Identifying the Immune Interactions Underlying HLA Class I Disease Associations

Elife. 2020 Apr 2;9:e54558. doi: 10.7554/eLife.54558.

Abstract

Variation in the risk and severity of many autoimmune diseases, malignancies and infections is strongly associated with polymorphisms at the HLA class I loci. These genetic associations provide a powerful opportunity for understanding the etiology of human disease. HLA class I associations are often interpreted in the light of 'protective' or 'detrimental' CD8+ T cell responses which are restricted by the host HLA class I allotype. However, given the diverse receptors which are bound by HLA class I molecules, alternative interpretations are possible. As well as binding T cell receptors on CD8+ T cells, HLA class I molecules are important ligands for inhibitory and activating killer immunoglobulin-like receptors (KIRs) which are found on natural killer cells and some T cells; for the CD94:NKG2 family of receptors also expressed mainly by NK cells and for leukocyte immunoglobulin-like receptors (LILRs) on myeloid cells. The aim of this study is to develop an immunogenetic approach for identifying and quantifying the relative contribution of different receptor-ligand interactions to a given HLA class I disease association and then to use this approach to investigate the immune interactions underlying HLA class I disease associations in three viral infections: Human T cell Leukemia Virus type 1, Human Immunodeficiency Virus type 1 and Hepatitis C Virus as well as in the inflammatory condition Crohn's disease.

Keywords: CD8 T cell; GWAS; HLA; computational biology; disease association; human; immunogenetics; immunology; inflammation; natural killer cell; systems biology.

Plain Language Summary

When considering someone’s risk of disease, every person is different but some similarities can be found when looking across populations. Some people are more likely to develop a certain disease, while others are protected in some way. Part of this variation is explained by the individual’s genes, while their lifestyle and environment are other factors. Numerous studies have looked for associations between different versions of genes, known as gene variants, and the occurrence of disease to identify who is at risk. There is one cluster of genes called the HLA genes that is a well-known hotspot for disease associations. The HLA cluster is named for the group of proteins it encodes, called the human leukocyte antigen (HLA) complex. These cell-surface proteins regulate the immune system in humans. These proteins are present on the surface of cells, and they help the immune system distinguish foreign invaders such as viruses and bacteria from the body’s own cells. Variants in the HLA genes are associated with more than 100 diseases, including infectious diseases like HIV, autoimmune conditions such as multiple sclerosis, and some cancers. However, while identifying which genetic variants are associated with an increased or decreased risk of disease is relatively simple, understanding why those genetic variants are associated with a particular disease is much harder. Debebe et al. have developed a new method to find out why certain gene variants in the HLA cluster are associated with disease in humans. They used this method to investigate known genetic variants associated with three viral infections: HIV, hepatitis C, and human leukemia virus – and one inflammatory disease: Crohn’s disease. Critically, Debebe et al. looked at the interactions between different immune cells and the cell-surface proteins encoded by the HLA gene variants in different cases of these diseases. In doing so, the analysis was able to identify which cells of the immune system were responsible for the associations between gene variants and diseases. In principle, this method could be applied to study any disease in any species. It could also be used in classic gene association studies to test for false positive results and “passenger” mutations, two common problems that beset sound interpretations from these studies.