My website should have been named FunctionalHealth4Autoimmune, because sadly in my office, we uncover a lot of autoimmune issues. According to the American Autoimmune Related Diseases Association, 50 million Americans suffer from some type of autoimmune disease. Per the National Institute of Health, autoimmunity has now become more common than heart disease which affects around 22 million or cancer affecting 9 million.

Researchers have identified 80-100 different autoimmune diseases and suspect at least 40 other diseases having an autoimmune basis. Autoimmune disease is one of the top 10 leading causes of death in female children and women in all age groups up to 64 years of age.

Studies also indicates that having one autoimmune disease makes you susceptible to developing others, so it is really important to uncover issues early to help keep the immune system nice and calm.

What are some common autoimmune disease?

• Addison’s disease
• Celiac disease
• Dermatomyositis
• Graves’ disease
• Hashimoto’s thyroiditis
• Multiple sclerosis
• Myasthenia gravis
• Pernicious anemia
• Reactive arthritis
• Rheumatoid arthritis
• Sjogren syndrome
• Lupus
• Colitis/Crohn’s
• Diabetes
• more…

What is the underlying cause of autoimmune disease?  

We believe that environmental risk factors trigger inflammation that disrupts the proper function of our immune system. 

Let’s try to simplify this. We are born with an innate adaptive immunity called the Th1 response. After we encounter a specific pathogen or antigen, we also create antibodies so that the next we see it, it can be can easily recognize and destroyed. This is called the Th2 response. These two are designed to help when appropriate and back off when they are not needed, maintaining a balance–just like a seesaw. In addition, our immune system is regulated to send help when needed and suppress itself when the job is done. This is referred to as the Th3 regulatory immune system.

With autoimmunity, our bodies start to make antibodies against our own self as well as dysregulate the immune system. There may be imbalance with the Th1/Th2 response as one side becomes overactive and/or the Th3 system forgets when to itself turn off. Th1 dominance may result in inflammation and autoimmunity, while Th2 dominance may result in asthma, allergies, and hyper-sensitivities to environmental factors.

These conditions can lead to an inappropriate inflammatory response called Th17, which ends up ramping up the immune system even more.

Why do we develop autoimmune diseases? 

Our body is designed to detect and protect against foreign invaders. But what happens if the immune system becomes so dysfunctional that it starts to attack our perfectly healthy cells, tissues, organs, or worse, our DNA?  There are a few schools of thought as to why.

Theory 1 : Genetic Susceptibility

The most common theory is that someone is born with a genetic susceptibility to a particular disorder. This doesn’t necessarily mean that they will develop the disease, but if they are exposed to certain risk factors over a period of time, genes may get “turned on”  .Over time, loss of function  occurs and disease develops. Keep in mind, autoimmunity could affect anything produced by the body: cells, tissues, organs, gland, enzymes, hormones, etc.

To see how this works, let’s look at autoimmune thyroid. Hashimoto’s thyroiditis affects 1 to 2 percent of people in the United States and is found more often in women. This disease causes the immune system to attack hormones responsible for thyroid hormone production and disbursement. 

So say you have a genetic weakness with one of  the genes associated with the thyroid such as CTLA4  and you really enjoy eating bread. Maybe you are really low in vitamin D (or have an issue with the VDR gene which makes it difficult for you to utilize it). You might potentially have blood sugar or estrogen swings, some undiagnosed infection, leaky gut, exposure to lots of chemicals, or some other risk factor that causes the gene to express. All of the sudden, your thyroid is not just a gland, but a beast the immune system must slay.

As the immune system tries to defend you, inflammation is generated which causes your thyroid to stop effectively producing hormones. Suddenly, you are gaining weight, losing hair, getting cold, and feeling dogged tired. Finally, you go to see the doctor and they check your TSH and low and behold, it comes back high (see my thyroid article to see why this test is not enough). You are put you on replacement hormone which seem to help, for a short time. But since the underlying cause is an issue with the immune system attacking your thyroid gland and not the gland itself, these hormones do nothing to address root of the problem, which is the inflammation.

With a little inflammation, your thyroid may not work so well and you appear hypothyroid. But what if there is a lot? Hormones may spill out of excessively inflamed tissue and the next thing you know you are having symptoms of hyperthyroidism. And so the game begins, the degree of functionality affected by the amount of inflammation present.

Theory 2: Stealth Pathogens such as Cell Wall Deficient Bacteria

It turns out the immune system may be taking a bad rap in regards to autoimmunity. Instead of being overactive, maybe it is just doing its job by protecting us from “stealth” pathogens such as cell wall deficient bacteria (CWD) like mycoplasma or mycotoxins. Biofilms can also be a contributing factor, but we are going to skip that for now.

There are lots of types of bacteria living in our gut, but CWDs goes unnoticed since they are only 1/100th the size of a normal cell. They act as scavengers by releasing toxins to digest and recycle the garbage left behind by degenerating cells and tissues. CWDs are unable to make cholesterol for themselves so they are commonly located in our cholesterol rich areas such as our brain, muscles, thyroid, liver, glands, joints, and nerves.

So these appear friendly, what is the problem?

Most bacteria, viruses, or fungi have cell walls which make them susceptible to antibiotics. CWD have this amazing ability to shape shift and even shed their cell walls depending on their environment (pH, temperature, oxygen, etc.). This means that many of the antibiotics and immune system tricks that kill other pathogens don’t work against CWD. So if they grow out of control, they can overwhelm our immune system.

Case studies have implicated these microbes in almost every chronic human degenerative, inflammatory, and autoimmune disease. Mycoplasma and Ureaplasma have been found in about 70% of those with Sjogrens and 40% lupus. 

How do the CWD bacteria flourish?

Increased levels of CWD are seen in folks with increased metabolic acidity. This may be caused by a combination of dietary choices, chlorinated water, compromised mitochondria (that lead to production of more acids and less energy), and gut dysfunction which lowers the ratio of good/bad bacteria leading to fermentation. This leads to the proliferation of CWD since they love a high acidic, anaerobic environment.

CWD can also enter the body through overuse of drugs such as antibiotics, synthetic estrogens, and statins, which are really just CWD mycotoxins. Even our food supply contributes with its mycotoxin containing foods like stored moldy grains and nuts as well as antibiotic fed livestock.

How do CWD lead to autoimmunity?

As these colonies continue to grow in unnaturally high quantities, they require more and more cholesterol. Where do they get it? From healthy cells in those critical locations which have been shown to be the birthplace of autoimmune dysfunction. In addition, the toxins produced by CWD may even be more damaging to the immune system.

That being said, the high levels of DNA antibodies and autoantibodies seen in those autoimmune could indicate CWD and/or their toxins destroying cellular DNA causing both it, and the remaining debris to be marked by the immune system for destruction. As more and more cell are destroyed, inflammation increases, tissue is destroyed, loss of function occurs, and the immune system goes into overdrive.

So could some autoimmunity really just be a response to a cascade of CWD infected, cholesterol depleted, dying cells?  And might the Th1/Th2 imbalance be the required response based on the CWD’s current morphology?

Theory 3: Underlying Infection

Another theory that has validity is an underlying infection—be it bacterial, fungal, stealth, mold, parasite, virus or retrovirus. EBV, h. Pylori, Yersinia, and Hepatitis are just a few pathogens commonly linked to autoimmune conditions. Let’s discuss a couple.

COVID-19 and Autoimmunity

A paper released in the January 2021 edition in Frontiers in Autoimmunity, tested the autoimmune response to COVID-19 on 55 target tissues and organs. They found that “SARS-CoV-2 antibodies had reactions with 28 out of 55 tissue antigens, representing a diversity of tissue groups that included barrier proteins, gastrointestinal, thyroid and neural tissues, and more. “

This implies is that if there is a genetic susceptibility in a particular tissue and you have an immune response to the virus, you may be triggering an autoimmune response in that genetically vulnerable area.

This could help explain the diverse symptoms and outcomes associated with COVID infections and possibly the “long haul syndrome” that some folks with COVID are experiencing.. 

“Extensive immune cross-reactivity between SARS-CoV-2 antibodies and different antigen groups may play a role in the multi-system disease process of COVID-19, influence the severity of the disease, precipitate the onset of autoimmunity in susceptible subgroups, and potentially exacerbate autoimmunity in subjects that have pre-existing autoimmune diseases.”

You can read the paper in its entirety here.

EBV and Autoimmunity

EBV is a common infection that has been shown to lead to autoimmunity. Michael P. Pender, MD, PhD, of the University of Queensland proposed that autoimmune is “based primarily on the unique ability of EBV to infect, activate, and latently persist in B lymphocytes, including autoreactive B cells.”

He referenced a sizable body of epidemiologic evidence suggesting that EBV infection was a prerequisite for the development of both lupus and multiple sclerosis — two quite different autoimmune diseases.

“Most people who were interested in this concept thought the connection was through molecular mimicry, whereby a person would mount an immunologic response to components of EBV that resembled structures in the brain in MS or anti-double stranded DNA or other lupus antigens for lupus. This immune response intended to control EBV then by ‘friendly fire’ could lead to organ damage.”

Theory 4: Microbiome

As we mentioned in our posts on microbiome and leaky gut, without healthy gut flora to maintain a healthy gut barrier and immune system, we will have a hard time keeping our immune system under control. 

Theory 5: Toxic Load

The immune system can be either dysfunctional, depleted or overactivated by pathogenic and toxin load. Food, chemicals, certain medications, radiation, etc. can cause a direct immune response or possibly bind to proteins thereby, confusing the immune system and leading to additional triggers of autoimmunity. 

Theory 6; Sulfate Deficiency

According to a MIT scientist, Dr. Seneff, ”Deficiencies in cholesterol and sulfate supplies to the blood and tissues are the most important factor behind modern diseases “. Why? If sulfate supplies are low, the body will attack organs and tissues in order to get the sulfate it needs.

One function of sulfate is that it supplies negatively charged ions which get bound to exterior of our cholesterol. This separation of charge becomes an energy gradient, almost like a magnet, which forces the movement of red blood cells from our artery to our veins. This electrical movement also creates an EMF field that signals nitric oxide (NO) to be released. NO relaxes blood vessels so that the blood can flow easily. You might supply the body sulfate through structured water and sunlight. 

Turns out, NO is the “magical” protein that also creates more sulfates to replenish the supply. Since nitric oxide production is reduced by triggers such as glyphosate, aluminum, and mercury, could the increase in the rise of these toxins be leading to decreased sulfate production which causes the rise in autoimmunity that we are witnessing today?

Autoimmune = 1+2+3+4+5+6+more?

Scientists are now beginning to understand the huge impact our diet, microbiome, and infection and toxic load have on genetic expression and degenerative disease.

But might there also be a “pseudo-autoimmune” as well caused by pathogenic load and an immune system just trying to do its job? And could pathogenic load also contribute cellular debris to possibly feed the CWD? Environmental toxins be paying a huge role? 

We need to respect that individuals will each have their own combination of immune dysfunction patterns, triggers, and reactions and support as such.

What can trigger autoimmunity?

The following have been associated with leading to the expression of autoimmune conditions….

• Gluten issues: linked in the scientific literature to 55 diseases so far
• Insulin surges
• Estrogen surges
• Viral, bacterial, or fungal loads including CWD and biofilm
• Pregnancy
• Heavy metals
• Vitamin D deficiency
• Iodine excess (controversial)
• NF-κB uncoupling: protein that helps code for DNA and regulate immune system
• Leaky barriers
• Stress
• Detoxification issues
• Sedentary lifestyle
• Poor diet
• more….

Can autoimmune conditions be cured?

Unfortunately, autoimmunity is a chronic condition with periods of remission and relapse depending on an individual’s triggers and their environment.

There are 3 stages of autoimmunity that someone may experience:

• Silent: Elevated antibodies with no symptoms or loss of tissue
• Reactive: Elevated antibodies with some symptoms but no noticeable loss of tissue
• Disease: Elevated antibodies with symptoms and measurable tissue destruction.

Please note that it is not the “number” of antibodies that determine dysfunction, but the level of affected tissue. Antibody counts could decrease if our immune system just become too depleted. This may create issues with autoimmune diagnosis or mistakenly lead us to believe we are in remission.

Unfortunately, some folks have autoimmune condition that affect cellular DNA, rather than a select organ or tissue and may become more susceptible greater dysfunction and more frequent cycling between the stages.

How is autoimmunity managed?

We following should be addressed.

• Find any other undiagnosed autoimmunity. If you have one, you may have more.
• Identify the stage of autoimmunity to best determine level of immune support
• Determine lifestyle, dietary protein, chemical, or underlying infection triggers
• Strengthen general immune function
• Improve health of immune barriers: gut/brain/lungs/nose 
• Manage autoimmune “flares” or worsening of symptoms with specialized support

Lifestyle and diet are the most powerful tools that we have to help keep autoimmune symptoms at bay. It is extremely important to get proper sleep (that is where the healing magic happens), participate in light/moderate exercise, consume an anti-inflammatory-mild-ketogenic diet, and reduce stress as much as possible.

Supporting Th1/Th2/Th3/Th17 response often helps to correct proper immune function.

Reducing inflammation is key. Maintaining  gut, immune, liver, adrenal, and brain health, eradicating infections, regulating blood sugar, etc., will provide your immune system a relative vacation, so that when faced with a real pathogen, it can do the job the way it is supposed to.

Is there a diet for autoimmunity?

Unfortunately, your “healthy” diet could be inflammatory for you if you are eating foods that might be unknowingly affecting your immune system. It is important to uncover the trigger foods that promote inflammation (as well as support CWD and yeast overgrowth in the gut) that can lead to intestinal permeability. By calming inflammation in the gut, you will be able to better calm inflammation throughout the entire body.

In addition, diets high in sugar and carbohydrates may be have a greater susceptibility to glycation, which attaches a sugar molecule to a protein or fat. If a protein gets oxidized, it changes shape and may confuse the immune system into thinking it is a foreign invader.

It isn’t sugar alone, foods like lectins and nightshades can also trigger changes in protein structure. Avoidance of gluten and gluten “cross cousin” foods such as dairy is essential. In addition, latex foods have also been shown to upregulate autoimmune. Salt can also be an issue for some.

Eating a diet composed with pH balance in mind provides a better environment to reduce CWD colonies. Additionally, fruits and veggies are high in healthy polyphenols, help enhance the microbiome, stabilize blood sugar, and contain necessary cofactor vitamins and minerals.

Finally, keep in mind that foods can become inflammatory if cooked or combined with other food choices or by not being organically grown. Some folks may need to go to a strict Ketogenic diet with intermittent fasting to best balance blood sugar and inflammation. Basically, each individual responds differently to dietary interventions.

What are the best supplements for autoimmunity?

Vitamin D, essential fatty acids, glutathione (for some), multivitamin, and barrier support are the basics for helping re-regulate the immune system. Opioids obtained through appropriate exercise may also help.

Individualized support of the TH1/TH2/TH3, CWD and biofilm support may be necessary. It is really dependent on an individual’s triggers and imbalances.

Please note that periods of relapse may require more directed support or medication. Support is best done under the guidance of a functional medicine professional or medical doctor.

How can I test for autoimmune disease?

I believe that it is best to first order a comprehensive blood test analyzed by Functional Blood Chemistry Analysis to help find uncover dysfunction that may be contributing to inflammation. In addition, markers such as CRP, SED, ANA, antibody and autoantibody tests are suggested to provide inflammatory status.

Cyrex Labs has a great panel for testing for many antibodies related to specific autoimmune conditions as well pathogenic, food, and chemical trigger antibodies. They also offer a panel to help differentiate immune system imbalances.

You may also have to delve deeper into acquired or innate immunity markers depending on stage of your condition to determine your immune system robustness.