Novel mechanisms of early defense against virus infections

Project Information

ENVISION

Grant agreement ID: 786602

DOI

10.3030/786602

Project closed

EC signature date 22 June 2018

Start date 1 December 2018

End date 30 November 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 480 338,00

EU contribution

€ 2 480 338,00

Coordinated by

AARHUS UNIVERSITET
Denmark

Periodic Reporting for period 4 - ENVISION (Novel mechanisms of early defense against virus infections)

Reporting period: 2023-06-01 to 2024-11-30

Summary of the context and overall objectives of the project

The innate immune system represents the first line of defense against infections, and in the case of virus infections, it is believed that the type I interferon (IFN) represents the initial response. However, IFN can also be pathological, and it can seem paradoxical, to have a potentially damaging system as the one activated most frequently. Therefore, the purpose of the project is to explore whether there are innate immune mechanisms which work independet of the IFN system to enable host defense reactions that control viruses but have less inflammatory activity. Identification of such novel immune mechanisms would potentially provide a knowledge basis for novel antiviral therapies. The project is divided into four sections, each exploring one aspect of early innate antiviral defense: (i) identification of mechanisms of immune sensing of viruses at epithelial surfaces; (ii) exploration of the importance and mechanisms of action of tonic IFN signaling, (iii) identification of novel restriction factors; (iv) identification of mechanisms initiating IFN expression during viral infection, including the possible interaction with constitutive immune mechanisms.
Key results from the project include discovery of TMEFF1, HIF1a and the autophagy pathway as central and non-redundant mechanisms exerting early control of HSV infections in epithelial cells and neurons. The project also led to deeper understanding of the signaling mechanisms governing the antiviral interferon response, and mechanisms through which viruses evade these host responses. Finally, the project took advantage of muse models and deep phenotyping omics technologies to uncover and characterize protective and pathological processes in the early immune response to HSV infections.
Altogether, ENVISION has lead to important new understanding of the early events that govern antiviral defense. In addition, the project trained a number of early career scientists, some have remained in academia, and some have moved to a job in the pharma sector. The identified novel antiviral mechanisms, molecules, and pathways could lead to new vaccines, therapeutics, and diagnostic tools for a number of different diseases.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The purpose of ENVISION is to explore the existence of novel innate antiviral mechanisms. The project has successfully identified several novel innate immune mechanisms, and we propose that these mechanisms in fact represent what may be a new layer of the immune system.
First, we have demonstrated that Viral replication at epithelial surfaces (HSV2 and SARS-CoV2) activates autophagic responses as well as activation of the stress-sensing Nrf2 and HIF pathways, and that all of these homeostasis-maintaining systems have potent antiviral activity independent of type I IFN. These discoveries represent the first indication that the underlying hypothesis in ENVISION is correct.
Second, we have uncovered novel mechanisms of immune receptor signaling to drive tonic and inducible antiviral IFN responses. For instance, we identified STEEP as a novel molecule governing cGAS-STING signaling through control of the essential ER-to-Golgi trafficking. We also showed that activation of this pathway leads to sorting of immunostimulatory DNA into exosomes, thus inducing paracrine activation of IFN responses.
Third, through genome-wide CRISPR screens, we have identified TMEFF1 as a restriction factors against HSV. TMEFF1 is constitutively expressed and specifically in CNS neurons. We have identified the mechanisms of antiviral action of TMEFF1 and also demonstrated that mice deficient in the restriction factor are highly susceptible to HSV1 infection in the brain. Finally, we have additionally identified HSV encephalitis patients with loss-of-function mutations in TMEFF1. These data provides a strong support of the idea of constitutive immune mechanisms being important for defense against infections.
Finally, we have seeked to identify mechanisms through which epithelial initially are restricted in their production of type I IFN. This part of the project has received least attention, and was the one most affected by the pandemic. However, we managed to clearly demonstrate that the autophagy, Nrf2, and HIF1a pathways all exert negative regulation of the virus-activated cGAS-STING pathway, and that defect in these pathways leads to higher inflammatory gene expression in different culture systems and in vivo.
The project has lead to a large panel of high-impact publications, and we have also communicated the research in layman articles and engaged in science communication with the public. This includes for instance, seminars for high school students and national fora.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The results from the project has led to discovery of a panel of fundamentally novel antiviral effector, and characterization of their regulation and physiological importance. The support the hypothesis that the interferon system is in fact not the first line of antiviral defense, but rather there exists a layer of constitutive and and stress-induced immune mechanisms, which exert the initial defense actions. These mechanisms are specific, and do not induce inflammatory activity.

Images of release of virus DNA (green) into macrophages upon HSV infection.