Autoimmune diseases and the Human Leukocyte Antigen (HLA) system have a close relationship. HLA antigens are coded for within a region of genes known as the Major Histocompatibility Complex (MHC). Although HLA and MHC are often used interchangeably, HLA in fact refers specifically to the MHC system in humans. The MHC is found in most vertebrates. In the mouse system it is referred to as the H-2 system.

The primary role of the HLA molecules is to present pathogen derived peptides to T cells thereby eliciting a T cell mediated adaptive immune response. The T cell recognises both the HLA molecule and the peptide it presents. T cell recognition of pathogen is therefore said to be MHC restricted. However in autoimmunity, autoreactive T cells become activated. Diseases associated with HLA include:


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