Interplay of cGAS with chromatin

Recognition of DNA is an evolutionarily highly conserved mechanism of immunity. In mammals, the cGAS-STING pathway plays a central role in coupling DNA sensing to the execution of innate immune mechanisms, both in contexts of infection as well as in noninfectious settings of cellular stress and injury. The indiscriminate ability of double-stranded DNA (dsDNA) to activate cGAS challenges our understanding on how engagement of this pathway is prevented on genomic selfDNA under homeostatic conditions. Here, we review recent discoveries on the regulation of cGAS on chromatin and we discuss implications for cGASdependent inflammatory phenotypes. We close by highlighting emerging developments on the role of nuclear cGAS and related open questions for future research.

Mitochondrial stress signalling and its impacts on physiology

Adrienne Joëlle Laurence Mottis

Mitochondria are responsible for respiration and energy harvesting across the eukaryotic kingdom. They also take part in other cellular processes like intermediary metabolism. As a result, mitochondrial function directly impacts organismal features such as metabolic homeostasis, fitness and aging. Moreover, mitochondrial dysfunction is involved in numerous pathologies, such as neurodegenerative disease, obesity, diabetes and cancer. Several surveillance pathways constantly monitor mitochondria to ensure their proper function. Among the pathways triggered by stress, the mitochondrial unfolded protein response (UPRmt) aims to restore proteostasis within this organelle. A better understanding of the cellular response to mitochondrial stress would expand our fundamental knowledge of physiological and pathological processes involving mitochondria, leading to potential new therapeutics that target these organelles. This thesis focuses on the mechanistic and physiological characterization of the mitochondrial stress response in several organisms. I used the model organism Caenorhabtis elegans to screen for novel players of the UPRmt and found the poly(A)-binding protein pab-1. Using transcript profiling, we showed that the induction of immune genes is a common consequence of several mitochondrial stressors. We demonstrated that pab-1 regulates the activation of the mitochondrial stress response and innate immunity as well. On top, pab-1 is required for the survival of C. elegans upon bacterial infection. Transcriptomic data from multiple human tissues suggest that the human pab-1 orthologue, PABPC1, has a conserved role in immunity. In mice, I explored the regulation of the mitochondrial stress response using a combination of bioinformatics and in vivo experimental approaches. Combined transcriptomic and proteomic analyses in the BXD mouse genetic reference population revealed a tight co-regulation of the orthologues of the UPRmt under normal physiological conditions. As a complementary approach, we triggered mitochondrial stress pharmacologically in newly born and adult mice. Due to the bacterial ancestry of mitochondria, the effects of the antibiotic doxycycline (dox) are also deleterious to this organelle. We found that dox impairs mitochondrial proteostasis and oxygen consumption in adult mice. However, mitochondrial stress induced by post-natal dox treatment did not cause long-lasting effects on mouse physiology and longevity, which is very distinct from observations in C. elegans. The mammalian gut flora plays an important role in organismal homeostasis. The use of an antibiotic causes perturbations of the microbiota, with repercussions on metabolism, inflammation, and the nervous system. To eliminate these confounding effects, we also treated germ-free mice with dox to characterize the response of the mouse to a so-called âpureâ mitochondrial stress. Using multi-omics profiling, we found that organs highly dependent on mitochondria display specific transcriptomic and proteomic signatures following dox treatment. In the kidney, we observed an inhibition of translation and of the mTOR pathway, accompanied by an activation of the ATF4 integrated stress response (ISR). In the liver, dox led to a remodelling of lipid metabolism. In both organs, target transcripts of type I interferon anti-viral response were induced. This thesis demonstrates that the response to mitochondrial stress is a multi-faceted process with conserved aspects acr

EPFL2018

An unexpected role for RNA in the recognition of DNA by the innate immune system

Andrea Ablasser

A central function of our innate immune system is to sense microbial pathogens through the presence of their nucleic acid genomes or their transcriptional or replicative activity. In mammals, a receptor-based system is mainly responsible for the detection of these "non self" nucleic acids. Tremendous progress has been made in the past years in identifying the host constituents that are required for this intricate task. With regard to the sensing of RNA genome based pathogens by our innate immune system, a picture is emerging that includes certain families of the toll-like receptor family (TLR3, TLR7, TLR8) and the RIG-I like helicases (RIG-I, MDA5 and LGP2). Genetic loss of function studies implicate that the absence of these pathways can lead to a complete lack of recognition of certain RNA viruses. At the same time, intracellular DNA can also trigger potent innate immune responses, yet the players in this field are less clear. We and another group have recently identified a role for RNA polymerase III in the conversion of AT-rich DNA into an RNA ligand that is sensed by the RIG-I pathway. In this review article, we will discuss the mechanisms and implications of this novel pathway.

2010

cGAS regulation and activity during genotoxic stress

Sélène-Véronique Glück

The innate immune system has evolved to detect pathogens through germlineencoded pattern recognition receptors (PRRs). Nucleic acid sensors, a defined class of PRRs, bind to microbial and viral nucleic acids and trigger the production of type I interferons and cytokines which mediate the first line of host defense. In the past, these sensors have been primarily studied in the context of infections. Yet, the DNA sensor cyclic GMP-AMP synthase (cGAS) has been recently described to detect not only microbial and viral derived dsDNA but also self-DNA in a sequenceindependent manner. At steady state, the organization of nuclear self-DNA is tightly controlled by a complex network of multiple factors that can become imbalanced during genotoxic stress. Whether and how this stress can be sensed by cGAS in the absence of infection are the main questions of this thesis. Observing the fate of cGAS in space and time in the presence of several genotoxic insults including chemotherapeutics allowed me to gain novel insights into processes regulating the localization and activation of cGAS. In this thesis, I demonstrate that cGAS localizes to both nuclear and cytosolic compartments of the cell. We show that cGAS is inactive in the nucleus due to binding to the acidic patch on H2A-H2B heterodimers. Upon genotoxic stress, cGAS is removed from the nucleus in a manner that is dependent on histones and remains inactive. Moreover, with time cGAS transcription is repressed resulting in a gradual decrease of cGAS levels. On the other hand, cGAS-activating DNA substrates such as cytosolic chromatin fragments accumulate in the cytosol of senescent cells deficient in Lamin B1 when cGAS levels are already decreased. Along with the occurrence of these chromatin fragments, cGAS mediates an inflammatory response dependent on STING (Stimulator of interferon genes), referred to as the senescence-associated secretory phenotype (SASP). Overall, we conclude that acute genotoxic stress does not result in cGAS-STING signaling, whereas the chronic DNA damage response, senescence, activates the cGAS-STING pathway. Moreover, the results presented in this work suggest a new role for cGAS-STING signaling during senescence beyond the recognition of pathogens.