GEO series

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

GSE302670 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 13 samples Submitted 2025/08/04 Platform GPL34284

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 13 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Homo sapiens (human)
Samples: 13 samples: 3 × MD901 vehicle vs 3 × MD901 HDAC3i vs 3 × MD901 AZA vs 3 × MD901 HDAC3 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 GSE302670 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE302670_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1291701 and SRA study SRP600951. 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 HDAC3 AZA

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 13 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

GSM9108538 MD901 vehicle_rep1 MD901 vehicle
GSM9108539 MD901 vehicle_rep2 MD901 vehicle
GSM9108540 MD901 vehicle_rep3 MD901 vehicle
GSM9108541 MD901 HDAC3i_rep1 MD901 HDAC3i
GSM9108542 MD901 HDAC3i_rep2 MD901 HDAC3i
GSM9108543 MD901 HDAC3i_rep3 MD901 HDAC3i
GSM9108544 MD901 AZA_rep1 MD901 AZA
GSM9108545 MD901 AZA_rep2 MD901 AZA
GSM9108546 MD901 AZA_rep3 MD901 AZA
GSM9108547 MD901 HDAC3 AZA_rep1 MD901 HDAC3 AZA
GSM9108548 MD901 HDAC3 AZA_rep2 MD901 HDAC3 AZA
GSM9108549 MD901 HDAC3 AZA_rep3 MD901 HDAC3 AZA
GSM9108550 INPUT

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