Foundry120 atlas

Immunomolecular and reactivity landscapes of gut IgA subclasses in homeostasis and inflammatory bowel diseases.

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Dataset overview

Participants None
Samples 1
Reuse readiness 3.3/10 evidence-backed score

Immunomolecular and reactivity landscapes of gut IgA subclasses in homeostasis and inflammatory bowel disease.

Abstract

The human gut includes plasma cells (PCs) expressing immunoglobulin A1 (IgA1) or IgA2, two structurally distinct IgA subclasses with elusive regulation, function, and reactivity. We show here that intestinal IgA1+ and IgA2+ PCs co-emerged early in life, comparably accumulated somatic mutations, and were enriched within short-lived CD19+ and long-lived CD19- PC subsets, respectively. IgA2+ PCs were extensively clonally related to IgA1+ PCs and a subset of them presumably emerged from IgA1+ precursors. Of note, secretory IgA1 (SIgA1) and SIgA2 dually coated a large fraction of mucus-embedded bacteria, including Akkermansia muciniphila. Disruption of homeostasis by inflammatory bowel disease (IBD) was associated with an increase in actively proliferating IgA1+ plasmablasts, a depletion in long-lived IgA2+ PCs, and increased SIgA1+SIgA2+ gut microbiota. Such increase featured enhanced IgA1 reactivity to pathobionts, including Escherichia coli, combined with depletion of beneficial A. muciniphila. Thus, gut IgA1 and IgA2 emerge from clonally related PCs and show unique changes in both frequency and reactivity in IBD.

Study facts

Organism
Homo sapiens
Platform
Illumina NovaSeq 6000
Age group
Disease groups
Anatomical sites

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Sample counts are documented

Limitations

  • Not documented: feature/otu tables are advertised
  • Not documented: taxonomic tables are advertised
  • Not documented: participant counts are documented
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.platform Illumina NovaSeq 6000
Sequencing was done on a NovaSeq 6000 S2 platform (Illumina).

Section Materials and methods—Cell isolation, single-cell RNA, and V(D)J-seq library preparation, sequencing, and analysis, offset 46200

Data_Assets

FieldValueEvidence
data_assets.raw_reads True
Raw and processed sequencing reads of scRNA and V(D)J-seq are available in Gene Expression Omnibus under accession number GSE268929.

Section Data availability, offset 56500

Specimens

FieldValueEvidence
specimens.body_site terminal ileum
scRNA and V(D)J sequencing of alive lamina propria cells from an histological normal human ileal sample.

Section study.overall_design, offset 8500

specimens.number_of_samples 1
from an histological normal human ileal sample

Section study.overall_design, offset 8500