GEO series

BCG vaccination impacts the epigenetic landscape of progenitor cells in human bone marrow (scRNA-Seq)

GSE248728 Homo sapiens (human) Single-cell RNA-seq 28 samples Submitted 2024/08/21 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 28 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 28 samples: 14 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: BCG vaccination alters the epigenetic landscape of progenitor cells in human bone marrow to influence innate immune responsesImmunity · 2024

Summary (written by the submitters)

While the Bacille-Calmette-Guérin (BCG) vaccine is used to prevent tuberculosis, it also offers protection against a diverse range of non-mycobacterial infections. However, the underlying protective mechanisms in humans are not yet fully understood. Here, we surveyed at single-cell resolution the gene expression and chromatin landscape of human bone marrow, aspirated before and 90 days after BCG vaccination or placebo administration.

Read the full summary ↓

We show that BCG vaccination significantly alters both the gene expression and epigenetic profiles of human hematopoietic stem and progenitor cells (HSPCs). Changes in gene expression occur primarily on the most uncommitted stem cells and are reflective of a persistent myeloid bias. In contrast, BCG-induced changes in chromatin accessibility are most prevalent within differentiated progenitor cells at sites influenced by Kruppel-like factor (KLF)/SP and EGR transcription factors (TFs). These TFs are also activated in the most uncommitted stem cells, indicating that activated TFs, which drive persistent changes in HSC gene expression, likely also drive chromatin dynamics appearing within downstream progenitor cells. This perspective contests the prevailing notion that epigenetic modifications linked to innate immune memory transfer directly from stem cells to their differentiated derivatives. Finally, we show that alterations in gene expression and chromatin accessibility in HSPCs due to BCG vaccination were highly correlated (r>0.8) with the IL-1β secretion capacity of paired PBMCs upon secondary immune challenge. Overall, our findings shed light on BCG vaccination's profound and lasting effects on HSPCs and its influence on innate immune responses.

Published in

BCG vaccination alters the epigenetic landscape of progenitor cells in human bone marrow to influence innate immune responses

Sun SJ, Aguirre-Gamboa R, de Bree LCJ et al. · Immunity 2024 · PMID 39153479 · doi:10.1016/j.immuni.2024.07.021

This dataset

Open GSE248728 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 GSE248728_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 PRJNA1045667 and SRA study SRP474474. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39153479) ↗

Study design

14 conditions, mostly in duplicate

B1_c ×2 B2_c ×2 B3_c ×2 B4_c ×2 B5_c ×2 B6_c ×2 B7_c ×2 B8_c ×2 +6 more

Supports a between-group comparison across 28 samples.

How we read this: 14 replicated groups read from 28 sample titles; they account for 28 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

GSM7919184 B1_c1 B1_c
GSM7919185 B1_c2 B1_c
GSM7919186 B2_c1 B2_c
GSM7919187 B2_c2 B2_c
GSM7919188 B3_c1 B3_c
GSM7919189 B3_c2 B3_c
GSM7919190 B4_c1 B4_c
GSM7919191 B4_c2 B4_c
GSM7919192 B5_c1 B5_c
GSM7919193 B5_c2 B5_c
GSM7919194 B6_c1 B6_c
GSM7919195 B6_c2 B6_c
GSM7919196 B7_c1 B7_c
GSM7919197 B7_c2 B7_c
GSM7919198 B8_c1 B8_c
GSM7919199 B8_c2 B8_c
GSM7919200 B9_c1 B9_c
GSM7919201 B9_c2 B9_c
GSM7919202 B10_c1 B10_c
GSM7919203 B10_c2 B10_c
GSM7919204 B11_c1 B11_c
GSM7919205 B11_c2 B11_c
GSM7919206 B12_c1 B12_c
GSM7919207 B12_c2 B12_c
GSM7919208 B13_c1 B13_c
GSM7919209 B13_c2 B13_c
GSM7919210 B14_c1 B14_c
GSM7919211 B14_c2 B14_c

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GSE270296 TGF-β Signaling Pathway and Cell-Cell Interactions in the Tumor Microenvironment Drive Bladder Cancer Progression after BCG Instillation Treatment: Insights from longitudinal Single-Nucleus RNA-Seq 14 samples shares bcg
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GSE249632 Longitudinal analysis of antigen-specific T cells after Shingrix vaccination 2866 samples shares vaccination

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