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Affinity maturation broadens influenza vaccine-induced antibody responses in humans [bcr]

GSE211869 Homo sapiens (human) RNA-seq (gene expression) 128 samples Submitted 2024/06/13 Platform GPL15520Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 128 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
128 samples: 42 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
Maturation of germinal center B cells after influenza virus vaccination in humansThe Journal of experimental medicine · 2024
Summary (written by the submitters)
Influenza virus vaccination remains the best strategy for combating virus infection, but vaccine efficacy is highly variable. An ideal influenza vaccine must have two attributes: one, it should be capable of inducing broadly cross-reactive antibodies that can neutralize diverse influenza virus strains; and two, it must induce long-lived antibody responses to maintain protective immunity for extended periods.
Read the full summary ↓
Germinal center (GC) reactions are the major sites where diversification and affinity maturation of B cells occur. Whether a persistent GC response could expand the breadth of responding B cell clones following influenza vaccination in humans remains unknown. Here, we show that influenza virus vaccine-specific GC B cells persist for over nine weeks post vaccination in two out of seven individuals. These late vaccine-specific GC B cells exhibited increased somatic hypermutation (SHM) of their B cell receptors compared to early vaccine-specific GC B cells. After re-immunization with seasonal influenza virus vaccine, individuals with a persistent GC engaged vaccine-specific plasmablasts (PBs) with higher SHM frequency. Tracking the maturation of three clonally related GC B cell lineages over time revealed that late GC B cells had receptors that recognized and neutralized heterologous influenza virus strains. Thus, SHM induced by persistent GCs can broaden the antibody response to influenza virus vaccination. This indicates that seasonal influenza virus vaccination in humans can induce broadly cross-reactive antibodies that target diverse influenza virus strains.
Published in
Maturation of germinal center B cells after influenza virus vaccination in humans
McIntire KM, Meng H, Lin TH et al. · The Journal of experimental medicine 2024 · PMID 38935072 · doi:10.1084/jem.20240668
This dataset
Open GSE211869 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 GSE211869_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 PRJNA838986 and SRA study SRP393513. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38935072) ↗
Study design
42 conditions, mostly in duplicate
scBCR, adult male, subject P05, Lymph Node, y… ×4 scBCR, adult male, subject P04, PBMC enriched… ×3 scBCR, adult male, subject P04, PBMC enriched… ×3 scBCR, adult male, subject P05, Lymph Node, y… ×3 scBCR, adult male, subject P05, Lymph Node, y… ×3 scBCR, adult male, subject P05, Lymph Node, y… ×3 scBCR, adult male, subject P05, Lymph Node, y… ×3 scBCR, adult male, subject P05, Lymph Node, y… ×3 +68 more

Supports a between-group comparison across 94 samples.

How we read this: 42 replicated groups read from 128 sample titles; they account for 94 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

+ 88 more — browse all 128 samples with per-sample file links →

Datasets on a similar topic

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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.