Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing

Author:

Mazzurana Luca,Czarnewski PauloORCID,Jonsson Viktor,Wigge Leif,Ringnér MarkusORCID,Williams Teresa C.,Ravindran Avinash,Björklund Åsa K.ORCID,Säfholm Jesper,Nilsson Gunnar,Dahlén Sven-Erik,Orre Ann-Charlotte,Al-Ameri Mamdoh,Höög Charlotte,Hedin CharlotteORCID,Szczegielniak Sylwester,Almer SvenORCID,Mjösberg Jenny

Abstract

AbstractThe impact of the microenvironment on innate lymphoid cell (ILC)-mediated immunity in humans remains largely unknown. Here we used full-length Smart-seq2 single-cell RNA-sequencing to unravel tissue-specific transcriptional profiles and heterogeneity of CD127+ ILCs across four human tissues. Correlation analysis identified gene modules characterizing the migratory properties of tonsil and blood ILCs, and signatures of tissue-residency, activation and modified metabolism in colon and lung ILCs. Trajectory analysis revealed potential differentiation pathways from circulating and tissue-resident naïve ILCs to a spectrum of mature ILC subsets. In the lung we identified both CRTH2+ and CRTH2 ILC2 with lung-specific signatures, which could be recapitulated by alarmin-exposure of circulating ILC2. Finally, we describe unique TCR-V(D)J-rearrangement patterns of blood ILC1-like cells, revealing a subset of potentially immature ILCs with TCR-δ rearrangement. Our study provides a useful resource for in-depth understanding of ILC-mediated immunity in humans, with implications for disease.

Funder

Knut och Alice Wallenbergs Stiftelse

Cancerfonden

Vetenskapsrådet

Publisher

Springer Science and Business Media LLC

Subject

Cell Biology,Molecular Biology

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