What is Autoimmunity

By Dr. Roxanna Garcia, NMD / May 24, 2022

What is Autoimmunity

Chronic inflammatory diseases are the most significant cause of death in the world and the greatest threat to human health. [12]

More alarming is that diseases associated with chronic inflammation in the U.S. are expected to increase dramatically over the next 30 years. [12] 

What does inflammation have to do with autoimmune disease? In autoimmune diseases, inflammation is a critical contributing factor affecting the development, progression, and management of illness. 

The incidence of these diseases is increasing, meaning more people are being diagnosed with autoimmune diseases than they were in the past. [1] 

Approximately 23.5 million people are confirmed to be affected by autoimmune disease in the U.S. Still, according to the American Autoimmune Related Diseases Association, this number is suspected to be closer to 50 million. [2][14]

You may be surprised to learn that 80% of those diagnosed with an autoimmune disease are women. [11] 

There are more than 80 types of autoimmune diseases that have been identified [1][2][3], and there can even be multiple autoimmune diseases occurring within one individual. [2]

Although conventional medicine says autoimmune diseases are life-long conditions, at NMD, we work towards reversal and remission using diet, lifestyle, and other natural modalities. 

What does that mean? 

In autoimmune diseases, there can be periods of time called “flares” where symptoms and disease activity are increased. In contrast, there are alternating periods of time when symptoms decrease or even disappear. We call this “remission.” [13]

This means you don’t have to live with negative symptoms impacting your daily life.

Are you ready to learn more about autoimmune disease, how it affects the body, and how to work towards remission?

Let’s get started!

The Immune System:

Basics of the Immune System

Autoimmune diseases are a dysfunction of the immune system. Therefore, it is essential to understand how the immune system functions normally to understand autoimmune disease. 

Your immune system protects you from harmful substances like germs, bacteria, viruses, fungi, etc. We call these pathogens. On the surface of pathogens are proteins called antigens, which help the immune system identify it as an invader of the body. [6] Once the immune system has discovered an antigen, a series of processes is triggered. [6] This process includes making antibodies, which are proteins that specifically recognize and attack the antigen. [7] Other immune cells will also be signaled to help get rid of the pathogen. [7]

Analogy Part 1:

Think of the body as a high-security building where a security guard checks each person using a metal detector wand. If the metal detector is set off, an alarm will sound. Not only will that person be denied access to the building, but security is calling for backup and enthusiastically escorting them out. 

Now think of an antigen as a metal top hat that the pathogens wear as they try to enter the body (i.e., the building). The immune system acts as our metal detector, alarm, and security guard, meaning the immune system helps to identify antigens and manage these pathogens. The extra backup guards are our antibodies, who will not stop until the pathogen is out of that building. Antibodies are serious about their job and, after dealing with the intruder, keep a “not welcome here” photo in case they try to come back again.

What is inflammation?

Inflammation, specifically chronic or long-term inflammation, is a critical contributing factor in developing an autoimmune disease.

But you may be surprised to learn that short-term inflammation is healthy for the body! 

This is another situation where we must first understand how inflammation normally works to understand why dysfunction leads to developing an autoimmune disease fully. Let me explain. 

The process of making antibodies and signaling other cells to help remove the pathogen will create inflammation in that area of the body. [8] Think of a time when you cut or scraped your skin. You may have noticed that the area was slightly pink and puffy. This was inflammation and the healing process at work! Eventually, that cut or scrape healed, and the pink puffiness went away. Once the cells recognize that the pathogen has been removed, inflammation will naturally reduce in the body.

However, in cases of chronic inflammation, inflammation does not reduce after healing. We will discuss this in more detail later.

The immune system also keeps a record of the antigen. This allows for a quick response and antibody production should the body come in contact with the antigen again in the future. [6] 


Antibodies are a crucial player in the immune system and, when not functioning properly, in autoimmune disease. 

When the immune system is not working properly, it can lead to a variety of health problems. When the antibodies fail to fight off infection, autoimmune disease can develop.

Earlier, we said that antibodies are proteins that specifically recognize and attack antigens, which are found on the surface of pathogens. [6][7] They also keep a record of all antigens they’ve come in contact with in the past, allowing them to identify and respond to reinfection with that pathogen quickly. 

You may have gotten symptoms from chickenpox the first time you were exposed to it as a child but did not get symptoms when exposed again. Instead, your body created antibodies, which identified the antigen on the surface of the chickenpox virus and quickly worked to destroy the virus before it could grow and cause symptoms. An antibody’s memory of an antigen is also the premise of how vaccinations work, such as the chickenpox vaccine.

Now that we understand the normal function of antibodies, we can talk about what happens with dysfunction…

What is Autoimmune Disease?

Dysfunction of the Immune System: Autoantibodies & Autoreactivity

Autoimmune diseases are a dysfunction of the immune system which causes the development of abnormally functioning antibodies, called autoantibodies.

We discussed how the immune system works to identify pathogens. We haven’t mentioned that our immune cells also work to identify “self,” meaning. Our body can distinguish between our body tissues and a pathogen. Typically, our body is very good at doing this. However, our immune cells can occasionally confuse and mistake “self” for a pathogen. When this happens, the immune system is activated just as it would be during infection, and immune cells will attack and damage the body’s organ tissues. This process is called autoreactivity. [1][4]  

Now, everyone has some amount of autoreactivity in their body. 

So you may be asking: if everyone has autoreactivity, why does it cause tissue damage and symptoms for some and not others? This is partially asking why some people develop an autoimmune disease while others do not. 

This is an excellent question that researchers have been asking for years, and the answer is complex and still not 100% determined yet, but I will do my best to explain what we know so far.

The difference between “normal” autoreactivity and the development of an autoimmune disease is the creation of autoantibodies

Remember, our antibodies record any antigen they’ve come into contact with. When autoreactivity happens, and the immune system is activated, our antibodies see our own cell’s protein and mistakenly believe it to be an antigen. This is what we call an autoantibody. [15]

The autoantibody then remembers this “antigen,” allowing for a quick response should it come in contact with it again. Unfortunately, because this “antigen” is our own cell’s protein, the antibody does come in contact with it again. Autoantibodies act as enthusiastically and forcefully as a regular antibody against a pathogen. The autoantibody signals for an immune response to attack our own body’s tissue and causes damage to that tissue. [7] This tissue damage then causes symptoms. [1][4] 

This is the beginning of an autoimmune disease.

But there’s more to the story! 

Another critical aspect of tissue damage (i.e., symptoms and disease) is the inflammation process. We know that inflammation is a normal and helpful part of healing when it occurs for a short duration. Long-term inflammation, however, contributes to tissue damage and allows autoreactivity to become an autoimmune disease. [7]

This is because the presence of inflammation creates an environment in the body that allows for autoreactivity to occur more freely. [4]

More autoreactivity = more autoantibodies = more tissue damage

Tissue damage causes more inflammation in an attempt to heal, which allows for more autoreactivity to occur, and this becomes a continuous cycle of chronic inflammation and illness. The immune system is always activated, and inflammatory pathways are constantly amplified. [1] .

Essentially, increased inflammation in the body and long-term or chronic inflammation is the main contributing factor in the development of autoimmune diseases.

Analogy Part 2:

Our immune system, specifically our antibodies, will remember any antigen it has come into contact with in the past so that it may recognize it again if exposed.

Remember the analogy from earlier? 

Let’s say that our security guards keep a “not welcome here” photo of past intruders. With autoreactivity, the enthusiastic security guards see our normal cells walking around the building. Our normal cell might be wearing a fancy tophat. But security thinks that it looks just like the “not welcome here” photo of the metal tophat-wearing pathogen. So they mistakenly attack our normal cells just as they would the antigen, sounding the alarm and calling for backup. 

This is autoreactivity and the development of an autoimmune disease. 

Now that we understand the immune system better and know what an autoimmune disease is let’s discuss some treatment options.

Conventional V.S. Naturopathic Approach to Treatment

Conventional Treatment

Conventional treatments tend to be generalized and focus on immunosuppression to address the dysfunction of the immune system found in autoimmune conditions. 

Immunosuppressants will target the immune system unspecifically. This means that both the autoimmune components and the healthy normal immune system will be suppressed. At this point, you’ve already learned about the role that our immune system plays in autoimmune disease, but also how helpful it is to our daily lives in maintaining health and fighting away infection. This is why complete immunosuppression using conventionally prescribed pharmaceuticals has many side effects. For more details on this, read about 14 Natural Ways to Support Your Immune System.

Let’s talk about the different options you may have already encountered. 

Most patients who walk into a conventional medicine clinic with an autoimmune disease will be prescribed one or all of the following: 

Over-the-Counter (OTC) Pain Medication

This includes NSAIDs (Aspirin, Ibuprofen, Naproxen) and Acetaminophen/Tylenol. Some practitioners will even prescribe these OTCs at higher doses. These meds act as anti-inflammatory pain relievers, which are helpful for short-term flares. But ultimately, none of these targets the immune component of autoimmune diseases, meaning a considerable part of the cause of the autoimmune disease is not being addressed.


Next up is the most prescribed drug class worldwide. This includes things like Prednisone or Cortisone shots. They are anti-inflammatory and immunosuppressive. Something to note about these is both the many adverse effects reported and the frequency of side effects. For example, 90% of patients who take a corticosteroid for more than 60 days reported adverse effects. One of the most common adverse effects is weight gain. This is interesting because most patients are told that losing weight will help manage their symptoms, yet they are recommended a pharmaceutical that causes them to gain weight. What an uphill battle!


Methotrexate is an immunosuppressant often prescribed for severe cases of autoimmune diseases. This may also be prescribed to reduce the amount/dose of corticosteroid to minimize adverse effects; however, even at low doses, Methotrexate comes with many documented adverse effects. From nausea and vomiting to hair loss, liver damage, and possible seizure.

This is not to say that conventional treatments should be completely avoided. On the contrary, conventional treatments are a helpful tool to use during severe acute flares of autoimmunity. Where these treatments fall short are long-term healing, individualization, and treating the cause. 

Luckily, these areas are where naturopathic treatments shine! 

Naturopathic Treatment

Naturopathic treatments target the root cause of autoimmune diseases (chronic inflammation, immune dysfunction such as autoreactivity, autoantibodies, and tissue damage resulting in symptoms). 

Rather than immunosuppression, we focus on immune modulation. Essentially, calming the immune system without completely shutting it off. Similarly, inflammation modulators target chronic inflammation without disturbing the healthy healing process.

In addition, we consider the different types of autoimmune diseases and evaluate the patients who come to our office. 

You are more than just an autoimmune disease. You are a person! 

With naturopathic medicine, we treat the person, not the disease. And we do so by treating the cause, not just through palliative symptom management. (Although we do that, too, so you can feel better!)

Here are a few of my favorite naturopathic treatments to address autoimmune diseases.


Have you heard of the anti-inflammatory spice turmeric? Curcumin is the active component of turmeric! Curcumin is a strong inflammation modulator and helps regulate the immune system. There are even research studies supporting the benefits of curcumin on pain and inflammation in several autoimmune diseases.

Vitamin D

Suboptimal and even deficient Vitamin D is extremely common in the USA, especially in Arizona. This is unfortunate because Vitamin D plays many roles in our body, such as maintaining energy, immune function, bone health, hormone production, etc. Not only do we need to make sure we’re getting enough to maintain health, but many pharmaceuticals, such as Prednisone, actually deplete the body of Vitamin D.


This can include many different things depending on the person’s autoimmune disease. An example of dietary recommendations includes a gluten-free diet, which has been shown to help reduce autoantibodies. In addition, elimination diets can be highly beneficial in addressing food sensitivities, which will increase inflammation if not corrected. We also must consider fiber, omega-3 fatty acids, and maintaining the gut microbiome, to name a few other considerations. 

Naturopathic medicine offers many approaches to addressing and reversing autoimmunity. However, the therapies listed above are just the tip of the iceberg.


In this article, you learned about how a healthy immune system functions. First, we discussed how occasional inflammation helps the body to heal. From this, we understood how a dysfunctional immune system, such as chronic inflammation, autoreactivity, autoantibodies, and tissue damage, can lead to autoimmune disease and a significant presentation of symptoms. Chronic inflammation is a serious concern, especially for autoimmune diseases. We also briefly described some common conventional treatments, which target inflammation and are immunosuppressive. In addition, we covered naturopathic treatments, which help to modulate the immune system and manage inflammation. 

There are many tools we use to help manage autoimmune diseases and get you feeling better!

If you want to learn more about how natural medicine can help you manage your autoimmune disease, click here to book your free consultation today with Natural Med Doc! 

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