← BioTransfer GEO Dataset Finder
GEO series

Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-Azacitidine against diffuse large B-cell lymphoma [MD901_RNAseq_Day5]

GSE302692 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/08/04 Platform GPL18573
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 × MD901_vehicle vs 3 × MD901_HDAC3i vs 3 × MD901_AZA vs 3 × MD901_HDAC3i_AZAGroups 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
Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-azacitidine against diffuse large B-cell lymphomaBlood neoplasia · 2026
Summary (written by the submitters)
Diffuse large B-cell lymphoma (DLBCL) refers to an aggressive lymphoma that arises from germinal center (GC) B-cells, which differentiate into plasma cells (PC) to produce high affinity antibodies. 40% of DLBCL patients relapse or are refractory to the conventional immunochemotherapy treatment, usually with fatal consequences. DLBCL is characterized by profound alterations in the epigenome, which is correlated with poor survival.
Read the full summary ↓
The abnormal epigenetic landscape of DLBCL tumors is associated with a blockade in GC exit and differentiation programs, which are regulated by the transcription factor BCL6. This aberrant repression of BCL6-target genes is mediated by 1) increased DNA methylation and 2) loss of acetylation of the lysine 27 of histone 3 (H3K27ac)-through recruitment of histone deacetylase 3 (HDAC3). Thus, we investigated the efficacy against DLBCL of the hypomethylating agent (HMA) 5-Azacitidine (5-Aza) and a specific HDAC3 inhibitor (HDAC3i). We found that treatment with 5-Aza plus HDAC3i had a potent synergistic anti-tumor activity in vitro and in vivo, which was superior to the effect of each single drug or 5-Aza combined with non-specific HDACi and, importantly, was not associated with toxicity in normal cells. We also demonstrated that the combined 5-Aza and HDAC3i treatment induced the epigenetic remodeling of DLBCL cells, which resulted in a more potent re-expression of PC differentiation genes, including XBP1 and ATF4, compared to each drug used as single agents. Our results highlight the importance of specifically targeting multiple layers of the epigenome to maximize the efficacy of epigenetic-based therapies.
Published in
Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-azacitidine against diffuse large B-cell lymphoma
Calaud C, Serrano-Lopez EM, Cluse LA et al. · Blood neoplasia 2026 · PMID 42007249 · doi:10.1016/j.bneo.2026.100214
This dataset
Open GSE302692 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 GSE302692_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 PRJNA1291740 and SRA study SRP600938. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42007249) ↗
Study design
3 × MD901_vehicle vs 3 × MD901_HDAC3i vs 3 × MD901_AZA vs 3 × MD901_HDAC3i_AZA

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

Search all human RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.