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Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins

Lookup NU author(s): Professor Muzlifah Haniffa

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

Abstract

© 2023, The Author(s).Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here we introduce Dandelion, a computational pipeline for scVDJ-seq analysis. It enables the application of standard V(D)J analysis workflows to single-cell datasets, delivering improved V(D)J contig annotation and the identification of nonproductive and partially spliced contigs. We devised a strategy to create an AIR feature space that can be used for both differential V(D)J usage analysis and pseudotime trajectory inference. The application of Dandelion improved the alignment of human thymic development trajectories of double-positive T cells to mature single-positive CD4/CD8 T cells, generating predictions of factors regulating lineage commitment. Dandelion analysis of other cell compartments provided insights into the origins of human B1 cells and ILC/NK cell development, illustrating the power of our approach. Dandelion is available at https://www.github.com/zktuong/dandelion.

Publication metadata

Author(s): Suo C, Polanski K, Dann E, Lindeboom RGH, Vilarrasa-Blasi R, Vento-Tormo R, Haniffa M, Meyer KB, Dratva LM, Tuong ZK, Clatworthy MR, Teichmann SA

Publication type: Article

Publication status: Published

Journal: Nature Biotechnology

Year: 2024

Volume: 42

Pages: 40–51

Online publication date: 13/04/2023

Acceptance date: 07/03/2023

Date deposited: 05/05/2023

ISSN (print): 1087-0156

ISSN (electronic): 1546-1696

Publisher: Nature Research

URL: https://doi.org/10.1038/s41587-023-01734-7

DOI: 10.1038/s41587-023-01734-7

PubMed id: 37055623

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