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Jonathan Edwards thank you for thinking this through so clearly and taking the time to share/discuss it with us. That is so encouraging.
I have ANA (speckled as you said, increasing over some time into indisputably significant level, but no other markers for particular diseases; several have been checked... [edited to remove some individual specifics]
I didn't notice it in the early days but I now have PEM. In addition to that, I have fatigue. I did not find a lot of infections when we checked. [edited some individual specifics] My questions are:
I have trouble running a fever (seldom do, and if I seem to really need to, it is not consistent and not high, which confuses ER, for example). If I get an incidental infection I typically feel worse (e.g. aches, malaise, possibly trembles, chills, cough) but don't have all the signs and symptoms unless it's a flu, but still not even moderately high fever (& for others, not much by way of specific S&S of cold, noravirus, etc.). I have low NK cell function like those with infections. Is all this explained by autoimmune (or other expected immune) problems? (I have not had cytokine testing.) My temp is most often low.
How does muscle dysfunction fit into everything? I can't paste studies from this device and honestly some (all?) of the studies are very small, but Yves Jammes and Kieren Hollingsworth are finding a neurological muscle problem in both smooth and skeletal muscle. Could the body be attacking the ion channels (if I understand it correctly) that work the muscles in some cases? I have a test result that would support this kind of muscle problem in my case (but no MG, MS, etc.). Also, if I walk too far, particularly if I've not been getting enough rest in general, my legs drag.
If autoimmune disease similar to Sjogren's were attacking the GI system, would it necessarily look bad on various scopes and image testing? Could this cause severe problems like malabsorption and maldigestion while looking relatively unimpressive and unidentifiable to a thoughtful GI doctor, or would that be a different problem? Second thought, I searched and I see it's not uncommon for Sjogren's patients to be diagnosed with IBS. They have some similar and some opposite problems to me, but this is intriguing.
How do you find a new autoantibody?
Apologies if some of this has already been asked; I got too sick to follow the long thread.
Thanks again; this is a very interesting thread. I have always thought it most likely there would be at least two groups, possibly many, because as Alex said it's common to find a similar proportion split. Also because we have different groups finding disparate things.