Omics Analyses in Inflammatory Bowel Diseases and Pemphigus Vulgaris

Omics-based analyses have greatly enhanced our understanding of complex human diseases such as inflammatory bowel disease (IBD) and pemphigus vulgaris (PV). Multiple genetic and environmental factors are thought to contribute to the pathogenesis of these complex diseases. In this thesis, omics analysis of the two aforementioned diseases has been performed to investigate: a) the link between the host genome and the gut microbiome in IBD, and b) the metabolomic and lipidomic profiles of patients in PV.

Microbial dysbiosis is a typical feature observed in IBD patients. In addition, the composition of the microbiome and IBD risk have been linked to genetic variation. In this work, a family-based approach was adopted in the specific IBD scenario, using genotype, phenotype and microbiome data from a prospective study in Germany that comprises IBD patients and their families to examine possible associations between host genetics and gut microbiome in IBD. Our analyses resulted in the identification of novel chromosomal regions significantly linked to microbiome traits.

This thesis also examined two other omics fields, namely metabolomics and lipidomics in relation PV. Here, to gain deeper insights into disease aetiology targeted metabolomic and lipidomic analyses were performed. One of the main findings was that the metabolite profiles of patients differed before and after therapy and displayed distinct clustering. Further, the cluster of treated patients shifted towards that of healthy controls relative to their untreated stage.

In summary, the findings of this thesis will a) contribute to enhancing our understanding of how the genome and the microbiome join forces to shape IBD phenotype, b) inspire future large-scale omics-based studies on PV to better understand its pathogenesis, and c) help researchers to apply some of these methods to investigate other complex diseases.