Biology subjects

Haigis, M.

Publications and source records attributed to Haigis, M..

4 recordsLinked to original sources

bioRxiv2020

In Silico Modeling of Metabolic State in Single Th17 Cells Reveals Novel Regulators of Inflammation and Autoimmunity

Cellular metabolism, a key regulator of immune responses, is difficult to study with current technologies in individual cells Here, we present Compass, an algorithm to characterize the metabolic state of cells based on single-cell RNA-Seq and flux balance analysis. We applied Compass to associate metabolic states with functional variability (pathogenic potential) amongst Th17 cells and recovered a metabolic switch between glycolysis and fatty acid oxidation, akin to known differences between Th17 and Treg cells, as well as novel targets in amino-acid pathways, which we tested through targeted metabolic assays. Compass further predicted a particular glycolytic reaction (phosphoglycerate mutase -- PGAM) that promotes an anti-inflammatory Th17 phenotype, contrary to the common understanding of glycolysis as pro-inflammatory. We demonstrate that PGAM inhibition leads non-pathogenic Th17 cells to adopt a pro-inflammatory transcriptome and induce autoimmunity in vivo. Compass is broadly applicable for characterizing metabolic states of cells and relating metabolic heterogeneity to other cellular phenotypes.

genomics↗

bioRxiv2020

Metabolic and Epigenomic Regulation of Th17/Treg Balance by the Polyamine Pathway

Cellular metabolism can orchestrate immune cell function. We previously demonstrated that lipid biosynthesis represents one such gatekeeper to Th17 cell functional state. Utilizing Compass, a transcriptome-based algorithm for prediction of metabolic flux, we constructed a comprehensive metabolic circuitry for Th17 cell function and identified the polyamine pathway as a candidate metabolic node, the flux of which regulates the inflammatory function of T cells. Testing this prediction, we found that expression and activities of enzymes of the polyamine pathway were enhanced in pathogenic Th17 cells and suppressed in regulatory T cells. Perturbation of the polyamine pathway in Th17 cells suppressed canonical Th17 cell cytokines and promoted the expression of Foxp3, accompanied by dramatic shift in transcriptome and epigenome, transitioning Th17 cells into a Treg-like state. Genetic and chemical perturbation of the polyamine pathway resulted in attenuation of tissue inflammation in an autoimmune disease model of central nervous system, with changes in T cell effector phenotype.

immunology↗

bioRxiv2019

The human mitochondrial 12S rRNA m4C methyltransferase METTL15 is required for proper mitochondrial function

Mitochondrial DNA (mtDNA) gene expression is coordinately regulated pre- and post-transcriptionally, and its perturbation can lead to human pathologies. Mitochondrial ribosomal RNAs (mt-rRNAs) undergo a series of nucleotide modifications following release from polycistronic mitochondrial RNA (mtRNA) precursors, which is essential for mitochondrial ribosomal biogenesis. Cytosine N4 methylation (m4C) at position 839 of the 12S small subunit (SSU) mt-rRNA was identified decades ago, however, its biogenesis and function have not been elucidated in details. Here we demonstrate that human Methyltransferase Like 15 (METTL15) is responsible for 12S mt-rRNA methylation at C839 (m4C839) both in vivo and in vitro. We tracked the evolutionary history of RNA m4C methyltransferases and revealed the difference in substrates preference between METTL15 and its bacterial ortholog rsmH. Additionally, unlike the very modest impact on ribosome upon loss of m4C methylation in bacterial SSU rRNA, we found that depletion of METTL15 specifically causes severe defects in mitochondrial ribosome assembly, which leads to an impaired translation of mitochondrial protein-coding genes and a decreased mitochondrial respiration capacity. Our findings point to a co-evolution of methylatransferase specificities and modification patterns in rRNA with differential impact on prokaryotic ribosome versus eukaryotic mitochondrial ribosome.

molecular biology↗

bioRxiv2019

The UTX Tumor Suppressor Directly Senses Oxygen to Control Chromatin and Cell Fate

Mammalian cells express multiple 2-oxoglutarate (OG)-dependent dioxygenases, including many chromatin regulators. The oxygen affinities, and hence oxygen sensing capabilities, of the 2-oxoglutarate (OG)-dependent dioxygenases reported to date vary widely. Hypoxia can affect chromatin, but whether this reflects a direct effect on chromatin-modifying dioxygenases, or indirect effects caused by the hypoxic-induction of the HIF transcription factor or the endogenous 2-OG competitor 2-hydroxyglutarate (2-HG), is unclear. Here we report that hypoxia induces a HIF- and 2-HG-independent histone modification signature consistent with KDM inactivation. We also show that the H3K27 histone demethylase KDM6A (also called UTX), but not its paralog KDM6B, is oxygen-sensitive. KDM6A loss, like hypoxia, prevented H3K27me3 erasure and blocked differentiation. Conversely, restoring H3K27me3 homeostasis in hypoxic cells reversed these effects. Therefore, oxygen directly affects chromatin regulators to control cell fate.\n\nOne Sentence SummaryKDM6A demethylase activity is diminished under hypoxic conditions and causes changes in gene expression programs that govern cell fate.

biochemistry↗