Project J3-50114

Whole genome approach to decipher the genetic basis of anaphylaxis

Research project ARIS
Code: J3-50114
Period 1.10.2023 - 30.9.2026
Head: Assist Prof Matija Rijavec, BSc (Microbiol), PhD
ARIS classification: Medicine/Human reproduction     

Organisations:  University Clinic of Respiratory and Allergic Diseases Golnik; University of Ljubljana, Biotechnical Faculty

Description of the project

Anaphylaxis is an acute, life-threatening, systemic allergic reaction most often caused by food, drugs, or insect (Hymenoptera) stings (venom). The incidence of anaphylaxis continues to increase, with an estimated lifetime prevalence of having at least one anaphylactic episode reaching up to 5%. Even though anaphylaxis is a quite common disease, it is not well understood.

Hymenoptera venom-triggered anaphylaxis (HVA) represents the best “model” for severity studies. When stung, similar amounts of venom are always released into the blood, eliminating the effect of different amounts of allergens on the severity of the allergic reaction. Furthermore, the severity of reactions is repeatable since previous severe reactions to stings are associated with subsequent severe reactions.

Despite the well-established role of IgE antibodies in allergy and anaphylaxis, most people with increased specific IgE (sIgE) against a particular allergen do not react to the allergen at all. This is particularly true for HVA (honey bee and wasp), where the vast majority (∼80%) of people with increased sIgE for Hymenoptera venoms have no history of systemic reactions. On the other hand, some people get only a large local reaction (LLR) after contacting an allergen that causes an anaphylactic reaction in others.

The major goal of genetic predisposition studies is identifying the (epi)genetic risk factors, which could determine the accurate risk for an individual patient to develop a disease, in our case, severe anaphylaxis. Importantly, over the last three years, we have demonstrated that the risk for severe anaphylaxis is associated with inherited differences in α-tryptase–encoding copies at TPSAB1 gene, known as hereditary α-tryptasemia (HαT). Furthermore, besides heritable factors, activating somatic missense variant in the KIT gene, p.D816V (c.2447A>T), also influences the development and severity of anaphylaxis. HαT and/or KIT p.D816V are present only in 30-40% of most severe HVA patients, leaving the reaction severity still largely unpredictable.

This project will allow us to identify the (epi)genetic risk factors for anaphylaxis. Identifying variants in a single or more probably in several genes with additive effects and explaining individual's susceptibility to anaphylaxis will allow us to better understand and manage patients with an increased risk for developing anaphylaxis.

The project will comprise several conceptually similar work packages (WPs). WP1 will be oriented towards the discovery of genetic loci/variant(s) associated with anaphylaxis and reaction severity. Genome-wide association studies (GWAS) using low-coverage whole genome sequencing (lcWGS) will be performed on HVA patients (clinical, laboratory data, DNA already available) with different reaction severities and controls. The association analysis will take into account also the HαT and KIT D816V status (data already available). In the second work package, WP2, we will identify epigenetic characteristics of anaphylaxis using epigenome-wide association study (EWAS). Our study will examine DNA methylation using a bisulfite conversion-based approach on the same individuals as in WP1. The selection of genes from WP1 and WP2 will be functionally and biologically characterized. WP3 will be oriented towards comprehensive and integrative analysis of the results from WP1 (GWAS) and WP2 (EWAS) with transcriptional analysis during anaphylaxis (RNA-seq; data already available). WP4 will be a replication study aimed at confirming the relevance of the most strongly associated variant(s)/gene(s) from WP1, WP2 and WP3 on an independent HVA cohort (recruitment ongoing) using targeted NGS-based (methyl) sequencing. In WP5, the biological and functional relevance of the detected variants and genes will be assessed using different approaches. In the last, WP6, we will use the multi-omics approach to integrate all available genomic, epigenomic, transcriptomic and proteomic data into an anaphylaxis atlas.

Project timeline

Project work packages and their realization

As part of the aforementioned project, we conducted a comprehensive systematic review of literature and data related to anaphylaxis with the aim of creating a multi-omics atlas of anaphylaxis. The results of this multi-omics insight into the understanding of anaphylaxis were published in the prestigious scientific journal Clinical Reviews in Allergy & Immunology (impact factor 11.3), underscoring the significance and relevance of our work in the field of anaphylaxis.

Towards a Multi-omics Understanding of Anaphylaxis

Anaphylaxis is an acute, life-threatening hypersensitivity reaction whose variability and unpredictability pose major challenges in both clinical practice and scientific research. Despite numerous studies, a comprehensive understanding of its pathogenesis remains incomplete. However, with the advancement of high-throughput technologies in the omics fields – including genomics, metagenomics, epigenomics, transcriptomics, proteomics, and metabolomics – new opportunities are emerging for an integrated, multi-layered analysis of the disease, known as the multi-omics approach. In our recently published article (Svetina et al., 2025), we reviewed all relevant studies from the past 25 years that have investigated individual omics layers in relation to anaphylaxis. The goal of this review was to synthesize their findings, highlight key molecular mechanisms, and identify potential biomarkers for early detection as well as for safer and more effective treatment of anaphylaxis. The analysis of over one hundred studies revealed that numerous factors contribute to the development and progression of anaphylaxis. Genomic studies have identified gene variants associated with an increased risk of severe systemic reactions. Epigenomic research has uncovered changes in DNA methylation that may influence gene expression and modulate the intensity of immune responses. Transcriptomic analyses demonstrated a rapid activation of genes involved in innate immunity during anaphylaxis, including signaling pathways that lead to the release of inflammatory mediators, which could serve as diagnostic markers. Additionally, findings from metagenomic and metabolomic studies suggest that both the composition of the microbiome and an individual’s metabolic profile may affect susceptibility to anaphylaxis. Collectively, these findings indicate that anaphylaxis results from a complex and interconnected interplay across all omics levels. The study highlights the need for integrated multi-omics research approaches to help identify distinct clinical subtypes (endotypes) of anaphylaxis. Such approaches are crucial for ensuring appropriate treatment and more accurate risk prediction in the future.

Read the full paper here:

https://link.springer.com/article/10.1007/s12016-025-09069-8

Figure: Findings across various omics levels and established associations between single-omics datasets in anaphylaxis.

Markedly Increased Diamine Oxidase During Acute Anaphylaxis Is Associated With an Underlying Clonal Mast Cell Disorder

As part of the aforementioned project, and with the aim of elucidating the molecular background of anaphylaxis, we showed that during acute anaphylaxis, a pronounced increase in diamine oxidase (DAO) is closely associated with clonal mast cell disorders. In this study, we provide the first evidence that a pronounced DAO release during anaphylaxis is restricted to patients with clonal mast cell disorders, providing functional support for the reported association between KIT p.D816V and anaphylaxis severity. In these patients, we detected KIT p.D816V in peripheral blood leukocytes using a highly sensitive qPCR assay and observed that DAO rises markedly during the acute reaction, whereas the increase in patients without detectable KIT p.D816V is typically moderate or substantially smaller. Importantly, individuals with clonal mast cell disorders may remain clinically unrecognized because they can have normal baseline tryptase levels; therefore, additional biomarkers are essential for improved identification of those at risk. Notably, despite very high DAO concentrations, histamine degradation capacity in acute plasma/serum was impaired, suggesting complex mechanisms that are not yet fully understood and regulating histamine metabolism during anaphylaxis.

The results, published in Clinical & Experimental Allergy (impact factor 6.4), indicate that measuring DAO during acute anaphylaxis may help identify individuals at the highest risk of the most severe outcomes, thereby improving risk stratification and clinical management.

The full article is available at the following link:

https://onlinelibrary.wiley.com/doi/10.1111/cea.70227

Figure: Graphical abstract.