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Journal Articles Cell Reports Year : 2023

Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes

Anastasiia Gainullina
Denis Mogilenko
  • Function : Author
Li-Hao Huang
  • Function : Author
Helena Todorov
  • Function : Author
Vipin Narang
  • Function : Author
Ki-Wook Kim
  • Function : Author
Lim Sheau Yng
  • Function : Author
Andrew Kent
  • Function : Author
Baosen Jia
  • Function : Author
Kumba Seddu
  • Function : Author
Karen Krchma
  • Function : Author
Jun Wu
  • Function : Author
Elena Tomasello
  • Function : Author
Regine Dress
  • Function : Author
Peter See
  • Function : Author
Charlotte Scott
  • Function : Author
Sophie Gibbings
  • Function : Author
Geetika Bajpai
  • Function : Author
Jigar Desai
Barbara Maier
  • Function : Author
Sébastien This
  • Function : Author
Peter Wang
  • Function : Author
Stephanie Vargas Aguilar
  • Function : Author
Lucie Poupel
  • Function : Author
Sébastien Dussaud
  • Function : Author
Tyng-An Zhou
  • Function : Author
Veronique Angeli
  • Function : Author
J. Magarian Blander
  • Function : Author
Kyunghee Choi
Marc Dalod
  • Function : Author
Ivan Dzhagalov
  • Function : Author
Claudia Jakubzick
  • Function : Author
Kory Lavine
  • Function : Author
Michail Lionakis
  • Function : Author
Helena Paidassi
Michael Sieweke
  • Function : Author
Florent Ginhoux
  • Function : Author
Martin Guilliams
  • Function : Author
Christophe Benoist
  • Function : Author
Miriam Merad
  • Function : Author
Gwendalyn Randolph
  • Function : Author
Alexey Sergushichev
Maxim Artyomov

Abstract

The diversity of mononuclear phagocyte (MNP) subpopulations across tissues is one of the key physiologicalcharacteristics of the immune system. Here, we focus on understanding the metabolic variability of MNPsthrough metabolic network analysis applied to three large-scale transcriptional datasets: we introduce (1)an ImmGen MNP open-source dataset of 337 samples across 26 tissues; (2) a myeloid subset of ImmGenPhase I dataset (202 MNP samples); and (3) a myeloid mouse single-cell RNA sequencing (scRNA-seq) data-set (51,364 cells) assembled based on Tabula Muris Senis. To analyze such large-scale datasets, we developa network-based computational approach, genes and metabolites (GAM) clustering, for unbiased identifica-tion of the key metabolic subnetworks based on transcriptional profiles. We define 9 metabolic subnetworksthat encapsulate the metabolic differences within MNP from 38 different tissues. Obtained modules revealthat cholesterol synthesis appears particularly active within the migratory dendritic cells, while glutathionesynthesis is essential for cysteinyl leukotriene production by peritoneal and lung macrophages.
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hal-04040831 , version 1 (22-05-2023)

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Anastasiia Gainullina, Denis Mogilenko, Li-Hao Huang, Helena Todorov, Vipin Narang, et al.. Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes. Cell Reports, 2023, 42 (2), pp.112046. ⟨10.1016/j.celrep.2023.112046⟩. ⟨hal-04040831⟩
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