Inflammation is a normal reaction of the immune system in response to infections or tissue damage. Inflammation is a component of the innate immune response that is elicited by a broad range of triggers, comprises a broad range of mechanisms and signaling pathways, all of which converging towards the production of soluble mediators of inflammation (cytokines and chemokines). Beneficial inflammatory responses are generally initiated locally, at the site of infection or injury, and constitute a central signaling step towards the activation of adaptive immune responses. Once the infection cleared or the wound healed, the inflammatory response is resolved, in order to limit the activation of the immune system over time.
When inflammatory responses are unresolved and persist in time, they are pervasive and may lead to systemic damage, affecting tissues heterogeneously. As a consequence, chronic inflammation is associated with a vast range etiologically distinct human pathologies, including cancer, auto-inflammatory and auto-immune disorders, but also metabolic diseases or neurodegenerative disorders and other non-communicable diseases. As such, chronic inflammation associated human pathologies weigh heavily on both socio-economic and healthcare systems, calling for innovative therapeutic routes.
The goal of the Molecular Basis of Inflammation laboratory is to provide a comprehensive view of the pathways governing the activation, maintenance and resolution of inflammatory responses. Furthermore, we aim to uncover the moelcualar mechanisms governing tissue-specific inflammatory responses. Our current research interests revolve around the study of inflammatory responses triggered by pathological nucleic acid species, that include cytosolic dsDNAs, ssDNAs and RNA:DNA hybrids. These moieties can arise in the cytosol following genotoxic or mitochondrial stress or following pathogen infection. Although they are all known to trigger inflammatory processes, it is also well established that they promote cell type-specific signatures, that may in turn promote differential tissue responses. To decipher how deregulation of inflammatory processes promote pathologies, we combine a broad array of approaches, ranging from mechanistic studies in vitro, to phenotyping in vivo. Combining several scales of study should allow charting the impact of pathological nucleic acids on cellular pathways and assessment of their impact at the whole organism level, potentially identifying key signalling nodes that can be acted upon to hinder pathological inflammation. In a nutshell:
• At the molecular level: we identify and characterize new pathways involved in triggering inflammatory pathologies,
• At the cellular level: we characterize how these pathways are regulated depending on cellular identity,
• At the tissue level: we study how cellular heterogeneity within tissues dictates the outcome of inflammatory response and impacts homeostasis
• At the organism level: we study inflammatory responses and the consequences of their pathological activation on integrated in vivo models.
Current interests of the Molecular Basis of Inflammation Team revolve around the theme of nucleic acid immunity. Pathological nucleic acids susceptible of triggering uninflammatory responses include cytosolic dsDNA, ssDNAs and DNA:RNA hybrids. Those may arise in the cytosol of cells following pathogen infection, genotoxic or mitochondrial stress and/or aberrant endogenous retroelement activity. Several detection routes for cytosolic nucleic acid species have been described in the past decade, although the molecular mechanisms underlying their cell type-specific activation and coordination remain poorly described. Additionally, for each given nucleic acid trigger, the ensuing inflammatory response and the associated physiopathological consequences, are governed by parameters that remain to be uncovered.
The major team’s projects aim to describe the molecular mechanisms involved in the activation of nucleic acid immunity, study their evolutionary conservation, and unravel how they feed pathological inflammation and tissue-specific alterations.
Projects developed by the team include:
• Detection and regulation of cytosolic DNA:RNA hybrids in tumorigenesis
• Novel cytosolic nucleic acids detection routes
• The crosstalk between inflammatory and metabolic responses
• Chromatin control of inflammatory responses
• ssDNA detection and regulation in chronic and acute inflammatory responses
• Cyclic dinucleotide in the control of inflammatory and physiological responses
• Harnessing co-regulators of nucleic acid detection pathways for boosting antitumoral responses
1.Detection and regulation of cytosolic DNA:RNA hybrids in tumorigenesis
We have shown that the reverse transcription (RT) activity associated with endogenous retroelements generates immunogenic cytosolic nucleic acids. These nucleic acids are recognized via the cGAS-STING pathway, central to the detection of cytosolic nucleic acids. Activation of this signaling pathway feeds chronic inflammation associated with the Fanconi Anemia cancer predisposition syndrome (Brégnard et al. EBioMed, 2016).
We next focused on identifying pathways regulating RT-generated immunogenic nucleic acids - in particular DNA:RNA hybrids. We have identified the Lysyl-tRNA synthetase (LysRS), a key player in protein translation of, as involved in the regulation of inflammation associated with the cytosolic DNA:RNA hybrids (Guerra et al. Science Adv, 2020).
Currently, we are studying the impact of LysRS on tumorigenesis, notably in the context of pancreatic adenocarcinoma (PDAC).
2.Novel cytosolic nucleic acids detection routes
Genotoxic stress is a complex phenomenon engaging numerous molecular interactions and post-translational modifications, induced by genetic instability and DNA replication stress. Genotoxic stress response proteins are direct regulators of the innate immune response via (i) their ability to recognize non-canonical nucleic acid structures, including endogenous DNAs present in the cytosol, and (ii) regulation of DNA repair. Our recent work has established that the DNA-PK holoenzyme, involved in the repair of double strand breaks by non-homologous end-joining, plays a major role in boosting the activation of the canonical cGAS-STING pathway, which is involved in the detection of cytosolic dsDNAs (Taffoni et al 2022). Using a range of in vivo and in vitro approaches, we showed that DNA-PK and cGAS cooperate to drive cancer-associated inflammatory responses, ultimately regulating the breadth of anti-tumor immune responses.
Because several tumors present with mutations in DNA-PK or cGAS, we now wish to investigate whether the cooperation of these two pathways could be harnessed to boost anti-tumoral responses, or to the contrary prevent deleterious, cancer-promoting inflammatory responses.
3.The crosstalk between inflammatory and metabolic responses
Chronic inflammation can be fueled by high fat diets that promote concerted alterations of inflammatory and metabolic pathways. We recently identified the STING protein, central to the production of type I Interferons in the presence of cytosolic nucleic acids, as a central regulator of polyunsaturated fatty acid (PUFA) metabolism (Vila et al. Cell Metabolism 2022). We are exploring the communication between these inflammatory and metabolic pathways, at the cellular, tissue and whole-body levels, to reveal their impact on the maintenance of homeostasis and in chronic inflammatory pathologies.
To this aim:
(i) We interrogate the role of potential imbalances in PUFA desaturation in pathologies presenting with chronic STING-dependent inflammation
(ii) We investigate whether metabolic regulation is the primordial function of STING.
(iii) We question how type I IFN responses are achieved in metabolic cells.
4.Chromatin control of inflammatory responses
Although most immunogenic nucleic acids are detected in the cytosol, the proteins mediating this recognition are, to a large extent, nuclear and associated with the chromatin when inactive. This for example the case of the cGAS protein, central to the detection of nucleic acids in the cytosol. Our current work shows that the cytosolic presence of immunogenic nucleic acids leads to the mobilization of numerous chromatin proteins, beyond already described receptors. We study the consequences of cytosolic mobilization of nuclear proteins and their impact on the regulation of inflammatory responses.
5.ssDNA detection and regulation in chronic and acute inflammatory responses
Physiologically, ssDNAs occur in cells upon replication stress and resolution of DNA damage. In cancer cells and certain immunopathologies, ssDNAs seem to accumulate and trigger inflammatory signaling. In addition, ssDNA can be pathogen-associated molecular patterns (PAMP) that arise during viral infection. In contrast to double-stranded DNA (dsDNA), the mechanisms of and requirements for ssDNA sensing are poorly defined. We wish to increase the understanding of ssDNA sensing and to better define the sensors, pathways and modulators involved.
6.Cyclic dinucleotide in the control of inflammatory and physiological responses
The cyclic AMP-GMP (cGAMP) second messenger is synthesized by the cGAMP synthase (cGAS) upon detection of cytosolic nucleic acids, including dsDNAs. cGAMP is the major activator of the adaptor protein STING and therefore plays a crucial role in the activation of type I Interferon and inflammatory responses. The production of cGAMP is a tightly regulated process for which, for example, we have shown that the DNA-PK DNA repair complex is necessary (Taffoni et al, EMBOJ 2022). Beyond this function of cGAMP in STING activation, there is growing evidence the implication of cyclic dinucleotides in numerous cellular functions, such as the regulation of polyunsaturated fatty acid metabolism (Vila et al Cell Metabolism 2022). In addition, dinucleotides of bacterial origin can elicit inflammatory responses in host cells upon infection. Altogether these evidences suggest that cyclic dinucleotides such as cGAMP are major players in the regulation of homeostasis.
We currently study the molecular mechanisms involved in the regulation of the production, propagation and degradation of cyclic dinucleotides.
7.Harnessing co-regulators of nucleic acid detection pathways for boosting antitumoral responses
The STING adaptor protein is a target of growing interest for the reactivation of anti-tumor immunity. We have identified several STING partners and screened for inhibitors and co-activators, amongst which druggable target have been validated. We wish to validate the efficiency of identified therapeutic combinations for their ability to boost anti-tumour responses in preclinical models of breast cancer, melanoma and pancreatic adenocarcinoma.