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Mucosal inflammation and pre-existing antibodies define protection and disease outcomes in human Bordetella pertussis challenge

GSE310241 Homo sapiens (human) RNA-seq (gene expression) 414 samples Submitted 2026/07/22 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 414 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
414 samples: 51 conditions, mostly with about 7 replicates eachGroups 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
Pre-existing antibodies predict protection while mucosal inflammation correlates with symptomatic Bordetella pertussis infectionmedRxiv : the preprint server for health sciences · 2026
Summary (written by the submitters)
Whooping cough, caused by Bordetella pertussis (BP), persists despite widespread vaccination with acellular pertussis (aP) vaccines, which protect against disease but provide incomplete and short-lived immunity against infection and transmission. To define correlates of protection and mechanisms underlying symptom development, we characterized systemic and mucosal immune responses in a North American BP-controlled human infection model (CHIM).
Read the full summary ↓
Healthy adults, primed in infancy with either whole-cell or aP vaccines, were intranasally challenged with escalating BP doses and classified as symptomatic, asymptomatic, or non-infected. Longitudinal paired blood and nasal samples were analyzed to measure antibody titers, cell subset frequencies, cytokine concentrations, gene expression, and T cell polarization and activation. Non-infected participants exhibited significantly higher pre-challenge serum antigen-specific IgG titers, identifying these antibodies as potential correlates of protection. Only symptomatic individuals developed robust antigen-specific IgG responses post-challenge and displayed pronounced nasal transcriptional inflammation peaking on day 7, characterized by induction of interferon and NF-κB signaling and the presence of HLA-DR⁺ myeloid cells. Systemic responses were modest: plasma cytokine concentrations decreased following challenge regardless of outcome, peripheral blood mononuclear cell transcriptomes remained largely unchanged, and antigen-specific T cell activation and polarization were unaffected. Together, these findings reveal that protection from BP colonization associates with pre-existing serum antibodies, whereas symptom development is driven by localized mucosal inflammation dominated by myeloid cells. The predominance of nasal over systemic immune activation highlights the importance of mucosal immunity in controlling BP and provides critical insights to guide the design of next-generation vaccines aimed at preventing both disease and transmission.
Published in
Pre-existing antibodies predict protection while mucosal inflammation correlates with symptomatic Bordetella pertussis infection
Willemsen L, Ren Z, Shinde P et al. · medRxiv : the preprint server for health sciences 2026 · PMID 42465938 · doi:10.64898/2026.06.26.26356067
This dataset
Open GSE310241 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 GSE310241_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 PRJNA1354793. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42465938) ↗
Study design
51 conditions, mostly with about 7 replicates each
PBMC_8325_CD ×8 PBMC_8334_CD ×8 PBMC_8336_CD ×8 PBMC_8589_CD ×8 PBMC_8590_CD ×8 PBMC_8778_CD ×8 PBMC_8779_CD ×8 PBMC_8780_CD ×8 +91 more

Supports a between-group comparison across 352 samples.

How we read this: 51 replicated groups read from the first 400 of 414 sample titles; they account for 352 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

+ 374 more — browse all 414 samples with per-sample file links →

Datasets on a similar topic

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