GEO series
Mapping immune cellular landscapes and vaccine responses across a spectrum of health and immunodeficiency [CITE-seq]
GSE334503
Homo sapiens
Expression profiling by high throughput sequencing; Other
10 samples
Submitted 2026/06/12
Platform GPL34284
Summary
Immune responses to infection and vaccination exhibit diversity between individuals that can be shaped by differences in their immune cell landscapes and the signalling, transcriptional, and genetic mechanisms that coordinate immune cell function. Specific antibody deficiency (SAD) and common variable immunodeficiency (CVID) are common forms of predominantly antibody deficiencies that result in poor responses to vaccination. While molecular and cellular causes of the immune dysfunction and poor vaccination responses for individuals with CVID have been reported, immune cell or molecular defects have not yet been identified in SAD. Here, we have used single-cell multi-omics to define the cellular landscapes, transcriptional states, adaptive immune repertoires and protein expression of patients with SAD and CVID before and after polysaccharide vaccination. We discovered that while SAD and CVID exhibit overlapping immune defects, including accumulation of exhausted NK memory cells and dysregulated expression of genes that mediate lipopolysaccharide sensing and clearance by monocytes, individuals with SAD have a unique expansion of cytotoxic CD4+ T cells that correlates with reduced regulatory T cells. In response to vaccination, we observed rapid changes in gene expression associated with lipopolysaccharide responses by monocytes and NF-kB pathway activation in B cells, and an apparent expansion of a CD95+ class-switched memory B cell population that does not occur in patients with lower antigen-specific responses. Together, our findings reveal cellular and molecular factors that underpin variability in vaccine responses and define SAD in a broader spectrum of immune dysfunction.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE334503_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 10 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1475356 and SRA study SRP707188. Searching any of these in the dataset finder brings you back here.
Study design
10 conditions, each sampled once — no replicated groups
Read from 10 sample titles: 10 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9789808 Human PBMCs CITE-seq library, 10X Batch 1, GEX
- GSM9789809 Human PBMCs CITE-seq library, 10X Batch 1, ADT + HTO
- GSM9789810 Human PBMCs CITE-seq library, 10X Batch 2, GEX
- GSM9789811 Human PBMCs CITE-seq library, 10X Batch 2, ADT + HTO
- GSM9789812 Human PBMCs CITE-seq library, 10X Batch 3, GEX
- GSM9789813 Human PBMCs CITE-seq library, 10X Batch 3, ADT + HTO
- GSM9789814 Human PBMCs CITE-seq library, 10X Batch 4, GEX
- GSM9789815 Human PBMCs CITE-seq library, 10X Batch 4, ADT + HTO
- GSM9789816 Human PBMCs CITE-seq library, 10X Batch 5, GEX
- GSM9789817 Human PBMCs CITE-seq library, 10X Batch 5, ADT + HTO
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