Multi-OMICs analysis of metabolites, proteins, and histone modifications during human macrophage polarization reveals novel regulatory pathways

ABSTRACT: Macrophages are phagocytic cells in the innate immune system that infiltrate into resident tissues and subsequently polarize into at least two classical phenotypes: ‘pro-inflammatory’ M1 and ‘anti-inflammatory’ M2. Aberrant polarization can aggravate the pathophysiology of infectious diseases such as tuberculosis. Understanding the mechanisms that influence macrophage biology can lead to pharmacological control of polarization. We have developed a novel triomics approach utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS) to perform simultaneous analysis of metabolites, proteins, and histone modifications. Using human blood derived monocytes that were polarized in vitro towards M1- (IFN-γ) and M2- (IL-4) phenotypes, we found that elevated nitric oxide production in M1 macrophages, inhibits oxidative phosphorylation and upregulates glycolytic pathways. Due to the uncoupling of glycolysis and the citric acid cycle/oxidative phosphorylation, an accumulation of acetylated amino acids was measured. Stable isotope tracing of glucose revealed reduced histone acetylation of certain key markers such as H3K27Ac, and others. We propose that the reduction could be due to trapping of excess acetyl-coA into acetylated amino acids. Furthermore, nitric oxide seems to irreversibly bind B12, a necessary co-factor for methionine synthase, inhibiting endogenous methionine synthesis, which could alter the histone epigenetic methylation and therefore downstream gene and protein expression. Triomics also allowed us to identify novel arginine methylation and Nα-acetylation of aspartate, glutamate, and ornithine. We conclude that triomics approach demonstrates a dynamic interplay between cellular metabolism and epigenetics and this axis can ultimately influence macrophage phenotype and gene expression.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood, Macrophage

DISEASE(S): Disease Free

SUBMITTER: Kangling Zhang  

LAB HEAD: Kangling Zhang

PROVIDER: PXD030701 | Pride | 2022-10-13

REPOSITORIES: Pride