CoSpar identifies early cell fate biases from single-cell transcriptomic and lineage information.
Journal
Nature biotechnology
ISSN: 1546-1696
Titre abrégé: Nat Biotechnol
Pays: United States
ID NLM: 9604648
Informations de publication
Date de publication:
07 2022
07 2022
Historique:
received:
06
05
2021
accepted:
04
01
2022
pubmed:
23
2
2022
medline:
20
7
2022
entrez:
22
2
2022
Statut:
ppublish
Résumé
A goal of single-cell genome-wide profiling is to reconstruct dynamic transitions during cell differentiation, disease onset and drug response. Single-cell assays have recently been integrated with lineage tracing, a set of methods that identify cells of common ancestry to establish bona fide dynamic relationships between cell states. These integrated methods have revealed unappreciated cell dynamics, but their analysis faces recurrent challenges arising from noisy, dispersed lineage data. In this study, we developed coherent, sparse optimization (CoSpar) as a robust computational approach to infer cell dynamics from single-cell transcriptomics integrated with lineage tracing. Built on assumptions of coherence and sparsity of transition maps, CoSpar is robust to severe downsampling and dispersion of lineage data, which enables simpler experimental designs and requires less calibration. In datasets representing hematopoiesis, reprogramming and directed differentiation, CoSpar identifies early fate biases not previously detected, predicting transcription factors and receptors implicated in fate choice. Documentation and detailed examples for common experimental designs are available at https://cospar.readthedocs.io/ .
Identifiants
pubmed: 35190690
doi: 10.1038/s41587-022-01209-1
pii: 10.1038/s41587-022-01209-1
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
1066-1074Subventions
Organisme : NHLBI NIH HHS
ID : R01 HL095993
Pays : United States
Organisme : NCATS NIH HHS
ID : U01 TR001810
Pays : United States
Organisme : NHLBI NIH HHS
ID : 75N92020C00005
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA218579
Pays : United States
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.
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