Hi Sarah,
Autoimmune disorders arise when your "adaptive immune system" starts working too well. Instead of just forming antibodies to bacteria, viruses, and parasites (which is essential for your survival), it starts forming antibodies that recognize your own organs, blood cells, nerves, DNA, etc... Ideally, this is not supposed to happen, but it does is about 20% of the human population. In many autoimmune disorders, these antibodies destroy the target. I have Hashimoto's disease, for example, and my immune system has been making antibodies (probably for a loooong time) that have damaged my thyroid to the point where it no longer makes enough thyroid hormones to keep me functioning normally. What your doctor is looking for is antibodies that are attacking and destroying your ganglion... nerve cells in your autonomic nervous system. If you have these antibodies it would definitely explain a LOT.
In some ways, the autoimmune version of MCAD that I have is a little different from most autoimmune disorders. It doesn't destroy my mast cells (or the high-affinity IgE receptors) it just causes them to degranulate... as if I had a peanut allergy.
Now here's the really tricky thing... any kind of autoimmune disorder will make a mast cell disorder worse, regardless of whether they're related or not. When antibodies lock on to their targets (allergens, organs, DNA, etc...) they form "antibody-antigen complexes." If there are not too many, your body can usually flush them out with "complement" so they don't cause any further damage. People with lupus or a severe infection (TB, malaria, AIDS, etc...) are making so many antibodies that their complement system can't keep up. So... the complexes get stuck in predictable places... joints, kidneys, heart, lungs, small blood vessels, ciliary body of the eye, and choroid plexus in the brain. This causes joint pain, headaches, petechiae, kidney damage, and sometimes worse (heart failure, seizures, etc...). The goal of treatment for lupus is to reduce the antibody production so you're not making so many complexes. That can work for someone like me too... it's the next step if I start feeling bad again. Now here's the part that a lot of doctors don't know...
the combination of a mast cell disorder (any type) and autoimmune disorder (any type) is going to make your symptoms worse. There are a couple of reasons for this. One is because all the histamine and leukotrienes make those antibody-antigen complexes really sticky. Even if you have normal levels of complement (like I do), you can still get that joint pain, kidney damage, headaches, etc... Another reason is because when our mast cell degranulate they release cytokines... these cytokines stimulate the production of antibodies, including autoantibodies. It can turn into a really vicious cycle!
It's GREAT that your doctor is thinking "autoimmune." Even if you can't pinpoint the antibodies that are causing the problems, you might be able to get some relief from treatments that reduce the production of antibodies... immunosuppressants (more than just steroids), IVIG, or even a monoclonal antibody like Rituxan.
I hope this answers your question. It IS complicated... just keep reading and it will eventually make more sense.
Heather