Introduction: Allergies and autoimmune conditions are both immune system issues, so it is natural to explore their possible connections. Let us start with some definitions from wikipedia
- Allergy: A hypersensitivity disorder of the immune system to substances in the environment. Such substances are called allergens. Allergens (pollens, peanuts,..) can be common to a large number of people . The allergen causes excessive activation of certain white blood cells called mast cells and basophils by a type of antibody called Immunoglobulin E (IgE)
- Autoimmune Disease: an inappropriate immune response of the body against substances and tissues that are normally present in the body.
Standard definition of a vaccine : “A vaccine is a biological preparation that improves immunity to a particular disease.” (Wikipedia). This kind of vaccine maximizes and prepares the body’s defense against an infector.
Broader definition of a vaccine: Cancer vaccines, where the immune system is “trained” to turn against cancerous cells. This is done either by training the immune system to recognize certain proteins belonging to the cancerous cell or to recognize Tumor-Specific Antigens (TSA) or tumor associated antigens. The trick is to convince the immune system that the cancerous related protein is to be eliminated.
Like the allergens, antigens trigger an aggressive response from the immune system.
Now immunotherapy treatments of allergies go the other way: The immune system has to be trained to declassify that allergen into a tolerated protein or compound.
1.0 Vaccines against pathogens: Can they trigger an autoimmune disease like Multiple Sclerosis, Lupus etc..?
Clearly the medical community is doing a balancing act between to much or too little of immune system familiarization with the infector.
2.0 Allergy immunotherapy and their vaccines:
As we said in the introduction, in an allergy attack, the immune system identify a benign part of the body as a threat
Immunotherapies are currently studied in an attempt to pacify the immune system. The treatments attempt to coax the Immune System to declassify the body component under allergy attack from threat to benign.
Vaccines are also a form of immunotherapy studied as allergy treatment . Quoting the HAL company:
“…Scientists discovered that administering small quantities of substances that people were allergic to put the disrupted immune system back on track and diminished the severity of the reactions..”
The parallel between allergens and noxious virus or bacteria is clear: Both will trigger an immune response. The difference is that the reaction by the immune system against the live pathogen is serving a genuine purpose. However the “allergen” quality of the foreign body involved is a case of mistaken identity by the immune system. A little bit like your watch dog mistakenly taking your favorite chair for an intruder with bad intentions…
So here the object of the vaccine is to pacify the immune system and training it to recognize the “chair” of the above metaphor as harmless. Here are the main approaches:
2.1 Use allergen molecules without major modifications : ” extracts containing intact allergen molecules.. treatment [are administered in] …an incremental dose fashion which ultimately achieves a plateau (maintenance dose) that may be continued for several years…” . Some such immunotherapy treatments are really treatment over substantial periods of time ”
The allergens can be administered under the tongue or by injections under the skin.
However, such treatments using the allergen directly are not without risks and serious allergic reaction (anaphylaxis ) can occur, which is what the treatment was trying to avoid in the first place.The parallel for infections vaccines would be a person getting the full brunt of the flu from a flu vaccine…
2.2 So the research community has come up with more subtle variants to the presenting the immune system with unmodified allergen
Peptides based vaccines: [5,6,7]. Here selected pieces of allergens [called epitopes] are presented to the body as opposed to the whole antigen compound. The idea is to reduce violent allergic reaction [anaphylaxis] risk.
Quoting  :
“…An alternative strategy for the generation of an effective but hypoallergenic preparation for immunotherapy is to modify T cell epitope peptides by, for example, single amino acid substitution….There is mounting evidence that the administration of peptide(s) containing immunodominant T cell epitopes from an allergen can induce T cell nonresponsiveness (immunotherapy).
Note : An epitope is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. and a peptide is a small protein (Wikipedia)
Ref.  discusses a immunotherapy study done on mice to tame peanut allergies, which can be life threatening. So they […… attached peanut proteins onto white blood cells called leukocytes and infused those back into the mice…” Sounds simple, but the “attachment” method is probably a lot of the work.
3.0 Conclusions remarks about vaccines, immunotherapies and autoimmune diseases
3.1 Vaccines against infection: We mentioned in 1.0 that live anti infectious vaccines are usually not advisable for people at risk , or already having, autoimmune disease, because of concerns of triggering relapses. Actually even initiating the disease itself has occurred.
Quoting  “… Infrequently reported post-vaccination autoimmune diseases include Systemic Lupus Erythematosus, Rheumatoid Arthritis, Inflammatory myopathies, Multiple Sclerosis,…” Ref.  essentially concurs with that statement.
The word “infrequently, like the word “rare” is of concern because they often mean less than 1% of the general population. I suspect that such reports are by specific autoimmune disease. To get an accurate number for the occurrences, you would have to add all the autoimmune events together.
Obviously, if you do need a vaccine and you are at risk for an autoimmune disease, you have to weigh the risks with your Doctor
3.1 Vaccines and immunotherapies for allergies:
Targeted Immunotherapy is very complex indeed
“… no antigen-specific immunotherapy (SIT) trial should be undertaken without detailed investigation of immunological changes arising from the treatment; and intervention should be undertaken as early after diagnosis as possible. Finally, the dose of antigen required for SIT is the most critical consideration; dose escalation should allow for a safe increase in dose until an effective, tolerogenic dose is achieved…”
Interestingly, immunotherapy is also explored to treat autoimmune diseases themselves. For the Table of Immunotherapies for autoimmune diseases contained in  Click Here The table includes common autoimmune diseases such as Rheumatoid Arthritis, Lupus, and Multiple Sclerosis
The study shows how targeted and complex the immunotherapy should be. In other words the patients and their doctors should watch their back, this is not for the timid.
Should be concerned allergy immunotherapy triggering an autoimmune reaction?
Clearly that concern had to be addressed, since a study was done in Sweden . Their result is in the study title:
“Allergen immunotherapy does not increase risk of autoimmune disease”
Note, however, that this study is an epidemiology one. Which means that the question was answered not on grounds of understanding the fundamentals, but by statistics. Also the study has as a basis a general population. Quoting 
“…All Danish citizens without other known diseases were linked and followed through central registries on medications and hospital admissions..”
What about people at risk of auto-immune disease , by virtue of genetics, or otherwise? Hopefully ok too, but no “proof” yet.
Again before embarking on an immunotherapy, people at risk should have a medical team that is very knowledgeable in immunology science, well connected to current research, and who knows them well. Only then can they be explained candidly the risk/ benefit ratio.
- MS Society position on vaccinations
- Wikipedia ; vaccines
- respiratoryreviews.com ; “Do vaccines cause allergies or other chronic diseases? ” , 2003
- Hal -Allergy ; “anti-allergy vaccines for food allergies” ;
- Current Topics in Microbiology and Immunology ; “T cell epitope-based allergy vaccines.”; 2011
- Current protein and peptide science ; “Epitope peptides and immunotherapy”; 2007; “
- Allergy ; “Immunotherapy with peptides.” ; 2011
- Peanut Allergy Treatment ; ” attaching peanut proteins onto white blood cells called leukocytes”; Oct 2011
- Discovery Medicine ; “Vaccines and autoimmune diseases of the adult.”; 2010
- European Journal Of Dermatology ; “Autoimmune diseases and vaccinations”
- Pharmacology and Therapeutics ; “Allergen-related approaches to immunotherapy.” ; 2009
- Current Opinions Immunology ; “Antigen-specific immunotherapy of autoimmune and allergic diseases” ; 2010
- American Academy of Allergy, Asthma, and Immunology ; “Allergen immunotherapy does not increase risk of autoimmune disease” ; 2011