GEO series

Ex vivo-generated human CD1c+ regulatory B cells by a chemically defined system suppress immune responses and alleviate graft-versus-host disease

GSE279879 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2024/12/19 Platform GPL34284

At a glance

RNA-seq (gene expression) · human · 14 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: 14 samples: 6 conditions, mostly in duplicateGroups 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: Ex vivo-generated human CD1c(+) regulatory B cells by a chemically defined system suppress immune responses and alleviate graft-versus-host diseaseMolecular therapy : the journal of the American Society of Gene Therapy · 2024

Summary (written by the submitters)

IL-10+ regulatory B cells (Bregs) show great promise in treating graft versus host disease (GVHD), a life-threatening complication of post-hematopoietic stem cell transplantation. However, obtaining high-quality human IL-10+ Bregs in vitro remains a challenge due to the lack of unique specific marker and the triggering of pro-inflammatory cytokines expression.

Read the full summary ↓

Here, by uncovering the critical signaling pathways in Bregs induction by mesenchymal stromal cells (MSCs), we firstly established an efficient Bregs induction system based on MSCs and GSK-3β blockage (CHIR-99021), which had a robust capacity to induce IL-10+ Bregs while suppress TNF-α expression. Furthermore, these Bregs population could be identified and enriched by CD1c+. Mechanistically, MSCs induced the expansion of Bregs through the PKA-mediated phosphorylation of cAMP response element binding protein (CREB). Thus, we developed a chemical-defined inducing protocol by PKA-CREB agonist, instead of MSCs, which can also effectively induce CD1c+ Bregs with lower TNF-α expression. Importantly, induced CD1c+ Bregs suppressed the proliferation of PBMC and the inflammatory cytokines secretion of T cells. When adoptive transferred to a humanized mouse model of GVHD, induced CD1c+ Bregs effectively alleviated GVHD. Overall, we establish an efficient ex vivo induction system for human Bregs, which has implications in developing novel Bregs-based therapies for GVHD.

Published in

Ex vivo-generated human CD1c(+) regulatory B cells by a chemically defined system suppress immune responses and alleviate graft-versus-host disease

Bao Y, Liu J, Li Z et al. · Molecular therapy : the journal of the American Society of Gene Therapy 2024 · PMID 39489917 · doi:10.1016/j.ymthe.2024.10.026

This dataset

Open GSE279879 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 GSE279879_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 PRJNA1175029 and SRA study SRP539541. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39489917) ↗

Study design

6 conditions, mostly in duplicate

total B cells ,culture with MSC, ×3 total B cells, control, ×3 1c+ B cells,culture with MSC, ×2 1c- B cells,culture with MSC, ×2 1c+ B cells, control, ×2 1c- B cells, control, ×2

Supports a between-group comparison across 14 samples.

How we read this: 6 replicated groups read from 14 sample titles; they account for 14 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

GSM8582474 total B cells ,culture with MSC, rep1 total B cells ,culture …
GSM8582475 total B cells ,culture with MSC, rep2 total B cells ,culture …
GSM8582476 total B cells ,culture with MSC, rep3 total B cells ,culture …
GSM8582477 total B cells, control, rep1 total B cells, control,
GSM8582478 total B cells, control, rep2 total B cells, control,
GSM8582479 total B cells, control, rep3 total B cells, control,
GSM8582480 1c+ B cells,culture with MSC, rep1 1c+ B cells,culture wit…
GSM8582481 1c+ B cells,culture with MSC, rep2 1c+ B cells,culture wit…
GSM8582482 1c- B cells,culture with MSC, rep1 1c- B cells,culture wit…
GSM8582483 1c- B cells,culture with MSC, rep2 1c- B cells,culture wit…
GSM8582484 1c+ B cells, control, rep1 1c+ B cells, control,
GSM8582485 1c+ B cells, control, rep2 1c+ B cells, control,
GSM8582486 1c- B cells, control, rep1 1c- B cells, control,
GSM8582487 1c- B cells, control, rep2 1c- B cells, control,

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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.