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scAgeCom: a murine atlas of age-related changes in intercellular communication inferred with the package scDiffCom

Cyril Lagger, Eugen Ursu, Anaïs Equey, Roberto A. Avelar, Angela O. Pisco, Robi Tacutu, View ORCID ProfileJoão Pedro de Magalhães
doi: https://doi.org/10.1101/2021.08.13.456238
Cyril Lagger
1Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
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Eugen Ursu
2Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
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Anaïs Equey
3Department of Medicine, Karolinska Institutet, Stockholm, Sweden
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Roberto A. Avelar
1Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
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Angela O. Pisco
4Chan Zuckerberg Biohub, San Francisco, California, USA
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Robi Tacutu
2Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
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João Pedro de Magalhães
1Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
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  • ORCID record for João Pedro de Magalhães
  • For correspondence: jp@senescence.info
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Abstract

Dysregulation of intercellular communication is a well-established hallmark of aging. To better understand how this process contributes to the aging phenotype, we built scAgeCom, a comprehensive atlas presenting how cell-type to cell-type interactions vary with age in 23 mouse tissues. We first created an R package, scDiffCom, designed to perform differential intercellular communication analysis between two conditions of interest in any mouse or human single-cell RNA-seq dataset. The package relies on its own list of curated ligand-receptor interactions compiled from seven established studies. We applied this tool to single-cell transcriptomics data from the Tabula Muris Senis consortium and the Calico murine aging cell atlas. All the results can be accessed online, using a user-friendly, interactive web application (https://scagecom.org). The most widespread changes we observed include upregulation of immune system processes, inflammation and lipid metabolism, and downregulation of extracellular matrix organization, growth, development and angiogenesis. More specific interpretations are also provided.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://scagecom.org

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted August 15, 2021.
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scAgeCom: a murine atlas of age-related changes in intercellular communication inferred with the package scDiffCom
Cyril Lagger, Eugen Ursu, Anaïs Equey, Roberto A. Avelar, Angela O. Pisco, Robi Tacutu, João Pedro de Magalhães
bioRxiv 2021.08.13.456238; doi: https://doi.org/10.1101/2021.08.13.456238
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scAgeCom: a murine atlas of age-related changes in intercellular communication inferred with the package scDiffCom
Cyril Lagger, Eugen Ursu, Anaïs Equey, Roberto A. Avelar, Angela O. Pisco, Robi Tacutu, João Pedro de Magalhães
bioRxiv 2021.08.13.456238; doi: https://doi.org/10.1101/2021.08.13.456238

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