I have been geeking out on HLA lately. HLA stands for human leukocyte antigen. This is a set of genes that encode something called the Major Histiocompatibility Complex, which is on cells that present antigens (read - bad stuff) to T cells, so they can trigger mechanisms to destroy said bad things.
There are many different HLA permutations, depending on which types of T cells they want to send messages to (CD4 or CD8). So what is the relevance to me, asks the reader? AUTOIMMUNE diseases. Here, the body turns on itself, in that it recognizes certain cells in the body as foreign and wants to destroy them. Obviously not good, since the body actually needs those cells. A classic exam is type 1 diabetes, where the islet cells on the pancreas that make insulin are destroyed, so uptake of glucose into cells that need it in the body is impaired. These pancreatic cells are destroyed by the body itself! Not some outside interloper. Cool stuff, unless they are your islet cells.
Even more interestingly, certain autoimmune diseases are linked to the same HLA type. Diabetes type 1 is linked to Rheumatoid Arthritis, via HLADR4. There's a whole slew of arthritis oriented disorders linked to HLAB27, including arthritis that you can get after having chlamydia. Even if you treat the chlamydia, you are still at risk for developing this arthritis (called reactive arthritis - used to be called Reiter's arthritis, but they are trying to get away from it because Dr. Reiter was a Nazi doctor, and you know what those dudes were up to).
And with that...back to the thymus.