GEO series

Disruption of deoxynucleotide biosynthesis leads to RASproto-oncogene activation and perturbation of mitochondrial metabolism [RNA-seq]

GSE261895 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2024/10/02 Platform GPL30173

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)
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.
Paper: Disruption of deoxyribonucleotide triphosphate biosynthesis leads to RAS proto-oncogene activation and perturbation of mitochondrial metabolismThe Journal of biological chemistry · 2025

Summary (written by the submitters)

Perturbation of the deoxyribonucleotide triphosphate (dNTP) pool is recognized for contributing to the mutagenic processes involved in oncogenesis. The RAS gene family encodes well characterized oncoproteins whose structure and function are among the most frequently altered in several cancers. In this work, we show that fluctuation of the dNTP pool induces CG->TA mutations across the whole genome, including RAS gene at codons for glycine 12 and 13, known hotspots in cancers.

Read the full summary ↓

Cell culture addition of the ribonucleotide reductase inhibitor thymidine increases the mutation frequency in nuclear DNA and leads to disruption of mitochondrial metabolism. Interestingly, this effect is counteracted by the addition of deoxycytidine. Finally, screening for the loss of hydrogen bonds detecting CG->TA transition in RAS gene of 135 patients with colorectal cancer confirmed the clinical relevance of this process. All together, these data demonstrate that fluctuation of intracellular dNTP pool alters the nuclear DNA and mitochondrial metabolism.

Published in

Disruption of deoxyribonucleotide triphosphate biosynthesis leads to RAS proto-oncogene activation and perturbation of mitochondrial metabolism

Suspène R, Raymond KA, Guardado-Calvo P et al. · The Journal of biological chemistry 2025 · PMID 39722416 · doi:10.1016/j.jbc.2024.108117

This dataset

Open GSE261895 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 GSE261895_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 PRJNA1089527 and SRA study SRP496374. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39722416) ↗

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

GSM8153730 RASJP1_Non Treated Rep 1
GSM8153731 RASJP2_Non Treated Rep 2
GSM8153732 RASJP3_Non Treated Rep 3
GSM8153733 RASJP4_T 10 Rep 1
GSM8153734 RASJP5_T 10 Rep 2
GSM8153735 RASJP6_T 10 Rep 3
GSM8153736 RASJP7_T 30 Rep 1
GSM8153737 RASJP8_T 30 Rep 2
GSM8153738 RASJP9_T 30 Rep 3
GSM8153739 RASJP10_T 10 C 10 THU 100 Rep 1
GSM8153740 RASJP11_T 10 C 10 THU 100 Rep 2
GSM8153741 RASJP12_T 10 C 10 THU 100 Rep 3
GSM8153742 RASJP13_T 30 C 10 THU 100 Rep 1
GSM8153743 RASJP14_T 30 C 10 THU 100 Rep 2
GSM8153744 RASJP15_T 30 C 10 THU 100 Rep 3
GSM8153745 RASJP16_C 10 U 100 Rep 1
GSM8153746 RASJP17_C 10 U 100 Rep 2
GSM8153747 RASJP18_C 10 U 100 Rep 3

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