So the pattern for my autoimmune hypothesis is an infection that generates antibodies first by changing what it looks like. (pigment or morphology) Then a viral infection generates antibodies that induces cross-targeting. Antibodies from 2 different types of infections induces the autoimmune disease.
Alopeica aterata is an autoimmune hair loss from a follicle on skin. Thus the cross-targeting must focus on the skin.
Any infection of the skin could if more then one morphology or pigment was produced stimulating the immune system.
http://www.ncbi.nlm.nih.gov/pubmed/7742246
http://www.ncbi.nlm.nih.gov/pubmed/23700152
vitiligo: fungal
Rheumatoid arthritis: mycoplasmas
in some cases alopecia overlaps RA and diabetes where i have already suspected Mycoplasmas but i have not found a reference of direct connection between mycoplasmas and alopecia yet but i have them infecting the scalp
http://www.ncbi.nlm.nih.gov/pubmed/12506953
http://www.ncbi.nlm.nih.gov/pubmed/6657503
Alternaria chlamydospora.
http://www.ncbi.nlm.nih.gov/pubmed/23329992
A toxin could replace the skin infection because it still draws the immune system to the skin
ant bite
http://www.ncbi.nlm.nih.gov/pubmed/15347501
Any viral skin infection could cause the cross-targeting but one really seems to stand out is Herpes.
The virus that seems to come up the most:
Herpes zoster
http://www.sciencedirect.com/science/article/pii/S0190962208002090
http://www.ncbi.nlm.nih.gov/pubmed/23526118
http://www.ncbi.nlm.nih.gov/pubmed/22838088
http://www.ncbi.nlm.nih.gov/pubmed/23181541
Personal story:http://www.alopeciaworld.com/forum/topics/alopecia-areata-episodes
This is an unproven hypothesis but alopecia areata fits the pattern I am testing on autoimmune diseases with. An infection generating antibodies followed by a virus causing cross-targeting.
2016 update...we need to sort throught the HLAs
HLA-C alopecia
http://link.springer.com/article/10.1007/s00251-013-0703-z
HLA-C is the Tcell mailbox for the endoplasmic recticulum
The viruses that are known to infect the ER : polyomaviruses like jc and BK
https://www.ncbi.nlm.nih.gov/pubmed/20373089
alopecia and
http://www.jidsponline.org/article/S1087-0024(15)30280-X/pdf
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