Integrated transcriptomic and metabolomic analysis reveals the metabolic programming of GM-CSF- and M-CSF- differentiated mouse macrophages

Front Immunol. 2023 Sep 25:14:1230772. doi: 10.3389/fimmu.2023.1230772. eCollection 2023.

Abstract

Macrophages play a critical role in the inflammatory response and tumor development. Macrophages are primarily divided into pro-inflammatory M1-like and anti-inflammatory M2-like macrophages based on their activation status and functions. In vitro macrophage models could be derived from mouse bone marrow cells stimulated with two types of differentiation factors: GM-CSF (GM-BMDMs) and M-CSF (M-BMDMs), to represent M1- and M2-like macrophages, respectively. Since macrophage differentiation requires coordinated metabolic reprogramming and transcriptional rewiring in order to fulfill their distinct roles, we combined both transcriptome and metabolome analysis, coupled with experimental validation, to gain insight into the metabolic status of GM- and M-BMDMs. The data revealed higher levels of the tricarboxylic acid cycle (TCA cycle), oxidative phosphorylation (OXPHOS), fatty acid oxidation (FAO), and urea and ornithine production from arginine in GM-BMDMs, and a preference for glycolysis, fatty acid storage, bile acid metabolism, and citrulline and nitric oxide (NO) production from arginine in M-BMDMs. Correlation analysis with the proteomic data showed high consistency in the mRNA and protein levels of metabolic genes. Similar results were also obtained when compared to RNA-seq data of human monocyte derived macrophages from the GEO database. Furthermore, canonical macrophage functions such as inflammatory response and phagocytosis were tightly associated with the representative metabolic pathways. In the current study, we identified the core metabolites, metabolic genes, and functional terms of the two distinct mouse macrophage populations. We also distinguished the metabolic influences of the differentiation factors GM-CSF and M-CSF, and wish to provide valuable information for in vitro macrophage studies.

Keywords: GM-CSF; M-CSF; immunometabolism; macrophage differentiation; metabolome; transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Arginine / metabolism
  • Cell Differentiation
  • Fatty Acids / metabolism
  • Granulocyte-Macrophage Colony-Stimulating Factor* / metabolism
  • Humans
  • Macrophage Colony-Stimulating Factor* / metabolism
  • Macrophages / metabolism
  • Mice
  • Proteomics
  • Transcriptome

Substances

  • Granulocyte-Macrophage Colony-Stimulating Factor
  • Macrophage Colony-Stimulating Factor
  • Arginine
  • Fatty Acids

Grants and funding

This work was supported by the Shandong Province Major Scientific and Technological Innovation Project (2020CXGC010503), Shandong Provincial Key Laboratory Platform Project (2021ZDSYS11), National Natural Science Foundation of China Major Project (81991525), and Shaanxi Provincial Key R&D Program (2021SF-110).