GEO series

Investigating a Novel Interaction of c-MET and BACH1 in Head and Neck Squamous Cell Carcinoma Metastasis

GSE268537 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2024/05/30 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 18 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: 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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)

Metastasis is estimated to be responsible for 90% of cancer deaths, and fewer than 10% of patients with metastatic head and neck squamous cell carcinoma (HNSCC) survive beyond 5 years. HNSCC is responsible for upwards of 270,000 global deaths annually, with up to 30% more cases projected annually by 2030. The proto-oncogene MET encodes for the tyrosine kinase receptor c-MET, which is overexpressed in over 80% of human papilloma virus (HPV)-negative HNSCC cases and particularly enriched in metastatic lymph nodes.

Read the full summary ↓

c-MET is activated by its ligand, hepatocellular growth factor (HGF), and is known to promote cancer cell migration, proliferation, and metastasis through a variety of downstream effectors. Thus far, unfortunately, inhibition of c-MET has shown low efficacy as a single-agent therapy in clinical trials, which indicates a need for further understanding of the mechanisms underlying c-MET-mediated metastasis in HNSCC. We show here that human HNSCC cells upregulate expression of the transcription factor BACH1 through c-MET activation upon HGF treatment. In accordance with previous reports, HGF activation increased expression of epithelial-mesenchymal transition (EMT) markers. Similarly, BACH1 suppression reduced expression of these EMT markers. By pharmacological inhibition of c-MET by FDA-approved capmatinib in combination with hemin treatment to reduce BACH1 expression, migration was reduced compared to either treatment alone in scratch-wound migration assays. Collectively, these data indicate that BACH1 and c-MET are both necessary for the regulation of EMT and migration in HNSCC. Our data suggest the potential for combination therapy targeting both c-MET and BACH1 to reduce HNSCC metastasis.

This dataset

Open GSE268537 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 GSE268537_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 PRJNA1117756 and SRA study SRP510428. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

18 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 18 sample titles: 18 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

GSM8294002 Cal27 shControl cells, untreated
GSM8294003 Cal27 shControl cells, 3 hours HGF treatment
GSM8294004 Cal27 shControl cells, 6 hours HGF treatment
GSM8294005 Cal27 shBACH1 cells, untreated
GSM8294006 Cal27 shBACH1 cells, 3 hours HGF treatment
GSM8294007 Cal27 shBACh1 cells, 6 hours HGF treatment
GSM8294008 Detroit562 shControl cells, untreated
GSM8294009 Detroit562shControl cells, 3 hours HGF treatment
GSM8294010 Detroit562 shControl cells, 6 hours HGF treatment
GSM8294011 Detroit562 shBACH1 cells, untreated
GSM8294012 Detroit562 shBACH1 cells, 3 hours HGF treatment
GSM8294013 Detroit562 shBACh1 cells, 6 hours HGF treatment
GSM8294014 FaDu shControl cells, untreated
GSM8294015 FaDu shControl cells, 3 hours HGF treatment
GSM8294016 FaDu shControl cells, 6 hours HGF treatment
GSM8294017 FaDu shBACH1 cells, untreated
GSM8294018 FaDu shBACH1 cells, 3 hours HGF treatment
GSM8294019 FaDu shBACh1 cells, 6 hours HGF treatment

More Head and neck cancer datasets

GSE164690 Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing 51 samples same disease briefing · shares investigating, interaction, head, neck
GSE140042 Single-cell atlas of head and neck squamous cell carcinoma 18 samples same disease briefing · shares squamous, head, neck
GSE185965 Single cell RNA sequencing of head and neck squamous carcinoma (HNSCC) patient sample 3 samples same disease briefing · shares squamous, head, neck
GSE173647 Single-cell Sequencing Analysis of Head and Neck Squamous Cell Carcinoma 2 samples same disease briefing · shares squamous, head, neck
GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing · shares head, neck
GSE139324 Immune landscape of viral- and carcinogen-drived head and neck cancer 63 samples same disease briefing · shares head, neck
GSE181919 Single-cell transcriptome profiling of the stepwise progression of head and neck cancer 37 samples same disease briefing · shares head, neck
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

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.