The complete food digestion and reduction of residue antigens in the gut has a strong emphasis in the treatment of autoimmune diseases and the use of enzymes is one of the most frequently used weapons, like anti-inflammatory, immune regulators and probiotics in the treatment plan for each person.
Many think the autoimmune diseases like where you build antibodies against their own "self" that facilitate the self-destruction. The topic is debated because in fact many "normal" there are autoantibodies in people who do not have any kind of disturbance and in many situations, as in Hashimoto's Thyroiditis, the presence of autoantibodies, even at high levels, it does not necessarily mean that the thyroid stops working. What generates "disease" was inflammatory reaction, almost always also stimulated by contact between gut and food that assumes a role often decisive. Triggering this mechanism may be due to cytokines as BAFF (B Cell Activating Factor) and PAF (Platelet Activating Factor) that trigger a cascading immune response stream. The antibodies do not necessarily determine organ injury, but can instead create certain proteins absorbed from the intestine and not yet fully digested, complex patterns, almost real "lumps", which are filtered and retained by certain organs and that generate an activation cascade of inflammatory reactions with strong impact on the entire organism.
Intestinal malabsorption, inflammation from food and "leaky gut syndrome" (situation in which increased intestinal permeability) are all situations that facilitate the occurrence of autoimmune diseases. Just think for example to close relations between Hashimoto and Gluten sensitivity. As he described Fasano (1), increased intestinal permeability is the possible cause of many autoimmune diseases and the complete enzymatic digestion of the gliadin, obtained from protease produced by Aspergillus, is able to reduce or cancel the reactive response of T-cells responsive to gluten (2).
The latter work explains why the complete digestion of the gliadin can reduce the reaction that leads, in susceptible people, the development of celiac disease.
Autoimmune reactions are often stimulated by the presence of a indigerite protein pattern in which autoantibodies are the "Binder", triggering the action of complement (detectable in the blood as C3 and C4) that is consumed and occurs in these cases often reduced. The fact that the vast majority of autoimmune diseases, inflammatory, allergic and benefit from repeated use digestive enzymes suggests that poor digestion is an important contributory cause of these disorders and among the many surely a contributory cause easily solved.