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Ah-choo! Compelling Research About Allergies and Autoimmune Disease: Immune System, Root Cause, Disease Progression

Each year, millions of people suffer from allergies, autoimmune disease, or both.  These conditions can range from relatively mild to severe and debilitating, and patients with either can attest to the effects such disorders, even when occurring at moderate levels, tend to have on one’s health and well being.  Here we examine some of the things that link these two categories of disease together, as well as those that set them apart from each other.

What are the similarities and differences in allergies and autoimmune disease?

Both allergies and autoimmune disease can be considered hyperimmune responses, whereby the body’s immune system becomes supercharged, attacking or responding to substances that shouldn’t normally draw such attention.  Because these two classes of disorders involve a misplaced inflammatory response, they also tend to overlap somewhat with regard to symptoms.  During flares of each type, one may experience common symptoms such as redness, swelling, rash and itchiness.  This is a result of the inflammatory processes occurring during each acute episode, which are similar in some respects, but quite different in others.

The first major difference concerns the precise causes each condition:  allergies, whether seasonal, perennial or specific, are a response to external antigens (substances that antibodies recognize as foreign and attack), such as pollen, dust, peanuts or shellfish, among a host of others.  In contrast, autoimmune conditions are an immunological reaction mistakenly directed at internal antigens (various innate proteins and body tissues) that become targeted as if they were foreign invaders, despite being normal parts of the body.  One example would be the autoimmune reaction seen in rheumatoid arthritis, where certain joint tissues are attacked unnecessarily, resulting in painful inflammation and deformities in some areas.

Another difference between the two concerns the actual mechanisms by which these pathological processes achieve their intended effects.  Without getting too technical, the difference involves the immunological pathways used in each instance.  Most allergies are initiated by a specific type of T-lymphocyte (TH2), and then directly mediated by something called IgE (immunoglobulin E), which is one of five major immunoglobulins/antibodies produced by B-lymphocytes and involved in different immune reactions.  Its activation leads to release of histamine, which causes itching and swelling.  Such a response is commonly known as a delayed hypersensitivity reaction. In contrast, several types of immune cells can mediate autoimmune diseases, but most often they involve a combination of different types of T-cells (T-killers/regulators/helpers/suppressors), sometimes combined with B-cells, which play various roles in the immune response, whether normal or abnormal.  Depending on the condition, one or more immune processes (B- or T-cell mediated) may be responsible, but those above are considered some of the basic mechanisms for each category.

Finally, because the inciting factors are much more readily known and identifiable with allergies, testing and therapies tend to be quite a bit more specific and effective when compared with those for autoimmune conditions.  Even though there are plenty of lab tests and treatments available for autoimmune conditions, the lack of complete understanding regarding disease causes and mechanisms leaves them less amenable to targeted therapies.  While autoimmune diseases are generally diagnosed and treated with relatively non-specific measures (ANA and ESR; steroids and other immunosuppressants), allergies where individual allergens can be identified through testing are often much more readily treatable via desensitization therapies (allergy shots aimed at blunting/removing the allergic response).  However, allergies are also treated with non-specific methods such as antihistamines.

Is the root cause of allergies and autoimmune disease the same?

Common sense based on the above information tells us that there is undoubtedly a connection between the two types of disorders, since they are both the result of dysfunctional immune responses, albeit to completely different triggers.  For a long time the specific way in which these two conditions align with each other and the commonalities between them remained mostly a mystery.  However, in the last few decades, researchers who are starting to elucidate these mechanisms have made significant advances. One line of thinking that has been around for a while, but has recently gained traction within the medical community is something called the hygiene hypothesis.  This possible explanation for one or both categories of disease is based on the idea that through modern medicine and sanitization techniques, people in the developed world have actually become too clean, ridding themselves of evolutionarily protective microbes (bacteria, viruses, parasites), under the assumption that such bugs are purely harmful.

Evidence corroborating this theory includes identification of beneficial gut bacteria (probiotics) and epidemiological statistics that show far less allergies and autoimmune disease in developing countries with less focus on sanitization and the latest antimicrobial techniques, as discussed in this article published in the journal Clinical & Experimental Immunology. The bottom line thinking is that we have, over many years, inadvertently rid ourselves of certain necessary and beneficial bugs, under the mistaken assumption that all of these organisms are dangerous.  As a result, our immune systems find themselves with less to protect against, and turn towards other targets in the absence of traditional ones.  In essence, we have removed harmful antigens and bugs to the point where our immune systems are, for lack of a better word, bored and looking for something to do. And more recently, scientists at the NIH have identified a gene that is believed to control the expression of both allergic and autoimmune reactions.  This gene, named BACH2, may be the first major step in clarifying the connection between the two, as well as the exact mechanisms involved, although our understanding is still quite rudimentary.

Is there a link between seasonal allergies and autoimmune disease onset/progression/flares?

While a link has been fairly well established (though the mechanism remains unclear) between food allergies and autoimmune disease (e.g., gluten sensitivity and celiac disease), the same cannot be said for seasonal allergies, where the same connection is somewhat lacking in the literature.  Still, some work has been done that indeed supports the theory of seasonal allergies influencing and up-regulating the autoimmune response. Much more prominent are patient anecdotes and testimonials, which abound online and clearly indicate some sort of connection between the two.  One story related to me personally involves a woman who had terrible allergies during her last trimester of pregnancy that induced unbearable sinus headaches, and then subsequently developed Hashimoto’s thyroiditis postpartum.  Naturally she is suspicious about there being a connection between the two.

Whether these relationships are correlative or causal – or their exact nature and direction – can’t be accurately determined without scientific experimentation.  Still, such attestations certainly offer evidence that something is going on in terms of a connection between the two.  Patient observations unfortunately must begin to accumulate sometimes before the problem is officially recognized and research action is undertaken.  Therefore, it is crucial for anyone who suspects that their allergies and autoimmune issues are related to continue to report such suspicions to his or her physician, so that we may build evidence for this connection, in the hopes of spurring additional research efforts.

Questions for your doctor:

  • How can I know exactly which things I’m allergic to?
  • Am I a candidate for allergy desensitization?  Why or why not?
  • Can you explain the connection between allergies and autoimmune disease?
  • In your clinical experience, do seasonal allergies have a connection to autoimmune conditions?  What is the direction of that connection?
  • Can you give me your opinion on the hygiene hypothesis and what I can do personally to avoid such unintended consequences of being “too clean”?

About the Author
Dr. Rothbard is a professional medical writer and consultant based in New York City, specializing in medical education articles targeted at a variety of audiences, from children through clinicians.  After leaving medicine, he worked as a biology and medical science educator for several years, before deciding to pursue writing full-time.  He may be reached at

This blog post was originally published by, written by Dr. Rothbard, and first published on Oct 9, 2013.

This post contains the opinions of the author. Autoimmune Association is not a medical practice and does not provide medical advice, diagnosis, or treatment. It is your responsibility to seek diagnosis, treatment, and advice from qualified providers based on your condition and particular circumstances. Autoimmune Association does not endorse nor recommend any products, practices, treatment methods, tests, physicians, service providers, procedures, clinical trials, opinions or information available on this website. Your use of the website is subject to our Privacy Policy.

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