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


ABSTRACT: 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.

SUBMITTER: Gainullina A 

PROVIDER: S-EPMC10372199 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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

Gainullina Anastasiia A   Mogilenko Denis A DA   Huang Li-Hao LH   Todorov Helena H   Narang Vipin V   Kim Ki-Wook KW   Yng Lim Sheau LS   Kent Andrew A   Jia Baosen B   Seddu Kumba K   Krchma Karen K   Wu Jun J   Crozat Karine K   Tomasello Elena E   Dress Regine R   See Peter P   Scott Charlotte C   Gibbings Sophie S   Bajpai Geetika G   Desai Jigar V JV   Maier Barbara B   This Sébastien S   Wang Peter P   Aguilar Stephanie Vargas SV   Poupel Lucie L   Dussaud Sébastien S   Zhou Tyng-An TA   Angeli Veronique V   Blander J Magarian JM   Choi Kyunghee K   Dalod Marc M   Dzhagalov Ivan I   Gautier Emmanuel L EL   Jakubzick Claudia C   Lavine Kory K   Lionakis Michail S MS   Paidassi Helena H   Sieweke Michael H MH   Ginhoux Florent F   Guilliams Martin M   Benoist Christophe C   Merad Miriam M   Randolph Gwendalyn J GJ   Sergushichev Alexey A   Artyomov Maxim N MN  

Cell reports 20230127 2


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 sequenci  ...[more]

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