GEO series

DUSP1 and SOX2 expression determine Squamous cell carcinoma of the salivary gland progression.

GSE253468 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2024/05/01 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 10 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)
Samples: 10 samples
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)

Salivary gland squamous cell carcinomas (SG-SCCs) are a rare type of head and neck cancers which are linked to poor prognosis. Due to their low frequencies, the molecular mechanisms responsible for their aggressiveness are poorly understood. In this work we studied the function of the phosphatase DUSP1, a negative regulator of MAPK activity, in controlling the progression of SG-SCCs.

Read the full summary ↓

We generated DUSP1 KO clones in A253 human cells. These clones showed a reduced ability to grow in 2D, self-renew in ECM matrices and grow tumors in immunodeficient mice. This was caused by an overactivation of the stress and apoptosis kinase JNK1/2 in DUSP1-KO clones. Interestingly, RNAseq analysis revealed that the expression of SOX2, a well know self-renewal gene was decreased at the mRNA and protein level. Unexpectedly, CRISPR-KO of SOX2 did not recapitulate DUSP1-KO phenotype, and SOX2-null cells had an enhanced ability to self-renew and grow tumors in mice. Gene expression analysis demonstrated that SOX2-null cells have a decreased squamous differentiation profile -losing TP63 expression- and an increased migratory phenotype, with an enhanced epithelial to mesenchymal transition signature. In summary, our data indicates that DUSP1 and SOX2 have opposite functions in SG-SCC, being DUSP1 necessary for tumor growth and SOX2 dispensable, and with a tumor suppressor function. Our data will suggest that the expression SOX2 and DUSP1 could be a useful biomarker to predict the progression of patients with SG-SCCs.

This dataset

Open GSE253468 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 GSE253468_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 PRJNA1065852 and SRA study SRP484308. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 10 more — browse all 10 samples with per-sample file links →

Datasets on a similar topic

GSE275870 Expression profiling of primary and metastatic oral squamous cell carcinoma identifies progression-associated transcriptome changes and therapeutic vulnerabilities 108 samples shares progression, squamous
GSE253091 The Small Extracellular Vesicle-Mediated Intercellular Transformation of CXCR1Low to CXCR1High Tumor Cells Promotes the Progression of Head and Neck Squamous Cell Carcinoma 36 samples shares progression, squamous
GSE326337 Fusobacterium nucleatum FadA promotes the progression of esophageal squamous cell carcinoma through binding to TFRC 9 samples shares progression, squamous
GSE180791 Proteogenomic characterization reveals that lipid droplet formation promotes esophageal squamous cell cancer progression 102 samples shares progression, squamous
GSE304098 Profiling of histone modifications reveal tumor microenvironment-acquired super-enhancer regulates progression of esophageal squamous cell carcinoma 11 samples shares progression, squamous
GSE335924 RNA-seq Identifies FOS as a Potential Therapeutic Target Activating Neural Stem Cells via miR-21/SOX2 Pathway in Hypertensive Intracerebral Hemorrhage 53 samples shares sox2
GSE289499 Uncovering Stage-Specific Biomarkers in Colorectal Cancer: RNA-Seq Analysis of Adenoma and Carcinoma Progression 29 samples shares progression
GSE267820 Exploring the mechanism of AGR2 regulating the progression of pancreatic ductal adenocarcinoma and remodeling of the tumor microenvironment 24 samples shares progression

Search all human RNA-seq datasets in GEO →

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.