Autoimmune diseases are the bodies own immune system mistakenly attacking itself.
What exactly causes the immune system to react improperly isn’t known and is actively being researched.
Since we don’t know the cause, and don’t have a complete understanding of how the immune system works (we understand a lot about it, but not everything) our only effective treatment is to suppress the immune system with drugs or blow it away completely with something like radiation therapy and rebuild it with someone elses in the hope it fixes the problem. Not exactly ideal either way.
If we can figure out the mechanism, then maybe we can figure out how to cure an autoimmune disease.
The same research may also be the key to curing allergies, as the mechanism that causes your body to attack itself may also be why it chooses to attack things like food and pollen.
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