Microbiome-derived asthma and allergy protective substances for prevention

Project Information

APROSUS

Grant agreement ID: 101052876

DOI

10.3030/101052876

EC signature date 26 October 2022

Start date 1 January 2023

End date 31 December 2027

Funded under

• European Research Council (ERC)

Total cost

€ 2 500 000,00

EU contribution

€ 2 500 000,00

Coordinated by

HELMHOLTZ ZENTRUM MUENCHEN DEUTSCHES FORSCHUNGSZENTRUM FUER GESUNDHEIT UND UMWELT GMBH
Germany

Periodic Reporting for period 1 - APROSUS (Microbiome-derived asthma and allergy protective substances for prevention)

Reporting period: 2023-01-01 to 2025-06-30

Summary of the context and overall objectives of the project

Asthma and allergies are the epidemic of the 21st century after a sharp rise in prevalence since the middle of the last century. Around 355 million people worldwide suffer from asthma with significant mortality. Asthma is the most common chronic condition for children – at school age about every 10th pupil is affected in westernized countries. Likewise, allergic illnesses are very prevalent with 30- 50 % of the paediatric population being affected. Currently, there is neither cure nor effective prevention. Current therapies are administered over years and decades and are only able to suppress symptoms but cannot halt the progression of disease. Asthma poses a high individual and societal burden given side effects and enormous costs of medications. However, asthma and allergies are illnesses, which are largely environmentally determined. Exposures to the environmental microbiome greatly determine risk and protection from onset of illness in populations of common genetic make-up. My team and I have found populations highly protected from the illness. Children raised on traditional farms and exposed to cow sheds have an 80% reduction in asthma risk. We also have described relevant taxa of the environmental microbiome in these unique farm studies we pioneered. Very recently, we discovered the microbiome-derived functional agents conferring protection. These epidemiological findings while being scientifically cutting edge, cannot be directly back translated to children’s and their families’ benefit. The interdisciplinary APROSUS Project addresses this research gap. The aims are to characterize and synthetize these functional agents (aim 1), to understand the underlying mechanisms of protection (aim 2) and to validate the findings in the population-based farm studies (aim 3). Thereby we will lay the ground for translation into innovative and effective prevention strategies to stop the asthma and allergy epidemic.

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

I and my team made tremendous progress in understanding the underlying mechanisms by which the farm environment prevents allergic asthma, as observed in many human epidemiological studies. First, my team and I confirmed previous work by showing that intranasal administration of an extract prepared from dust collected in cow sheds (FD) prevents experimental allergic asthma in an ovalbumin (OVA)-induced murine model. Besides the known reduction in the cardinal features of allergic lung inflammation, i.e. airway hyperresponsiveness and airway eosinophilia, we observed that mice exposed to FD showed a strong increase in a specific type of immune cells in their lungs. We then applied single cell RNA sequencing (scRNA-seq) to 61,803 isolated lung cells. In contrast to allergic asthmatic mice these immune cells of FD-exposed mice displayed a significantly altered transcriptome, characterized by decreased expression of genes encoding for proteins which play a major role in the pathophysiology of asthmatic inflammation. Importantly, we confirmed these findings in human monocytes isolated from blood of healthy human donors. Treatment of these cells with FD also resulted in a downregulation of these genes even in the event of an additional inflammatory stimulus. Further mechanistic insights were obtained through multi-omic integration of RNA-seq and ATAC-seq data of FD treated murine immune cells in an ex vivo experiment. My team and I demonstrated that epigenetic silencing of these genes is facilitated by activation of an intracellular transcription factor that has previously been shown to bind bacterial metabolites.
To discover the active principle, we applied various extraction methods and fractionation steps to the farm dust. We analyzed the obtained fractions using NMR, proteomics and lipidomics, among other methods. Our knowledge of the involved receptor guided the next steps and allowed us to identify two relevant metabolites of presumably bacterial origin. We tested these in the same functional in vitro assays and in vivo models reported above and found that they fully replicated the asthma protective effects of the farm dust extracts. Therefore, I will now focus on further characterization of these metabolites.

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 most important achievement is to finally understand the mechanisms and the active principle of asthma protection in the farm environment – a question that has occupied my mind over the last 20 years. I now understand that the environmental exposure is most likely inhaled – since intranasal application has repeatedly been shown to be effective. The active principle are metabolites – we speculate that these are derived from farm-related microbes and plants – which are inhaled and incorporated by specific immune cells. The activation of an intracellular transcription factor leads to the epigenetic silencing of several inflammatory genes and thereby blocks already very upstream asthmatic airway inflammation This intriguing asthma-protective pathway is truly novel, though many components still need to be elucidated in more detail. These mechanistic studies will continue over the rest of the funding period.
The next major achievement is to have discovered the active principle. To our knowledge the naturally occurring identified bacterial metabolites have not previously been described as asthma-protective substances which supports the novelty of our findings and increases the likelihood of translation into drug development. We are preparing a patent application and further collaborate closely with tech transfer within Helmholtz Centre Munich.