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Berry-derived gold nanoparticles induce integrated oxidative stress-mediated apoptosis, immune modulation, and transcriptomic remodeling in 4T1 triple-negative cancer cells

GSE310210 Mus musculus (mouse) Single-nucleus RNA-seq 15 samples Submitted 2026/04/11 Platform GPL36317
At a glance

Single-nucleus RNA-seq · mouse · 15 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
15 samples: 5 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
Berry-derived gold nanoparticles induce integrated ROS-mediated apoptosis, immune modulation, and transcriptomic remodeling in 4T1 triple-negative cancer cellsCell death discovery · 2026
Summary (written by the submitters)
Comprehensive molecular and phenotypic characterization of tumor models is still needed for robust understanding of breast cancer mechanisms and therapies. Here, we explore genome, transcriptome, and proteome of treated and untreated 4T1 triple-negative breast cancer cells. Nanoencapsulation (AuNPs) of berry-derived polyphenolic compounds was influenced by limited clinical use due to poor stability and bioavailability.
Read the full summary ↓
Several physicochemical characterizations employed include TEM, FTIR, and targeted UPLC/MS-QQQ assays. We identified significant mutations to breast cancer-related tumor suppressor genes (Trp53, Brca2, Bard1, Cdh1, Nf1, and Chek2) and deciphered the function consequences leveraging on the higher throughput Illumina NovaSeq X and NextSeq 1000 sequencers and highly accurate predicting power of AlphaFold. We found ~5700000 single nucleotide variations (SNVs) and 329448 indels achieving an important upgrade over previous literature data. Key findings from differentially expressed gene enrichment analyses (GSEA) revealed positive gene enrichments of DNA repair regulators and TGF-β signaling while having negative enrichments of cell adhesion, cadherin and MAPK signaling via PI3K/AKT/MAPK/Wnt pathways, potentially influencing apoptosis and immune evasion intrinsic to cancer. Notably, decreased expression of PIK3CG, PALLD, PTPRZ1, and CDH8 and increased expression of SEMA6C, WWOX, NHEJ1, and MAML3 suggested suppression of epithelial-to-mesenchymal transition (EMT) and metastatic potential. Further assessment of immunohistochemical, immunofluorescent, and flow cytometric data revealed that berry-derived nanoparticles can modulate oncogenic transcription factors and induce caspase-dependent execution-phase ROS-mediated apoptosis through pPAK1Thr212 dephosphorylation, downregulation of pPI3Kp85αγ(Tyr467/199)/pAKT1Thr450/mTOR signaling, and modulation of pJAK3Tyr785/STAT3 pathway supporting transcriptomic and transcriptional reprogramming of 4T1 treated cells. Together, our findings uncover a new strategy to capture berry-derived polyphenols required to regulate apoptosis, autophagy, immune response, and metastasis-related gene networks in breast cancer thereby underscoring the therapeutic potential of functionalized AuNPs as delivery platforms for dietary phytochemicals.
Published in
Berry-derived gold nanoparticles induce integrated ROS-mediated apoptosis, immune modulation, and transcriptomic remodeling in 4T1 triple-negative cancer cells
Fagbohun OF, Oladipo AO, Gao C et al. · Cell death discovery 2026 · PMID 41963310 · doi:10.1038/s41420-026-03023-z
This dataset
Open GSE310210 in finder → Find more mouse 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 GSE310210_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1359542 and SRA study SRP644313. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41963310) ↗
Study design
5 conditions, mostly in triplicate
Untreated 4T1 Breast Cancer Cells ×3 Blackberry treated 4T1 Breast Cancer Cells ×3 Blueberry treated 4T1 Breast Cancer Cells ×3 4T1 Breast Cancer Cells treated with Blackber… ×3 4T1 Breast Cancer Cells treated with Blueberr… ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 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
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