What might case autoimmune diseases?

Confused cells. Immune system, especially, the adaptive part, views body organ systems as foreign invaders and attacks protectively. Our genetic makeup determines organ susceptibility, and environmental stimuli trigger the attack. This could be termed a biological mimicry. Classics include rheumatoid arthritis, ms, celiac disease, pernicious anemia, to name a few.
Excess immune stimul. A manifestation of excess immune stimulation which leads to inflammation of your tissues- myelin in ms, joints in ra... The immune stress can be environment edible, infectious... Chronic stress leads to compensatory changes in adrenal, thyroid & other hormones wreaking metabolic havoc in your system. Plus other stressors contribute- poor diet, lack of sleep... Genetics play roll.