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Persistence of mucosal CAR-T cells and inflammatory remodeling in enterocolitis associated with BCMA CAR-T cell therapy

GSE322796 Homo sapiens (human) Single-cell RNA-seq 23 samples Submitted 2026/07/29 Platform GPL34281
At a glance

Single-cell RNA-seq · human · 23 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
23 samples: 11 × Normal Voluntee vs 7 × CAR-T Enterocolitis vs 5 × CAR-T ControlGroups 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)
B cell-targeted therapies are expanding across oncologic and autoimmune indications, yet their consequences for immunity remain incompletely examined. Here, we define the mucosal pathophysiology of ciltacabtagene autoleucel CAR-T cell-induced enterocolitis (CAR-TEC), a severe complication of B cell maturation antigen (BCMA)-targeted CAR-T cell therapy in multiple myeloma.
Read the full summary ↓
Using single-cell transcriptomics, flow cytometry, and tissue imaging of intestinal biopsies from patients with CAR-TEC (n=10), CAR-T cell treated controls (CAR-TCTRL) without enterocolitis (n=7), and healthy volunteers (n=26), we identify profound depletion of mucosal B cells and plasma cells (PCs) accompanied by expansion of highly cytotoxic CAR-T cells and inflammatory myeloid, stromal, and glial cell remodeling to be associated with CAR-TEC. Cell-cell communication analyses suggest a compensated mucosal state in CAR-TCTRL, while telocyte-driven stromal niche dysfunction was noted in CAR-TEC. Interferon and JAK-STAT-associated reprogramming was noted across stromal, endothelial, and epithelial compartments, supporting JAK inhibition as a rational, mechanism-based therapeutic strategy. Upadacitinib, an oral selective JAK1 inhibitor resulted in clinical, endoscopic and histologic improvement in 2 individuals with CAR-TEC. Our findings define CAR-TEC as a multi-compartment syndrome of severe mucosal dysregulation with implications for the emerging field of B cell-targeted therapies.
This dataset
Open GSE322796 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 GSE322796_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 PRJNA1431538 and SRA study SRP680742. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
11 × Normal Voluntee vs 7 × CAR-T Enterocolitis vs 5 × CAR-T Control

Supports a between-group comparison across 23 samples.

How we read this: 3 replicated groups read from 23 sample titles; they account for 23 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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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.