Comparative analysis of cell-cell communication at single-cell resolution.
Journal
Nature biotechnology
ISSN: 1546-1696
Titre abrégé: Nat Biotechnol
Pays: United States
ID NLM: 9604648
Informations de publication
Date de publication:
Mar 2024
Mar 2024
Historique:
received:
28
03
2022
accepted:
05
04
2023
pmc-release:
11
11
2024
medline:
18
3
2024
pubmed:
12
5
2023
entrez:
11
5
2023
Statut:
ppublish
Résumé
Inference of cell-cell communication from single-cell RNA sequencing data is a powerful technique to uncover intercellular communication pathways, yet existing methods perform this analysis at the level of the cell type or cluster, discarding single-cell-level information. Here we present Scriabin, a flexible and scalable framework for comparative analysis of cell-cell communication at single-cell resolution that is performed without cell aggregation or downsampling. We use multiple published atlas-scale datasets, genetic perturbation screens and direct experimental validation to show that Scriabin accurately recovers expected cell-cell communication edges and identifies communication networks that can be obscured by agglomerative methods. Additionally, we use spatial transcriptomic data to show that Scriabin can uncover spatial features of interaction from dissociated data alone. Finally, we demonstrate applications to longitudinal datasets to follow communication pathways operating between timepoints. Our approach represents a broadly applicable strategy to reveal the full structure of niche-phenotype relationships in health and disease.
Identifiants
pubmed: 37169965
doi: 10.1038/s41587-023-01782-z
pii: 10.1038/s41587-023-01782-z
pmc: PMC10638471
mid: NIHMS1932261
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
470-483Subventions
Organisme : NIGMS NIH HHS
ID : T32 GM007365
Pays : United States
Organisme : NIAID NIH HHS
ID : DP2 AI112193
Pays : United States
Organisme : NIDA NIH HHS
ID : DP1 DA046089
Pays : United States
Organisme : NIDA NIH HHS
ID : DP1 DA053731
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI161803
Pays : United States
Organisme : Bill & Melinda Gates Foundation
ID : INV-027498
Pays : United States
Organisme : NICHD NIH HHS
ID : R01 HD103571
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA217377
Pays : United States
Organisme : Bill & Melinda Gates Foundation
ID : INV-027498
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI161803
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.
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