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Immune cells have unique metabolic requirements to support the energetic and biosynthetic burden during their activation. Delineation of the metabolic tuning of immune cells could lead to novel strategies in treating metabolically-demanding processes including autoimmune diseases. Among innate effectors, monocytes have a distinct role in systemic lupus erythematosus (SLE) pathogenesis. We have previously described robust type-I interferon (IFNα) signaling in patients with SLE. IFNα-stimulated monocytes from healthy individuals (IFN-Mo) develop mitochondrial hyperpolarization and increased oxidative stress resembling SLE monocytes (SLE-Mo). Here we sought to delineate the metabolic repercussion of IFNα-mediated signaling that could explain metabolic shifts pertaining to autoimmunity. To this end, we combined transcriptomic data with metabolic flux analysis (Seahorse technology) and Gas Chromatography (GC-MS) in healthy monocytes, IFN-Mo and SLE-Mo. Our preliminary results indicate an increased, glucose-dose dependent glycolytic flux in IFNα-treated healthy monocytes recapitulating the SLE-Mo phenotype. Blockade of hexokinase 2 (HK-2)-dependent glycolysis with the use of 2-DG inhibitor attenuated proinflammatory cytokine secretion and the expression of surface markers characteristic of activated monocytes, supporting the deregulated metabolic profile in SLE autoimmunity. Combination of these data with targeted metabolomics (LC-MS) analyses and the application of pathway-specific inhibitors are implemented in vitro to reverse the inflammatory state of SLE monocytes. Together, our data are expected to yield unique insights into the role of immunometabolism in SLE and the potential use of metabolites as novel therapeutic targets in autoimmunity.

A remarkable, yet poorly explained feature of Systemic Lupus Erythematosus (SLE) is the propensity to flare following a preceding period of disease inactivity. The clinical burden of lupus flares is substantial since they often tend to involve multiple or major organs, and carry a near two-fold increased risk for accrual of irreversible organ damage. The cellular and molecular mechanisms underlying the progression of SLE from inactive to active state remain ill-defined. Application of novel sequencing technologies together with cellular immunology assays, have illustrated the important role of multiple types of both innate and adaptive cells and associated pathways. We have previously described significant differences in the blood transcriptome of SLE patients at active versus inactive disease, and we have also defined genome regions (domains) with co-ordinated expression of genes implicated in the disease. In the present study, we aim to decipher the cellular and molecular basis of SLE exacerbations by utilising novel single-cell sequencing approaches, which allow us to characterise the transcriptional and epigenetic landscapes of thousands of cells in the peripheral blood of patients. The significance of the study lies in the detailed characterisation of the molecular and regulatory program of immune cell subpopulations that underlie progression from inactive to active SLE. Accordingly, our results may be exploited to identify biomarkers for disease monitoring and novel therapeutic targets.

microRNAs are of vital importance for the regulation of the adaptive and innate immune responses, modulating gene expression at the post transcriptional level. Although there is cumulative information regarding the steady state mature microRNA levels and their respective targets, little is known about the effect of the three-dimensional chromatin architecture on the transcriptional regulation of microRNA gene loci. Here, we sought to investigate the effect of subnuclear localization on the transcriptional activation of eight murine microRNA loci in the immune system. Our results show that microRNA genes display a preferential monoallelic gene expression profile accompanied with perinuclear localization irrespectively of their transcription status or differentiation state. The expression profile and perinuclear localization are developmentally conserved while microRNA gene loci localization outside constitutive lamin associated domains is cross-species conserved. Our findings provide support for an active nuclear periphery and its role in chromatin organization of the non-coding genome.

Metabolism is a critical immune regulator under physiologic and pathologic conditions. Culminating evidence has disentangled the contribution of distinct metabolic pathways, namely glucolysis, pentose phosphate, fatty acid oxidation, glutaminolysis, Krebs cycle and oxidative phosphorylation, in modulating innate and adaptive immune cells based on their activation/differentiation state. Metabolic aberrations and changes in the intracellular levels of specific metabolites are linked to the inflammatory phenotype of immune cells implicated in autoimmune disorders such as systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis and diabetes. Notably, targeting metabolism such as the mTOR by rapamycin, hexokinase by 2-deoxy-D-glucose, AMP-activated protein kinase by metformin, may be used to ameliorate autoimmune inflammation. Accordingly, research in immunometabolism is expected to offer novel opportunities for monitoring and treating immune-mediated diseases.

It is becoming increasingly appreciated that the non-coding genome may have a great impact on the regulation of chromatin structure and gene expression. The innate immune response can be mediated upon lipopolysaccharide stimulation of macrophages which leads to immediate transcriptional activation of early responsive genes including tumor necrosis factor alpha (Tnfα). The functional role of non-coding RNAs, such as lncRNAs and microRNAs, on the transcriptional activation of proinflammatory genes and the subsequent regulation of the innate immune response is still lacking mechanistic insights. In this study we wanted to unravel the functional role of the lncRNA SeT, which is encoded from the murine Tnfα gene locus, and miR-155 on the transcriptional regulation of the Tnfα gene. We utilized genetically modified mice harboring either a deletion of the SeT promoter elements or the mature miR-155 and studied the response of macrophages to lipopolysaccharide (LPS) stimulation. We found that decreased expression of the lncRNA SeT in murine primary macrophages resulted in increased mortality of mice challenged with LPS, which was corroborated by increased Tnfα steady state mRNA levels and a higher frequency of biallelically expressing macrophages. On the contrary, miR-155 deletion resulted in reduced Tnfα mRNA levels supported by a lower frequency of biallelically expressing macrophages upon stimulation with LPS. In both cases, in the absence of either lncRNA SeT or miR-155 we observed a deregulation of the Tnfα allele homologous pairing, previously shown to regulate the switch from mono- to bi-allelic gene expression. Although lncRNA SeT was not found to be a direct target of miR-155 its stability was increased upon miR-155 deletion. This study suggests a role of the non-coding genome in mediating Tnfα mRNA dosage control based on the regulation of homologous pairing of gene alleles and their subsequent biallelic expression.