapeutic vulnerabilities
GSE275870
Homo sapiens (human)
RNA-seq (gene expression)
108 samples
Submitted 2025/01/07
Platform GPL24676
At a glance
RNA-seq (gene expression) · human · 108 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
- 108 samples: 83 distinct titles, 20 of them repeatedGroups 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
- Expression profiling of primary and metastatic oral squamous cell carcinoma identifies progression-associated transcriptome changes and therapeutic vulnerabilitiesCancer communications (London, England) · 2025
Summary (written by the submitters)
Oral squamous cell carcinoma (OSCC) constitutes a subset of head and neck squamous cell carcinoma primarily caused by the excessive consumption of alcohol, tobacco, and areca nut. According to the latest estimates of the global burden of cancer (GLOBOCAN 2022), cancers of the lip and oral cavity account for 389,485 new cancer cases and 188,230 deaths annually.
Read the full summary ↓
Despite significant progress in OSCC diagnosis and therapy only about 65% of patients survive five years or longer. This poor prognosis is mainly due to the fact that about half of OSCC patients are diagnosed with advanced disease. Hence, a better understanding of the molecular mechanisms responsible for the development and metastatic progression of OSCC is needed in order to identify novel biomarkers and therapeutic targets. We isolated RNA from 87 primary tumours and 21 lymph node metastases from a total of 72 OSCC patients. The RNA was subjected to next-generation sequencing (~62 Mio. reads per sample) upon depletion of ribosomal RNA. Comprehensive transcriptome-wide expression and correlation analyses were performed in order to identify expression subtypes, disease-associated genes and isoforms. The functional and therapeutic relevance of selected candidates was further investigated in vitro using gain- and loss-of-function analyses. Unsupervised clustering of primary tumours identified three clusters (C1-C3) that show different overall survival (OS) probabilities, especially for C3. Furthermore, gene-level analyses identified SHMT2 as a prognostic biomarker associated with poor OS. Importantly, targeting of SHMT2 using siRNAs or a small molecule inhibitor (SHIN1/RZ-2994) decreased cell proliferation and induced apoptosis in a panel of OSCC cell lines and establish SHMT2 as a promising therapeutic target. Comparison of primary tumours and their matched lymph node metastases identified additional druggable metastasis-associated genes as well as several isoform switches. For example, the canonical full-length isoform of WNT5A was higher expressed in metastases and its overexpression in SAS enhanced cell invasion capacity. Our profiling study provides a valuable resource for the community that will foster functional analyses to gain insights into the molecular mechanisms of OSCC progression, and it will help to identify novel biomarkers and therapeutic targets in the future.
Published in
Pyko J, Glaß M, Rosemann J et al.
· Cancer communications (London, England) 2025
· PMID 39778089
· doi:10.1002/cac2.12660
This dataset
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.
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 GSE275870_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1153444 and SRA study SRP534523. Searching any of these in the dataset finder brings you back here.
Study design
83 distinct titles, 20 of them repeated
patient 037 primary tumor sample ×4
patient 034 primary tumor sample ×3
patient 042 metastasis ×3
patient 072 metastasis ×3
patient 001 metastasis ×2
patient 001 primary tumor sample ×2
patient 004 metastasis ×2
patient 005 primary tumor sample ×2
+12 more
How we read this: Read from 108 sample titles: 83 distinct titles with little repetition. 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
- GSM8486850 patient 001 metastasis 1
- GSM8486851 patient 001 metastasis 2
- GSM8486852 patient 001 primary tumor sample 1
- GSM8486853 patient 001 primary tumor sample 2
- GSM8486854 patient 002 primary tumor sample 1
- GSM8486855 patient 003 primary tumor sample 1
- GSM8486856 patient 004 metastasis 1
- GSM8486857 patient 004 metastasis 2
- GSM8486858 patient 004 primary tumor sample 1
- GSM8486859 patient 005 primary tumor sample 1
- GSM8486860 patient 006 primary tumor sample 1
- GSM8486861 patient 007 primary tumor sample 1
- GSM8486862 patient 008 primary tumor sample 1
- GSM8486863 patient 009 primary tumor sample 1
- GSM8486864 patient 010 primary tumor sample 1
- GSM8486865 patient 011 primary tumor sample 1
- GSM8486866 patient 011 primary tumor sample 2
- GSM8486867 patient 012 primary tumor sample 1
- GSM8486868 patient 013 primary tumor sample 1
- GSM8486869 patient 014 primary tumor sample 1
- GSM8486870 patient 015 primary tumor sample 1
- GSM8486871 patient 015 primary tumor sample 2
- GSM8486872 patient 016 primary tumor sample 1
- GSM8486873 patient 017 primary tumor sample 1
- GSM8486874 patient 018 primary tumor sample 1
- GSM8486875 patient 019 primary tumor sample 1
- GSM8486876 patient 020 primary tumor sample 1
- GSM8486877 patient 021 primary tumor sample 1
- GSM8486878 patient 022 primary tumor sample 1
- GSM8486879 patient 023 primary tumor sample 1
- GSM8486880 patient 024 primary tumor sample 1
- GSM8486881 patient 025 primary tumor sample 1
- GSM8486882 patient 026 primary tumor sample 1
- GSM8486883 patient 027 metastasis 1
- GSM8486884 patient 027 metastasis 2
- GSM8486885 patient 027 primary tumor sample 1
- GSM8486886 patient 027 primary tumor sample 2
- GSM8486887 patient 028 primary tumor sample 1
- GSM8486888 patient 029 primary tumor sample 1
- GSM8486889 patient 030 primary tumor sample 1
+ 68 more — browse all 108 samples with per-sample file links →
More Head and neck cancer datasets
- GSE114446 Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines 33 samples same disease briefing · shares changes
- GSE145057 Establishment of a human tongue cancer organoid biobank enables early diagnosis, prognosis, and identification of therapeutic targets 25 samples same disease briefing · shares therapeutic
- GSE140042 Single-cell atlas of head and neck squamous cell carcinoma 18 samples same disease briefing · shares squamous
- GSE185965 Single cell RNA sequencing of head and neck squamous carcinoma (HNSCC) patient sample 3 samples same disease briefing · shares squamous
- GSE173647 Single-cell Sequencing Analysis of Head and Neck Squamous Cell Carcinoma 2 samples same disease briefing · shares squamous
- GSE176077 RNA-seq profiling of salivary transcriptome reveals potential diagnostic RNAs and oral microbial dysbiosis in oral squamous cell carcinoma 28 samples same disease briefing · shares squamous
- GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing
- GSE139324 Immune landscape of viral- and carcinogen-drived head and neck cancer 63 samples same disease briefing
Share this dataset
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.