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Transcriptomic analysis of effects of cancer cell detachment after treatment with 2-deoxy-D-glucose alone or in co-treatment with metformin

GSE279580 Homo sapiens (human) RNA-seq (gene expression) 30 samples Submitted 2024/10/20 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 30 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
30 samples: 10 conditions, mostly in triplicateGroups 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
MDA-MB-231 breast cancer cells adapted to anchorage-independent growth reveal senescent-like phenotype and persistent downregulation of PD-L1 expressionFrontiers in oncology · 2025
Summary (written by the submitters)
Detachment of cancer cells from tumor, anchorage-independent survival, and maintenance of proliferative capacity upon reattachment are crucial steps in metastases formation. Better understanding of the underlying molecular mechanisms could help to improve targeted cancer therapies. We show reversible detachment of cancer cells using N-glycosylation inhibitors 2-deoxy-D-glucose (2DG) and tunicamycin, with re-attached cells retaining their proliferating capacity.
Read the full summary ↓
This phenomenon was enhanced by combining with inhibitors of the electron transport chain. Analysis of the detached MDA-MB-231 cells treated with 2DG or 2DG combined with metformin showed ER stress, upregulation of pentose phosphate pathway, stemness, and alterations in genes involved in EMT.
Published in
MDA-MB-231 breast cancer cells adapted to anchorage-independent growth reveal senescent-like phenotype and persistent downregulation of PD-L1 expression
Snedec T, Repas J, Lah D et al. · Frontiers in oncology 2025 · PMID 41103963 · doi:10.3389/fonc.2025.1667308
This dataset
Open GSE279580 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 GSE279580_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 PRJNA1173549 and SRA study SRP538891. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41103963) ↗
Study design
10 conditions, mostly in triplicate
ctrl, selected, ×3 4.8 mM 2DG, selected, ×3 5 mM meftormin + 0.6 mM 2DG, selected, ×3 polyHEMA, selected, ×3 ctrl, ×3 4.8 mM 2DG, attached, ×3 4.8 mM 2DG, dettached, ×3 5 mM meftormin + 0.6 mM 2DG, attached, ×3 +3 more

Supports a between-group comparison across 29 samples.

How we read this: 10 replicated groups read from 30 sample titles; they account for 29 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
Datasets on a similar topic

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