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A novel approach to single cell analysis to reveal intrinsic differences in immune marker expression in unstimulated macrophages from BALB/c and C57BL/6 mouse strains

View ORCID ProfileJeremie Breda, Arka Banerjee, Rajesh Jayachandran, View ORCID ProfileJean Pieters, View ORCID ProfileMihaela Zavolan
doi: https://doi.org/10.1101/2022.05.29.493868
Jeremie Breda
1Biozentrum, University of Basel
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Arka Banerjee
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Rajesh Jayachandran
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Jean Pieters
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Mihaela Zavolan
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  • For correspondence: mihaela.zavolan@unibas.ch
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Abstract

Macrophages are cells of the innate immune system that provide the first line of defense against pathogens. Their functional and morphological heterogeneity is well known, though the origin of this heterogeneity is still debated. Furthermore, while mouse strains differ in the type of immune responses that they mount to individual pathogens, the range of gene expression variation among their macrophages in the absence of a specific stimulus is not known. By applying single cell RNA sequencing we here reveal the gene expression variation in pre-stimulation macrophage populations from specific pathogen-free BALB/c and C57BL/6 mice, two mouse strains that give prototypical Th2 and Th1-biased immune responses, directed towards extracellular or intracellular pathogens, respectively. We show that intrinsic differences between the macrophages of these two strains are detectable before any specific stimulation and we place the gene expression profile of these cells within the range of variation that is measured upon in vitro stimulation with pro-inflammatory lipopolysaccharide (LPS) and interferon γ (IFN), or anti-inflammatory IL-4. We find that C57BL/6 mice show stronger evidence of macrophage polarization than BALB/c mice, which could explain their resistance to pathogens such as Leishmania. Our computational methods for analyzing single cell RNA sequencing data, controlling for common sources of stochastic variation, can be more generally adopted to uncover biological variation between cell populations.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-11814

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-NC 4.0 International license.
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Posted May 29, 2022.
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A novel approach to single cell analysis to reveal intrinsic differences in immune marker expression in unstimulated macrophages from BALB/c and C57BL/6 mouse strains
Jeremie Breda, Arka Banerjee, Rajesh Jayachandran, Jean Pieters, Mihaela Zavolan
bioRxiv 2022.05.29.493868; doi: https://doi.org/10.1101/2022.05.29.493868
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A novel approach to single cell analysis to reveal intrinsic differences in immune marker expression in unstimulated macrophages from BALB/c and C57BL/6 mouse strains
Jeremie Breda, Arka Banerjee, Rajesh Jayachandran, Jean Pieters, Mihaela Zavolan
bioRxiv 2022.05.29.493868; doi: https://doi.org/10.1101/2022.05.29.493868

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