From genome-wide association studies to antigenic triggers of PSC

Genome-wide association studies (GWAS) have shown that the genetic architecture of PSC closely resembles autoimmune disorders where the strongest genetic risk factors reside within the major histocompatibility complex (HLA). The project was set to understand the HLA associations in PSC and their immunological implications at the molecular level. Primary sclerosing cholangitis (PSC) is a cholestatic autoimmune liver disorder of unknown etiology characterized by hepatic immune infiltrates and extensive fibrotic strictures of the intra- and extra-hepatic biliary ducts. Genome-wide association studies (GWAS) have shown that the genetic architecture of PSC closely resembles other prototypical autoimmune disorders such as celiac disease and type 1 diabetes where the strongest genetic risk factors reside within the HLA alleles of the major histocompatibility complex. In PSC, the contribution of the overwhelming HLA association is unclear, and the project is aiming to understand these associations in PSC. The HLA genes encode molecules that bind and present peptide fragments (antigen) from proteins (from the body itself or from an exogenous source) and present them to the T cells of the immune system. The bacterial composition of the gut in PSC is different from that of patients with other bowel diseases and healthy individuals. The gut microbiota may serve as a source of specific antigens relevant for adaptive immune responses in PSC, but also other antigens are being explored. In brief, the current emphasis has been on the identification of peptides: • presented by PSC-associated HLA variants; • originated from PCS-specific gut microbiota; • which contribute to tissue injury in PSC either (1) by directly eliciting immune reactions (similar to the way gluten is driving gut pathology in celiac disease), or (2) by molecular mimicry (i.e. eliciting immune reactions that cross-react with endogenous peptides). The successful project has comprised two distinct pathways, one methodological - to overcome the bottlenecks related to antigen detection and discovery, the other one data production and analytical activities. Selected accomplishments in the methodological avenue include development and testing of methodology fr proteogenomic HLA-II typing at the 4-digit level and allele-specific quantification using targeted MS/MS (manuscript in preparation), establishment of a new method for T-cell receptor sequencing and analysis, published (PMID 28693542), establishing of novel methodology for isolation and genomic seqeuncing of antibody-binding (IgA emphasis) bacteria (manuscript in preparation), novel statistical analysis of HLA assessments which exploits differences in linkage disequilibrium between various ethnic subpopulations and disease specifities (two papers in submission). The methodological advances made throughout the project period has paved the way for studies along three future research pathways; a) detailed analyses of HLA-TCR and BCR immunoprofiles and interactions, b) assessments of antigenic determinants of the gut microbiome, and c) assessments of non-peptide, antigenic determinants. Selected accomplishments in the data production and analytical avenue includes several publications that vastly specified the immunoreactivity of T cells (e.g. PMID 26257205) and B cells (e.g. PMID 30094406) and the HLA associations in PSC and related immune-mediated diseases (e.g. PMID 28695657), along with potentially relevant microbiome factors (e.g. PMIDs 26887816, 27720803, 31243055 and 31250469). Papers related to the immunopeptidome assessments, which has been focusing on monoallelic cells expressing either DRB1*13:01 or DRB1*13:02 (for which there is only one amino acid difference between primary structures, i.e. susceptible DRB1*13:01 and protective DRB1*13:02), the microbiome antibody-biding, and the genomic HLA refinement will be published throughout 2020, i.e. after the formal project period, but resulting from the project. The project has had a relatively basic emphasis with translational opportunities deriving from the project rather than the project itself having impacted on the health services. For the health services directly, the most tangible output from the project has been the derivatives of the project related to the role of the gut microbiome in PSC, which we have identified as the likely source of the antigenic triggers - not only in PSC, but also in various other disease entities. This has led to several successful spin-off projects and grant appliacations, and the establishing of a broad portfolio of research activity - far beyond PSC, and included most recently the establishing of a Regional Research Network in Helse Sør-Øst related to gut microbiota medicine as well as a Oslo University Hospital focused research area on the gut microbiome. These research activities and the current query for antigenic triggers in PSC has positioned Oslo University Hospital and Helse Sør-Øst at the front of this rapidly developing research area, with major implications for many disease areas. Disease modeling that takes into account not only the genetic component of disease susceptibility (which for complex diseases may be far below 50%, for many diseases as low as 10-20%), but also their environmental co-factors - antigenic triggers included - clearly represents a valid paradigm - and one that we through the activities of this project has enabled by establishing a local methodological and conceptual framework to tackle, research wise, and in the near future also in the clinics for the benefit of the patients.