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.
Many prevention approaches or treatments of diseases that involve the immune system use controlling the immune system with a vaccine. The definition of what is a vaccine is rather loose:

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.

In the Bottle: Vaccines, Allergies, and Autoimmunity at Play

1.0  Vaccines against pathogens: Can they  trigger an  autoimmune disease like Multiple Sclerosis, Lupus etc..?

1.1 In a standard vaccine, the immune system is presented with a “picture” of what an infectious agent looks like so that it can recognize it quickly when the infectious agent mounts an attack, in other words the vaccine is a “heads up” . The question is is that “heads up” sufficient to provoke an autoimmunity response from people who have a ready autoimmune trigger. The answer is a qualified yes.
The Multiple Sclerosis Society is conceding that   live vaccines are not advisable for MS patients [1].
Quoting:   “…In general, MS specialist neurologists do not recommend any live-virus vaccine for people with MS because live-virus vaccines can precipitate an increase in disease activity…”
1.2  A live or attenuated vaccine [2]  coaxes a stronger response  than  a  vaccine made of  killed infectors.  Many are live viruses or bacteria  that have been cultivated under conditions that disable their virulent properties, or which use closely related but less dangerous organisms to produce a broad immune response.
The consensus is that vaccines made of killed infectors will not cause an autoimmune response. However, the MS society recommendation has many restrictions:
Quoting from [1]: “…A high-dose flu vaccine is available for people over age 65.  This high-dose vaccine has not been studied in people with MS of any age. At present, the Centers for Disease Control is not recommending the high-dose vaccine over the seasonal flu vaccine for the general population…”
Some in the medical community are dismissing concerns about vaccines causing allergies or autoimmunes diseases [3] . Quoting Dr Offit:
“…To induce autoimmunity, you need the tremendous immune system stimulation that only occurs with natural infection and not with a weakened vaccine pathogen..”
Weakened pathogen? The question is how weak. Are live vaccines weak enough?
However, Dr Offit has two interesting observations:
In order to be an autoimmune risk, the vaccine should present molecules to the immune system that,
a) “Look” similar to cells or cell components of the human body. For example:
“…. Influenza virus type A contains a protein that is similar to human myelin basic protein, and some studies have shown that natural infection with influenza virus exacerbates symptoms in patients with multiple sclerosis..” Then he presents studies that purport the Influenza vaccine , in fact , did not trigger MS exacerbations.
b) Quantity of the vaccine pathogen should be large:  “…the aggregation of hepatitis B surface antigen that occurs during natural hepatitis B infection far outweighs that given with the vaccine…”

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 [4].  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…” [5].  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 [6] :

“…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. [8] 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 [9] “… Infrequently reported post-vaccination autoimmune diseases include Systemic Lupus Erythematosus, Rheumatoid Arthritis, Inflammatory myopathies, Multiple Sclerosis,…” Ref. [10] 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

Quoting [12]:

“… 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 [12]  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 [13]. 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 [13]

“…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.


  1. MS Society position on vaccinations
  2. Wikipedia ; vaccines
  3. ; “Do vaccines cause allergies or other chronic diseases? ” , 2003
  4. Hal -Allergy ; “anti-allergy vaccines for food allergies” ;
  5. Current Topics in Microbiology and Immunology ; “T cell epitope-based allergy vaccines.”; 2011
  6. Current protein and peptide science ; “Epitope peptides and immunotherapy”; 2007; “
  7. Allergy ; “Immunotherapy with peptides.” ; 2011
  8. Peanut Allergy Treatment ; ” attaching peanut proteins onto white blood cells called leukocytes”; Oct 2011
  9. Discovery Medicine ; “Vaccines and autoimmune diseases of the adult.”; 2010
  10. European Journal Of Dermatology ; “Autoimmune diseases and vaccinations”
  11. Pharmacology and Therapeutics ; “Allergen-related approaches to immunotherapy.” ; 2009
  12. Current Opinions Immunology ; “Antigen-specific immunotherapy of autoimmune and allergic diseases” ; 2010
  13. American Academy of Allergy, Asthma, and Immunology ; “Allergen immunotherapy does not increase risk of autoimmune disease” ; 2011

3 Comments for this entry

  • carlos roman says:

    I develop Polychondritis during the course of SCIT, Polychondritis often appear around 40s and 60s, I contact Dr. Linneberg to ask his oppinion about the relation of SCIT and Autoimmune disease.

    It seems that there are many cases of autoimmune disease trigger during the course of SCIT that are not published on the literature, so it might be a probabilty that people to be prone to have autoimmune problems are on a risk during the use of SCIT.

    Doctors should publish all the cases to have better and safe treatment options with less risk.

    Carlos Román Castañeda

    • Yves Eljas says:

      Interesting comment, but who is Dr Linneberg?

      • carlos roman castañeda says:

        Hi Yves Elijas.

        Dr. Linneberg is the one who made the article about Allergen Immunotherapy and Autoimmune Disease. that is the Epidemeolgy study that is on this article.

        On the conclusions are that the risk is small, beacuse there are only few reported cases of autoimmune disease that have been trigger during the course of Allergen Immunotherapy (SCIT), but if you search on web forums of difernt types of autoimmune diseases you can see that exist many other cases that are not publicated on the web by doctors.

        I develop Polychondritis during the course of SCIT I was 13 years old, and as I said this disease often appear arround 40s and 60s.

        The principal immunologic change that SCIT make is a shift from Th2 to Th1 immune profile, wich seems tho be connected to autoimmune diseases.

        Maybe people who have genetic disposition to this immune problems should be informed before recive SCIT.

        Like in my case, we need more information about this topic.

        Carlos Roman.

        my email is if people need information about this.


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