Gluten can cause abnormalities in gut flora (the good bacteria in your gut). This is especially true for those with celiac disease. If the gut flora is compromised, your immune system becomes compromised because the pH of your intestines changes, allowing foreign bacteria to grow. The gut flora also helps digest food that provides you with the essential nutrients for your body to function.
Casein is a protein that is found in cows milk, and autoimmune patients generate an immune response to casein. If cows milk is introduced into the diet too early, casein can be flagged as a foreign invader and stimulate an immune response.
Lectins are a protein found in the cell membrane and facilitate cell to cell contact. Lectins bind to sugars found on the surface of other cell membranes. It is thought that lectins found in autoimmune patients strip away the sugars on the surface of other cells instead of binding to it. After the sugar is stripped away by the lectin, the body reads that cell as an invader and activates the immune system. A diet low in lectins for autoimmune patients could potentially help turn down the immune system.