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Unveiling the biological effects of DNA G-quadruplex ligands through multi-omics data integration

GSE286401 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/05/20 Platform GPL24676
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)
Samples
12 samples: 3 × HeLa cells, untreated, biol vs 3 × HeLa cells treated with RHPS4, biol vs 3 × HeLa cells treated with Berberine, biol vs 3 × HeLa cells treated with PDS, biolGroups 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
Unveiling the biological effects of DNA G-quadruplex ligands through multi-omics data integrationInternational journal of biological macromolecules · 2025
Summary (written by the submitters)
G-quadruplexes (G4s) are non-canonical DNA structures that have proved to play a pivotal role in various biological processes, including telomere maintenance and gene expression regulation. Owing to their prevalence in tumor cells, G4s have emerged as promising targets for cancer therapy, with a substantial body of research demonstrating the potential of G4 ligands as anti-cancer tools.
Read the full summary ↓
However, a more comprehensive understanding of G4 binders’ mode of action is imperative to successfully translate them into therapeutic agents. Herein, we employed a multi-omics approach, integrating transcriptomics, proteomics and metabolomics, to identify key signaling pathways that mediate the anti-cancer effects of well-characterized G4-binding agents (berberine, PDS and RHPS4) on HeLa cancer cells. Our results revealed that, under the investigated experimental conditions, berberine treatment only had negligible cellular effects, whereas PDS-treated HeLa cells underwent significant changes at the transcriptomic, proteomic and metabolomic levels, with marked impairment in glycolysis, antioxidant capacity, lipids and nucleotides biosynthetic processes. Notably, RHPS4 could selectively affect mitochondrial activity, possibly through the specific stabilization of mitochondrial G-quadruplex structures. Overall, our findings provide a valuable multi-omics perspective on the cellular changes driven by G-quadruplex binders, that may accelerate the development of G4-targeted therapies.
Published in
Unveiling the biological effects of DNA G-quadruplex ligands through multi-omics data integration
Romano F, Persico C, Barra A et al. · International journal of biological macromolecules 2025 · PMID 40383348 · doi:10.1016/j.ijbiomac.2025.144325
This dataset
Open GSE286401 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 GSE286401_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 PRJNA1209075 and SRA study SRP556539. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40383348) ↗
Study design
3 × HeLa cells, untreated, biol vs 3 × HeLa cells treated with RHPS4, biol vs 3 × HeLa cells treated with Berberine, biol vs 3 × HeLa cells treated with PDS, biol

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
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