Well HiV is immunodeficiency, and autoimmune disease seem to be an over active immune system, so not sure how that works?
Crohn's disease shows inflammation, and lots of cytokine are involved during active disease, but the innate immune system in crohn's disease and the genetic susceptibility show
immune deficiencies at particular loci, related to autophagy, macrophage deficiencies and there are lots of similarities between mycobacteria susceptibility.
Autoimmunity in crohn's disease is a nice theory but there is no evidence of this atm in any form. There are no known autoantigens, the "patchyness" of crohn's disease (skip lesions) contradict the autoimmune theory, genome studies contradict this, and antibiotics are able to induce remission. To this day there is no evidence of autoimmunity in crohn's disease, I think this point needs to be made somewhat more clear because I am under the impression that people think this is an accepted theory, it's not. It's a theory that is pretty much dead at this point. (A study showed they could create a continous T Cell response in rats even when the bacteria is removed, but there is no evidence this is happening crohn's disease at all)
In fact the first studies that showed immune deficiencies in crohn's disease used nothing other than Viagra to increase blood flow which increased bacterial clearance of non-pathogenic invaders which were artificially injected in people with crohn's disease to measure their immune status, which shows an underresponsive immune system.
If you can wrap your head around that, you can look at studies that show crohn's disease actually has an inflammation deficiency in the innate immune system. Lack of alpha defensin also.
There are also immune deficiencies in people with crohn's disease related to mutations in the VDR gene, the receptor for vitamin D.
There are a number of similarities between HIV and Crohn's disease. One that they both involve immune deficiencies, the second is that they are both in some way related to mycobacteria.
M. Avium Complex infections are common in people with HIV (although this is going down thanks to HIV treatment), MAC is part of the mycobacteria genus. Crohn's disease shows susceptibility to this genus, it actually shows a lot of similarities to M Leprae susceptibility shown in the Nature study published last month.
That one is a precursor for the other is something I don't think is rooted in evidence though. Never heard of an increase in crohn in HIV patients.