scDiffCom: a tool for differential analysis of cell–cell interactions provides a mouse atlas of aging changes in intercellular communication

Cyril Lagger; Eugen Ursu; Anaïs Equey; Roberto A. Avelar; Angela Oliveira Pisco; Robi Tacutu; João Pedro de Magalhães

doi:10.1038/s43587-023-00514-x

scDiffCom: a tool for differential analysis of cell–cell interactions provides a mouse atlas of aging changes in intercellular communication

Cyril Lagger, Eugen Ursu, Anaïs Equey, Roberto A. Avelar, Angela Oliveira Pisco, Robi Tacutu, João Pedro de Magalhães^*

^*Corresponding author for this work

Inflammation and Ageing

Research output: Contribution to journal › Article › peer-review

27 Downloads (Pure)

Abstract

Dysregulation of intercellular communication is a hallmark of aging. To better quantify and explore changes in intercellular communication, we present scDiffCom and scAgeCom. scDiffCom is an R package, relying on approximately 5,000 curated ligand–receptor interactions, that performs differential intercellular communication analysis between two conditions from single-cell transcriptomics data. Built upon scDiffCom, scAgeCom is an atlas of age-related cell–cell communication changes covering 23 mouse tissues from 58 single-cell RNA sequencing datasets from Tabula Muris Senis and the Calico murine aging cell atlas. It offers a comprehensive resource of tissue-specific and sex-specific aging dysregulations and highlights age-related intercellular communication changes widespread across the whole body, such as the upregulation of immune system processes and inflammation, the downregulation of developmental processes, angiogenesis and extracellular matrix organization and the deregulation of lipid metabolism. Our analysis emphasizes the relevance of the specific ligands, receptors and cell types regulating these processes. The atlas is available online (https://scagecom.org).

Original language	English
Pages (from-to)	1446-1461
Number of pages	16
Journal	Nature Aging
Volume	3
Issue number	11
Early online date	2 Nov 2023
DOIs	https://doi.org/10.1038/s43587-023-00514-x
Publication status	Published - Nov 2023

Bibliographical note

Acknowledgements
We thank J. Kimmel for helpful information regarding the Calico murine cell atlas, K. Tsuyuzaki for general discussion regarding intercellular communication at the early stage of this project, Z. Abidi for support to deploy the Shiny app and U. Castet for useful suggestions on the manuscript. C.L. is grateful for the funding provided by the Human Frontier Science Program (fellowship LT000741/2019-C). Our work in the Integrative Genomics of Ageing Group was further supported by grants from the Wellcome Trust (208375/Z/17/Z), LongeCity and the Biotechnology and Biological Sciences Research Council (BB/R014949/1) to J.P.d.M. R.T. and E.U. were supported by the National Authority for Scientific Research and Innovation and by the Ministry of European Funds, Romania, through the Competitiveness Operational Program 2014–2020, POC-A.1-A.1.1.4-E-2015 (grant no.: 40/02.09.2016, ID: P_37_778, to R.T.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Access to Document

10.1038/s43587-023-00514-xLicence: Creative Commons: Attribution (CC BY)

LaggerC2023scDiffComFinal published version, 5.67 MBLicence: Creative Commons: Attribution (CC BY)

GeneFriends: A gene and transcript co-expression resource
Lourenco Rocha De Magalhaes, J. P.
THE WELLCOME TRUST
1/09/22 → 28/08/24
Project: Research

Cite this

@article{27187e1d55f34365879299744a15cc38,

title = "scDiffCom: a tool for differential analysis of cell–cell interactions provides a mouse atlas of aging changes in intercellular communication",

abstract = "Dysregulation of intercellular communication is a hallmark of aging. To better quantify and explore changes in intercellular communication, we present scDiffCom and scAgeCom. scDiffCom is an R package, relying on approximately 5,000 curated ligand–receptor interactions, that performs differential intercellular communication analysis between two conditions from single-cell transcriptomics data. Built upon scDiffCom, scAgeCom is an atlas of age-related cell–cell communication changes covering 23 mouse tissues from 58 single-cell RNA sequencing datasets from Tabula Muris Senis and the Calico murine aging cell atlas. It offers a comprehensive resource of tissue-specific and sex-specific aging dysregulations and highlights age-related intercellular communication changes widespread across the whole body, such as the upregulation of immune system processes and inflammation, the downregulation of developmental processes, angiogenesis and extracellular matrix organization and the deregulation of lipid metabolism. Our analysis emphasizes the relevance of the specific ligands, receptors and cell types regulating these processes. The atlas is available online (https://scagecom.org).",

author = "Cyril Lagger and Eugen Ursu and Ana{\"i}s Equey and Avelar, {Roberto A.} and Pisco, {Angela Oliveira} and Robi Tacutu and {de Magalh{\~a}es}, {Jo{\~a}o Pedro}",

note = "Acknowledgements We thank J. Kimmel for helpful information regarding the Calico murine cell atlas, K. Tsuyuzaki for general discussion regarding intercellular communication at the early stage of this project, Z. Abidi for support to deploy the Shiny app and U. Castet for useful suggestions on the manuscript. C.L. is grateful for the funding provided by the Human Frontier Science Program (fellowship LT000741/2019-C). Our work in the Integrative Genomics of Ageing Group was further supported by grants from the Wellcome Trust (208375/Z/17/Z), LongeCity and the Biotechnology and Biological Sciences Research Council (BB/R014949/1) to J.P.d.M. R.T. and E.U. were supported by the National Authority for Scientific Research and Innovation and by the Ministry of European Funds, Romania, through the Competitiveness Operational Program 2014–2020, POC-A.1-A.1.1.4-E-2015 (grant no.: 40/02.09.2016, ID: P_37_778, to R.T.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.",

year = "2023",

month = nov,

doi = "10.1038/s43587-023-00514-x",

language = "English",

volume = "3",

pages = "1446--1461",

journal = "Nature Aging",

issn = "2662-8465",

publisher = "Nature Research",

number = "11",

}

TY - JOUR

T1 - scDiffCom

T2 - a tool for differential analysis of cell–cell interactions provides a mouse atlas of aging changes in intercellular communication

AU - Lagger, Cyril

AU - Ursu, Eugen

AU - Equey, Anaïs

AU - Avelar, Roberto A.

AU - Pisco, Angela Oliveira

AU - Tacutu, Robi

AU - de Magalhães, João Pedro

N1 - Acknowledgements We thank J. Kimmel for helpful information regarding the Calico murine cell atlas, K. Tsuyuzaki for general discussion regarding intercellular communication at the early stage of this project, Z. Abidi for support to deploy the Shiny app and U. Castet for useful suggestions on the manuscript. C.L. is grateful for the funding provided by the Human Frontier Science Program (fellowship LT000741/2019-C). Our work in the Integrative Genomics of Ageing Group was further supported by grants from the Wellcome Trust (208375/Z/17/Z), LongeCity and the Biotechnology and Biological Sciences Research Council (BB/R014949/1) to J.P.d.M. R.T. and E.U. were supported by the National Authority for Scientific Research and Innovation and by the Ministry of European Funds, Romania, through the Competitiveness Operational Program 2014–2020, POC-A.1-A.1.1.4-E-2015 (grant no.: 40/02.09.2016, ID: P_37_778, to R.T.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

PY - 2023/11

Y1 - 2023/11

N2 - Dysregulation of intercellular communication is a hallmark of aging. To better quantify and explore changes in intercellular communication, we present scDiffCom and scAgeCom. scDiffCom is an R package, relying on approximately 5,000 curated ligand–receptor interactions, that performs differential intercellular communication analysis between two conditions from single-cell transcriptomics data. Built upon scDiffCom, scAgeCom is an atlas of age-related cell–cell communication changes covering 23 mouse tissues from 58 single-cell RNA sequencing datasets from Tabula Muris Senis and the Calico murine aging cell atlas. It offers a comprehensive resource of tissue-specific and sex-specific aging dysregulations and highlights age-related intercellular communication changes widespread across the whole body, such as the upregulation of immune system processes and inflammation, the downregulation of developmental processes, angiogenesis and extracellular matrix organization and the deregulation of lipid metabolism. Our analysis emphasizes the relevance of the specific ligands, receptors and cell types regulating these processes. The atlas is available online (https://scagecom.org).

AB - Dysregulation of intercellular communication is a hallmark of aging. To better quantify and explore changes in intercellular communication, we present scDiffCom and scAgeCom. scDiffCom is an R package, relying on approximately 5,000 curated ligand–receptor interactions, that performs differential intercellular communication analysis between two conditions from single-cell transcriptomics data. Built upon scDiffCom, scAgeCom is an atlas of age-related cell–cell communication changes covering 23 mouse tissues from 58 single-cell RNA sequencing datasets from Tabula Muris Senis and the Calico murine aging cell atlas. It offers a comprehensive resource of tissue-specific and sex-specific aging dysregulations and highlights age-related intercellular communication changes widespread across the whole body, such as the upregulation of immune system processes and inflammation, the downregulation of developmental processes, angiogenesis and extracellular matrix organization and the deregulation of lipid metabolism. Our analysis emphasizes the relevance of the specific ligands, receptors and cell types regulating these processes. The atlas is available online (https://scagecom.org).

U2 - 10.1038/s43587-023-00514-x

DO - 10.1038/s43587-023-00514-x

M3 - Article

SN - 2662-8465

VL - 3

SP - 1446

EP - 1461

JO - Nature Aging

JF - Nature Aging

IS - 11

ER -

scDiffCom: a tool for differential analysis of cell–cell interactions provides a mouse atlas of aging changes in intercellular communication

Abstract

Bibliographical note

Access to Document

Fingerprint

Projects

GeneFriends: A gene and transcript co-expression resource

Cite this