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Effect of lactate accumulation on translation and transcription in MDA-MB-231 breast cancer cells

GSE297242 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/08/01 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 12 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
Breast cancerThis series is part of our curated briefing on it.
Samples
12 samples: 3 × total RNA, MDA-MB-231 cells, DMSO, vs 3 × total RNA, MDA-MB-231 cells, AZD0095, vs 3 × Ribosome protected fragments, MDA-MB-231 cells, DMSO, vs 3 × Ribosome protected fragments, MDA-MB-231 cells, AZD0095,Groups 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)
Dynamic coordination of energy metabolism and protein synthesis is pivotal to cell fitness, especially in cancer cells that frequently encounter microenvironmental challenges. Yet it remains unclear whether this rapid communication depends on complex regulatory signaling pathways or can be governed by a single molecule. Here, we show that intracellular accumulation of lactate, a central product of glycolysis, is sufficient to acutely repress mRNA translation.
Read the full summary ↓
Mechanistically, lactate is charged to the 3′ end of tRNA, a site canonically reserved for amino acids, generating translation-defective lactyl-tRNAs. This mechanism may have evolved to restrict protein synthesis during metabolic imbalance, such as when glycolytic activity exceeds lactate clearance, and is particularly relevant in highly glycolytic cancer cells, which frequently experience prolonged hypoxia and elevated lactate levels. Notably, triple-negative breast cancer (TNBC) cells evade this repression by maintaining low intracellular lactate, even under hypoxic stress. Blocking lactate export via monocarboxylate transporter (MCT) inhibition re-establishes translational repression, diminishes cancer cell fitness under metabolic stress, and impairs tumor progression. These findings uncover a unique metabolite-tRNA charging event that directly rewires translational output and reveal a metabolic vulnerability with therapeutic potential.
This dataset
Open GSE297242 in finder → Find more human RNA-seq datasets → Breast 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 GSE297242_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 PRJNA1263382 and SRA study SRP586076. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × total RNA, MDA-MB-231 cells, DMSO, vs 3 × total RNA, MDA-MB-231 cells, AZD0095, vs 3 × Ribosome protected fragments, MDA-MB-231 cells, DMSO, vs 3 × Ribosome protected fragments, MDA-MB-231 cells, AZD0095,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
More Breast cancer datasets

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