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

Authors :
Anastasiia Gainullina
Denis A. Mogilenko
Li-Hao Huang
Helena Todorov
Vipin Narang
Ki-Wook Kim
Lim Sheau Yng
Andrew Kent
Baosen Jia
Kumba Seddu
Karen Krchma
Jun Wu
Karine Crozat
Elena Tomasello
Regine Dress
Peter See
Charlotte Scott
Sophie Gibbings
Geetika Bajpai
Jigar V. Desai
Barbara Maier
Sébastien This
Peter Wang
Stephanie Vargas Aguilar
Lucie Poupel
Sébastien Dussaud
Tyng-An Zhou
Veronique Angeli
J. Magarian Blander
Kyunghee Choi
Marc Dalod
Ivan Dzhagalov
Emmanuel L. Gautier
Claudia Jakubzick
Kory Lavine
Michail S. Lionakis
Helena Paidassi
Michael H. Sieweke
Florent Ginhoux
Martin Guilliams
Christophe Benoist
Miriam Merad
Gwendalyn J. Randolph
Alexey Sergushichev
Maxim N. Artyomov
Source :
Cell Reports, Vol 42, Iss 2, Pp 112046- (2023)
Publication Year :
2023
Publisher :
Elsevier, 2023.

Abstract

Summary: The diversity of mononuclear phagocyte (MNP) subpopulations across tissues is one of the key physiological characteristics of the immune system. Here, we focus on understanding the metabolic variability of MNPs through 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 ImmGen Phase I dataset (202 MNP samples); and (3) a myeloid mouse single-cell RNA sequencing (scRNA-seq) dataset (51,364 cells) assembled based on Tabula Muris Senis. To analyze such large-scale datasets, we develop a network-based computational approach, genes and metabolites (GAM) clustering, for unbiased identification of the key metabolic subnetworks based on transcriptional profiles. We define 9 metabolic subnetworks that encapsulate the metabolic differences within MNP from 38 different tissues. Obtained modules reveal that cholesterol synthesis appears particularly active within the migratory dendritic cells, while glutathione synthesis is essential for cysteinyl leukotriene production by peritoneal and lung macrophages.

Details

Language :
English
ISSN :
22111247
Volume :
42
Issue :
2
Database :
Directory of Open Access Journals
Journal :
Cell Reports
Publication Type :
Academic Journal
Accession number :
edsdoj.8a6a390493e44f40a7321fccee2cd51c
Document Type :
article
Full Text :
https://doi.org/10.1016/j.celrep.2023.112046