Mitochondrial 2-hydroxyglutarate dehydrogenases modulate the cellular epitranscriptome

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There is increasing recognition of mitochondria as signaling organelles. An important facet of this “adjunct” mitochondrial function is epigenetic modulation, as exemplified by the generation of acetyl-CoA and S- adenosylmethionine used in the acetylation and methylation, respectively, of DNA and histones. In addition, alpha-ketoglutarate (αKG) and 2-hydroxyglutarate (2-HG), metabolites generated almost exclusively in the mitochondria, are found to modulate the activity of αKG-dependent dioxygenases, including TET DNA hydroxylases and histone demethylase (HDM), thus controlling DNA and histone methylation. Notably, our group discovered that αKG activates and 2-HG inhibits FTO and ALKBH5, RNA demethylases that act on N6- methyladenosine (m6A), a reversible chemical modification of mRNA (the epitranscriptome) that influences gene expression. Similar to other epigenetic marks, RNA methylation is dynamically controlled and m6A abundance influence various biological functions, while its misregulation associates with human diseases. Considering that αKG/2-HG are generated mainly by intermediary mitochondrial metabolism, and that the activity of RNA demethylases are modulated by these metabolites, it is reasonable to speculate that mitochondria play an important role in the control of RNA methylation homeostasis. In particular, we postulate that the mitochondrial enzymes D-2- and L-2-hydroxyglutarate dehydrogenase (D2HGDH and L2HGDH), which catalyze the interconversion of 2-HG to αKG, are integral to the interplay between mitochondrial metabolism and the control of RNA methylation. This hypothesis is supported by our earlier discovery that loss of function D2HGDH mutations leads to decreased activity of the αKG-dependent TET and HDM enzymes. We recently expanded on this concept by identifying upstream signals that regulate D2HGDH and L2HGDH expression/activity. Using ChIP assays, inducible cell lines and a transgenic mouse model we discovered that MYC transcriptionally activates D2HGDH and L2HGDH, and that in a D2/L2HGDH/αKG-dependent manner it induces FTO and ALKBH5 function leading to RNA demethylation in vitro and in vivo. Remarkably, we found that the MYC-D2/L2HGDH-αKG axis also promotes the nuclear accumulation of FTO and ALKBH5, in association with enhanced O-GlcNAcylation, a post-translational modification executed by another mitochondrial enzyme, O-GlcNAc transferase (OGT). Here, using multiple genetic models in vitro and in vivo, we will test the hypothesis that a novel mitochondrial signaling axis, which includes MYC at the proximal point, D2/L2HGDH and OGT at the center, and, distally, FTO/ALKBH5 activity, controls the cellular epitranscriptome. Our specific aims are: 1) characterize the contribution of D2HGDH/L2HGDH and of intermediate metabolites to the control of m6A levels, 2) determine the mechanistic basis for the increased O-GlcNAcylation mediated by the MYC-D2/L2HGDH-αKG axis and its role in promoting RNA demethylation, 3) define a mitochondrial metabolism-dependent methylRNA/gene expression signature in human cells.