Variant Enrichment Analysis to Explore Pathways Functionality in Complex Autoinflammatory Skin Disorders through Whole Exome Sequencing Analysis

Abstract

The challenge of unravelling the molecular basis of multifactorial disorders nowadays cannot rely just on association studies searching for potential causative variants shared by groups of patients and not present in healthy individuals; indeed, association studies have as a main limitation the lack of information on the interactions between the disease-causing variants. Thus, new genomic analysis tools focusing on disrupted pathways rather than associated gene variants are required to better understand the complexity of a disease. Therefore, we developed the Variant Enrichment Analysis (VEA) workflow, a tool applicable for whole exome sequencing data, able to find differences between the numbers of genetic variants in a given pathway in comparison with a reference dataset. In this study, we applied VEA to discover novel pathways altered in patients with complex autoinflammatory skin disorders, namely PASH (n = 9), 3 of whom are overlapping with SAPHO) and PAPASH (n = 3). With this approach we have been able to identify pathways related to neutrophil and endothelial cells homeostasis/activations, as disrupted in our patients. We hypothesized that unregulated neutrophil transendothelial migration could elicit increased neutrophil infiltration and tissue damage. Based on our findings, VEA, in our experimental dataset, allowed us to predict novel pathways impaired in subjects with autoinflammatory skin disorders.

Keywords: OMICs; PAPASH; PASH; SAPHO; hidradenitis suppurativa; whole exome sequencing.

Figure 1

Exploiting Variant Enrichment Analysis (VEA) results on the basis of molecular pathogenesis of PAPASH, PASH, and PASH/SAPHO. The figure represents the unregulated mechanisms of leukocyte transendothelial migration (TEM). VEA revealed that the pathways involved in neutrophil infiltration and activation are altered in PAPASH, PASH, and PASH/SAPHO patients.

Figure 2

Variant Enrichment Analysis. After sequencing all patients, we extracted common variants (CommonVar) from each studied group, PAPASH, PASH, and PASH/SAPHO. Then, we recovered all genes carrying CommonVar and performed a VEA. Finally, a Venn diagram (Figure S7: https://davinci.biohub.solutions/pash/data/data1/vea/#figure-s7-1) was used to set apart the exclusive enriched pathway (eEP) for each group.