Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples.

CP: Cell biology CP: Systems biology cell-cell communication context dependent ligand-receptor interactions multiple conditions single-cell RNA sequencing tensor decomposition

Journal

Cell reports methods
ISSN: 2667-2375
Titre abrégé: Cell Rep Methods
Pays: United States
ID NLM: 9918227360606676

Informations de publication

Date de publication:
10 Apr 2024
Historique:
received: 10 08 2023
revised: 22 12 2023
accepted: 22 03 2024
medline: 18 4 2024
pubmed: 18 4 2024
entrez: 17 4 2024
Statut: aheadofprint

Résumé

In recent years, data-driven inference of cell-cell communication has helped reveal coordinated biological processes across cell types. Here, we integrate two tools, LIANA and Tensor-cell2cell, which, when combined, can deploy multiple existing methods and resources to enable the robust and flexible identification of cell-cell communication programs across multiple samples. In this work, we show how the integration of our tools facilitates the choice of method to infer cell-cell communication and subsequently perform an unsupervised deconvolution to obtain and summarize biological insights. We explain how to perform the analysis step by step in both Python and R and provide online tutorials with detailed instructions available at https://ccc-protocols.readthedocs.io/. This workflow typically takes ∼1.5 h to complete from installation to downstream visualizations on a graphics processing unit-enabled computer for a dataset of ∼63,000 cells, 10 cell types, and 12 samples.

Identifiants

DOI: 10.1016/j.crmeth.2024.100758 PMID: 38631346
pubmed: 38631346
pii: S2667-2375(24)00089-4
doi: 10.1016/j.crmeth.2024.100758
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

100758

Informations de copyright

Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests J.S.-R. reports funding from GSK, Pfizer, and Sanofi and fees/honoraria from Travere Therapeutics, Stadapharm, Astex, Pfizer, and Grunenthal. N.E.L. reports funding during the course of this work from Sanofi, Amgen, Sartorius, and Ionis and is a co-founder of NeuImmune, Inc., and Augment Biologics.

Auteurs

Hratch M Baghdassarian (HM)

Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.

Daniel Dimitrov (D)

Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, 69120 Heidelberg, Germany.

Erick Armingol (E)

Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.

Julio Saez-Rodriguez (J)

Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, 69120 Heidelberg, Germany. Electronic address: pub.saez@uni-heidelberg.de.

Nathan E Lewis (NE)

Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: nlewisres@ucsd.edu.

Classifications MeSH