Genome-wide analysis of individual coding variants and HLA-II-associated self-immunopeptidomes in ulcerative colitis

Genome wide association studies contributed to a better understanding of the etiology of inflammatory bowel disease (IBD). While over 240 genetic associations with IBD have since been identified, functional follow-up studies are still in their infancy with the overall pathogenesis of IBD remaining unsolved. E.g., a functional understanding of the genetic association between the human leukocyte antigen (HLA) region and ulcerative colitis (UC) – one subtypes of IBD – is still lacking. Here, we analyzed whether an autoimmune reaction involving the HLA class II proteins HLA-DQ and -DR, both being strongly associated with UC, could be a disease trigger or driver. To this end, genotype data derived from whole exome sequencing and genome-wide SNP array data of 863 German UC patients as well as 4,185 healthy controls were analyzed. Association analyses identified novel variants in the NOD2 and SNX20 genes to be linked with UC and confirmed known HLA allele associations. Employing the genetic data, we generated patient-specific self-immunopeptidomes and in sili co predicted HLA-peptide binding. Peptidome-wide association analyses of peptide binding preferences in a set of candidate proteins yielded significant associations with 234 specific peptides. Interestingly, none of those peptides showed a differential presence in case and control samples. The disease-associated candidate peptides predicted to be presented by risk HLA proteins contained predominantly aromatic amino acids. In contrast, protective HLA proteins were predicted to bind peptides enriched in acidic amino acids. In summary, we present a proof-of-concept immunogenetic analysis that contributes to a better understanding of the HLA in UC. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement M.W. and H.E. were funded by the German Research Foundation (DFG) (Research Training Group 1743, Genes, Environment and Inflammation). T.L.L. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 437857095. The study received infrastructure support from the DFG Cluster of Excellence 2167 Precision Medicine in Chronic Inflammation (PMI) (EXC 2167-390884018). The funding agency had neither a role in the design, collection, analysis, and interpretation of data nor in writing the manuscript. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee of University Hospital Schleswig-Holstein (UKSH) gave ethical approval for this work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.