Single cell transcriptomic analysis of the immune cell compartment in the human small intestine and in Celiac disease

Nader Atlasy, Anna Bujko, Espen S. Bækkevold, Peter Brazda, Eva Janssen-Megens, Knut E. A. Lundin, Jørgen Jahnsen, Frode L. Jahnsen and Hendrik G. Stunnenberg ()
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Nader Atlasy: Radboud University
Anna Bujko: University of Oslo and Oslo University Hospital, Rikshospitalet
Espen S. Bækkevold: University of Oslo and Oslo University Hospital, Rikshospitalet
Peter Brazda: Radboud University
Eva Janssen-Megens: Radboud University
Knut E. A. Lundin: University of Oslo
Jørgen Jahnsen: Akershus University Hospital and University of Oslo
Frode L. Jahnsen: University of Oslo and Oslo University Hospital, Rikshospitalet
Hendrik G. Stunnenberg: Radboud University

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: Abstract Celiac disease is an autoimmune disorder in which ingestion of dietary gluten triggers an immune reaction in the small intestine leading to destruction of the lining epithelium. Current treatment focusses on lifelong adherence to a gluten-free diet. Gluten-specific CD4+ T cells and cytotoxic intraepithelial CD8+ T cells have been proposed to be central in disease pathogenesis. Here we use unbiased single-cell RNA-sequencing and explore the heterogeneity of CD45+ immune cells in the human small intestine. We show altered myeloid cell transcriptomes present in active celiac lesions. CD4+ and CD8+ T cells transcriptomes show extensive changes and we define a natural intraepithelial lymphocyte population that is reduced in celiac disease. We show that the immune landscape in Celiac patients on a gluten-free diet is only partially restored compared to control samples. Altogether, we provide a single cell transcriptomic resource that can inform the immune landscape of the small intestine during Celiac disease.

Date: 2022
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DOI: 10.1038/s41467-022-32691-5

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