GEO series

Targeting metastasis stem cells through the fatty acid receptor CD36 (DID+, DID- and CD44DIM).

GSE83346 Homo sapiens (human) Expression microarray 15 samples Submitted 2016/12/16 Platform GPL17077

At a glance

Expression microarray · human · 15 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: Head and neck cancerThis series is part of our curated briefing on it.
Samples: 15 samples: 5 × Detroit DID+ # vs 5 × Detroit DID- # vs 5 × Detroit CD44DIM #Groups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Metastasis is the leading cause of cancer-related deaths. For most human cancers, the identity of the cells that initiate and promote metastasis is still unknown, hampering our ability to develop therapies to prevent or inhibit the spread of tumour cells to distant sites. Using an orthotopic model of human oral squamous cell carcinoma (OSCC), we have now identified a subpopulation of CD44bright cells within the primary lesion with the highest potential to develop lymph node and lung metastasis.

Read the full summary ↓

This population is slow-cycling, expresses high levels of the receptor CD36 at the cell membrane and relies on fatty acid metabolism to thrive in lymph nodes and bronchoalveolar environments. Importantly, inhibition of CD36 by either shRNA or neutralizing monoclonal antibodies severely impairs metastatic spread of primary OSCC patient samples and established cell lines. Further underscoring its importance, CD36 overexpression in poorly disseminating tumours confers an aggressive metastatic behaviour. Analyses of public gene expression data indicate that the presence of the signature-defining CD36+ cells also strongly correlates with a poor prognosis in patients with lung SCC, ovarian cancer, bladder cancer, or luminal breast cancer. By identifying metastasis-promoting cells and then targeting them with CD36 inhibition, novel anti-metastatic therapies could be developed for patients with these types of tumours.

This dataset

Open GSE83346 in finder → Find more human microarray datasets → Head and neck cancer landscape →

Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE83346_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA325647. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 27974793) ↗

Study design

5 × Detroit DID+ # vs 5 × Detroit DID- # vs 5 × Detroit CD44DIM #

Supports a between-group comparison across 15 samples.

How we read this: 3 replicated groups read from 15 sample titles; they account for 15 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

GSM2199932 Detroit DID+ #1 Detroit DID+ #
GSM2199933 Detroit DID- #1 Detroit DID- #
GSM2199934 Detroit CD44DIM #1 Detroit CD44DIM #
GSM2199935 Detroit DID+ #2 Detroit DID+ #
GSM2199936 Detroit DID- #2 Detroit DID- #
GSM2199937 Detroit CD44DIM #2 Detroit CD44DIM #
GSM2199938 Detroit DID+ #3 Detroit DID+ #
GSM2199939 Detroit DID- #3 Detroit DID- #
GSM2199940 Detroit CD44DIM #3 Detroit CD44DIM #
GSM2199941 Detroit DID+ #4 Detroit DID+ #
GSM2199942 Detroit DID- #4 Detroit DID- #
GSM2199943 Detroit CD44DIM #4 Detroit CD44DIM #
GSM2199944 Detroit DID+ #6 Detroit DID+ #
GSM2199945 Detroit DID- #6 Detroit DID- #
GSM2199946 Detroit CD44DIM #6 Detroit CD44DIM #

More Head and neck cancer datasets

GSE173161 Comparative analysis of gene expression after Oct4 or Scrambled siRNA knockdown in HNSCC cell lines 18 samples same disease briefing
GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing
GSE159067 Immunologically hot phenotype is associated with response to PD-1/PD-L1 inhibitors in patients with advanced head and neck squamous cell carcinoma. 102 samples same disease briefing
GSE139324 Immune landscape of viral- and carcinogen-drived head and neck cancer 63 samples same disease briefing
GSE162738 Immune gene signatures in oropharyngeal cancers are associated with inverse prognosis by HPV-status 51 samples same disease briefing
GSE164690 Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing 51 samples same disease briefing
GSE181919 Single-cell transcriptome profiling of the stepwise progression of head and neck cancer 37 samples same disease briefing
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

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