Epimetabolites: discovering metabolism beyond building and burning

Abstract

Enzymatic transformations of primary, canonical metabolites generate active biomolecules that regulate important cellular and physiological processes. Roles include regulation of histone demethylation in epigenetics, inflammation in tissue injury, insulin sensitivity, cancer cell invasion, stem cell pluripotency status, inhibition of nitric oxide signaling and others. Such modified compounds, defined as epimetabolites, have functions distinct from classic hormones as well as removed from generic anabolism and catabolism. Epimetabolites are discovered by untargeted metabolomics using liquid- or gas chromatography-high resolution mass spectrometry and structurally annotated by in-silico fragmentation prediction tools. Their specific biological functions are subsequently investigated by targeted metabolomics methods.

Figure 1

The dark matter of metabolism. Known biochemical modules (colored) are interspersed with epimetabolites (black), in addition to exposome compounds (orange) detected by untargeted mass spectrometry such as household chemicals, pharmaceuticals, food components, pesticides.

Figure 2

Origin of novel metabolites. Specific enzymes modify or repair metabolites without creating new pathways.

Figure 3

The different effects of the enantiomeric forms of 2-hydroxyglutarate. Targeted methods must carefully distinguish chiral stereoisomers to unravel the different functions of the oncometabolites (R)- and (S)-2-hydroxyglutarate that impact histone methylations, or may be substrate to proline hydroxylases.

Figure 4

(a) Mass spectral deconvolution in untargeted metabolomics. In both GC–MS and data-independent LC–MS/MS, molecule fragments overlap for co-eluting metabolites. Following all MS/MS events (1–4) in MS-DIAL enables disentangling precursor and fragment ions to obtain pure MS¹ and MS/MS spectra. (b) Predicting elemental composition and MS fragmentation by in-silico tools. From accurate mass, isotope and MS/MS data, elemental formulas are calculated. List of isomer structures are downloaded from databases, MS/MS spectra are predicted, and structures are ranked by highest matching scores.