GEO series

Quadruple adenine base edited allogeneic CAR T cells outperform CRISPR/Cas9 nuclease engineered T cells [ATAC-seq]

GSE290620 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 25 samples Submitted 2025/04/09 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 25 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: 25 samples: 25 samples, each with a distinct title — no replicated groupsGroups 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.

Summary (written by the submitters)

Genome editing technologies have enabled the clinical development of allogeneic cellular therapies, yet the optimal gene editing modality for multiplex editing of therapeutic T cell product manufacturing remains elusive. In this study, we conducted a comprehensive comparison of CRISPR/Cas9 nuclease and adenine base editor (ABE) technologies in generating allogeneic chimeric antigen receptor (CAR) T cells, utilizing extensive in vitro and in vivo analyses.

Read the full summary ↓

Both methods achieved high editing efficiencies across four target genes, critical for mitigating graft-versus-host disease and allograft rejection: TRAC or CD3E, B2M, CIITA, and PVR. Notably, ABE demonstrated higher manufacturing yields and distinct off-target profiles compared to Cas9, with translocations observed exclusively in Cas9-edited products. Functionally, ABE-edited CAR T cells exhibited superior in vitro effector functions under continuous antigen stimulation, including enhanced proliferative capacity and increased surface CAR expression. Transcriptomic analysis revealed that ABE editing resulted in reduced activation of p53 and DNA damage response pathways at baseline, along with sustained activation of metabolic pathways during antigen stress. Consistently, ATAC-seq data indicated that Cas9-edited, but not ABE-edited, CAR T cells showed enrichment of chromatin accessibility peaks associated with double-strand break repair and DNA damage response pathways. In a preclinical leukemia model, ABE-edited CAR T cells demonstrated improved tumor control and extended overall survival compared to their Cas9-edited counterparts. Collectively, these findings position ABE as a superior choice of Cas9 nucleases for multiplex gene editing in therapeutic T cells.

This dataset

Open GSE290620 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 GSE290620_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 PRJNA1229423 and SRA study SRP566921. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

25 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 25 sample titles: 25 distinct titles with little repetition. 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

GSM8818268 CTL019 CAR T cells, No EP, D0, ND502, ATAC-seq
GSM8818269 CTL019 CAR T cells, ABE mRNA 4KO, D0, ND502, ATAC-seq
GSM8818270 CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, ND502, ATAC-seq
GSM8818271 CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, ND502, ATAC-seq
GSM8818272 CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, ND502, ATAC-seq
GSM8818273 CTL019 CAR T cells, No EP, D0, ND589, ATAC-seq
GSM8818274 CTL019 CAR T cells, ABE mRNA 4KO, D0, ND589, ATAC-seq
GSM8818275 CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, ND589, ATAC-seq
GSM8818276 CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, ND589, ATAC-seq
GSM8818277 CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, ND589, ATAC-seq
GSM8818278 CTL019 CAR T cells, No EP, D0, ND602, ATAC-seq
GSM8818279 CTL019 CAR T cells, ABE mRNA 4KO, D0, ND602, ATAC-seq
GSM8818280 CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, ND602, ATAC-seq
GSM8818281 CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, ND602, ATAC-seq
GSM8818282 CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, ND602, ATAC-seq
GSM8818283 CTL019 CAR T cells, No EP, D0, ND632, ATAC-seq
GSM8818284 CTL019 CAR T cells, ABE mRNA 4KO, D0, ND632, ATAC-seq
GSM8818285 CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, ND632, ATAC-seq
GSM8818286 CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, ND632, ATAC-seq
GSM8818287 CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, ND632, ATAC-seq
GSM8818288 CTL019 CAR T cells, No EP, D0, TMP511, ATAC-seq
GSM8818289 CTL019 CAR T cells, ABE mRNA 4KO, D0, TMP511, ATAC-seq
GSM8818290 CTL019 CAR T cells, Cas9 WT mRNA 4KO, D0, TMP511, ATAC-seq
GSM8818291 CTL019 CAR T cells, Cas9 SpyFi mRNA 4KO, D0, TMP511, ATAC-seq
GSM8818292 CTL019 CAR T cells, Cas9 SpyFi Protein 4KO, D0, TMP511, ATAC-seq

Datasets on a similar topic

GSE326661 Reprogramming engineered autologous T cells to overcome resistance in Merkel cell carcinoma [scRNA-seq] 22 samples shares car, engineered
GSE345979 Cellular and molecular mechanisms determining allogeneic CAR T cell rejection and expansion -- Submission 2 of 2 (scRNA/CITE-seq) 12 samples shares car, allogeneic
GSE267597 AP-1 Mediates Oncogenic Transcription and Predicts Fatality in Lung Squamous Cell Carcinoma Patients [ChIP-seq] 36 samples shares car
GSE278910 Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN] 30 samples shares crispr
GSE278073 Targeting VRK2 Enhances the Efficacy of Anti-PD-1 Therapy in Hepatocellular Carcinoma by Reducing Direct Phosphorylation and Stability of MYC: CUT-TAG sequencing for MYC in hepatocellular carcinoma cells 16 samples shares car
GSE14520 Gene expression data of human hepatocellular carcinoma (HCC) 488 samples shares car
GSE314310 Cardiopedia-Ligand: a Ligand Stimulation Atlas for Cardiac Function and Transcriptional Response 468 samples shares car
GSE71729 Virtual Microdissection of Pancreatic Ductal Adenocarcinoma Reveals Tumor and Stroma Subtypes. 357 samples shares car

Search all human ChIP / ATAC / CUT&Tag 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.