[rubatuga]

MHC (Major histocompatibility complex) plays a large role in this, essentially they are like hash functions for the peptides / proteins in your body. Cells then present these hashes on the outside of their membrane which then let them be either targeted for destruction or recognized as self.

Mistakes (or unfortunate genetics) in this process along with a mix of unknown environmental factors (smoking? EBV infection?) can affect how likely you are to develop autoimmune conditions where the body attacks itself. For example, people with the HLA-B27 "hash function" are much more likely to develop ankylosis spondylitis, but this gene may protect against viruses such as HIV or Hepatitis C. A lot of the research for the treatment of these autoimmune conditions now is on how to treat the condition without shutting down the entire immune system.