GEO series

Vaccines combining slow release and follicle targeting of antigens increase germinal center B cell clonal diversity and clonal expansion

GSE288450 Mus musculus (mouse) Single-cell RNA-seq 33 samples Submitted 2025/02/04 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 33 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: Mus musculus (mouse)
Samples: 33 samples: 33 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.
Paper: Vaccines combining slow release and follicle targeting of antigens increase germinal center B cell diversity and clonal expansionScience translational medicine · 2025

Summary (written by the submitters)

Vaccines incorporating slow release, multivalent antigen display, and/or immunomodulation through adjuvants have important roles in shaping the humoral immune response. Here, we analyzed mechanisms of action of a clinically relevant combination adjuvant strategy, where phosphoserine (pSer)-tagged immunogens bound to aluminum hydroxide (alum) adjuvant (promoting prolonged antigen release to draining lymph nodes) are combined with a potent saponin nanoparticle adjuvant termed SMNP (which alters lymph flow and antigen entry into lymph nodes).

Read the full summary ↓

When employed with a stabilized HIV Env trimer antigen in mice, this combined adjuvant approach promoted substantial enhancements in germinal center (GC) and antibody responses relative to either adjuvant alone. Using scRNA-seq and scBCR-seq, we found that the alum-pSer/SMNP combination augmented the clonal expansion and diversity of GC B cell repertoire, coincident with increased expression of positive selection markers and proportion of S-phase GC B cells. To gain insight into the source of these changes in the GC response, we analyzed antigen biodistribution and structural integrity in draining lymph nodes and found that the combination adjuvant approach, but not alum-pSer delivery or SMNP alone, promoted accumulation of intact antigen on follicular dendritic cells (FDCs), reflecting an integration of the effects by slowing antigen release and altering lymph node uptake. Ablating the Cr1/2 complex on FDCs significantly hampered antigen-specific GC response, corroborating enhanced FDC decoration as the key mechanism of improved vaccine response. These results demonstrate how adjuvants with complementary mechanisms of action impacting vaccine biodistribution and kinetics can synergize to enhance humoral immunity.

Published in

Vaccines combining slow release and follicle targeting of antigens increase germinal center B cell diversity and clonal expansion

Rodrigues KA, Zhang YJ, Lam J et al. · Science translational medicine 2025 · PMID 40531969 · doi:10.1126/scitranslmed.adw7499

This dataset

Open GSE288450 in finder → Find more mouse 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 GSE288450_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 PRJNA1217578 and SRA study SRP560824. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40531969) ↗

Study design

33 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 33 sample titles: 33 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

GSM8768106 AG1_SMNP
GSM8768107 AG2_pSer
GSM8768108 AG3_both
GSM8768109 AQ1_SMNP
GSM8768110 AQ2_pSer
GSM8768111 AQ3_both
GSM8768112 AQ4_both
GSM8768113 P1_pSer
GSM8768114 P2_pSer
GSM8768115 P3_pSer
GSM8768116 P4_pSer
GSM8768117 AG1_SMNP_HTO
GSM8768118 AG2_pSer_HTO
GSM8768119 AG3_both_HTO
GSM8768120 AQ1_SMNP_HTO
GSM8768121 AQ2_pSer_HTO
GSM8768122 AQ3_both_HTO
GSM8768123 AQ4_both_HTO
GSM8768124 P1_pSer_HTO
GSM8768125 P2_pSer_HTO
GSM8768126 P3_pSer_HTO
GSM8768127 P4_pSer_HTO
GSM8768128 AG1_VDJ
GSM8768129 AG2_VDJ
GSM8768130 AG3_both_VDJ
GSM8768131 AQ1_SMNP_VDJ
GSM8768132 AQ2_pSer_VDJ
GSM8768133 AQ3_both_VDJ
GSM8768134 AQ4_both_VDJ
GSM8768135 P1_pSer_VDJ
GSM8768136 P2_pSer_VDJ
GSM8768137 P3_pSer_VDJ
GSM8768138 P4_pSer_VDJ

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