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Overcoming resistance to anti-VEGF therapy via epigenetic regulation of BARD1 [BeadChip expression]

GSE249415 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/06/16 Platform GPL10558
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 × Control IgG-treated SKOV3ip1 tumors, biol vs 3 × Azacytidine-treated SKOV3ip1 tumors, biol vs 3 × B20-treated SKOV3ip1 tumors, biol vs 3 × Azacytidine+B20-treated SKOV3ip1 tumors, 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
Epigenetic modulation of BARD1 to enhance anti-VEGF therapyCell reports. Medicine · 2025
Summary (written by the submitters)
Despite widespread use of anti-vascular endothelial growth factor (VEGF) antibody (AVA) for cancer therapy, most patients develop progressive disease after initial response. Therefore, novel strategies are needed to understand and overcome AVA resistance. Here, we identify an unexpected role of BRCA1-associated RING domain 1 (BARD1) in overcoming adaptive resistance to AVA.
Read the full summary ↓
We investigated the effects of epigenetic modulation on cellular response to AVA; in particular, the molecular effects of both global and targeted DNA methylation. Using in vitro assays, BARD1 was identified as being specifically involved in angiogenesis. Sequential treatment with azacytidine overcame AVA therapy resistance in cancer models in vivo. We further demonstrated that specifically targeting BARD1 with either small-interfering RNA or CpG-targeted demethylation reduced tumor growth when combined with AVA therapy (compared with AVA alone) in mouse models of ovarian cancer. These results identify a previously unrecognized role for BARD1 in tumor angiogenesis and show that targeted restoration of BARD1 can enhance the efficacy of AVA therapy in cancer models. (Microarray was used to investigate altered genes that have signature of anti-VEGF therapy resistance.)
Published in
Epigenetic modulation of BARD1 to enhance anti-VEGF therapy
Bayraktar E, Rodriguez-Aguayo C, Stur E et al. · Cell reports. Medicine 2025 · PMID 40907495 · doi:10.1016/j.xcrm.2025.102329
This dataset
Open GSE249415 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 GSE249415_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 PRJNA1049004. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40907495) ↗
Study design
3 × Control IgG-treated SKOV3ip1 tumors, biol vs 3 × Azacytidine-treated SKOV3ip1 tumors, biol vs 3 × B20-treated SKOV3ip1 tumors, biol vs 3 × Azacytidine+B20-treated SKOV3ip1 tumors, 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
Datasets on a similar topic

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