The Functional Medicine Solution for Autoimmunity

The Functional Medicine Solution for Autoimmune Disease

If you’re reading this article, chances are you have an autoimmune disease or know someone who does.

These chronic conditions, once considered rare, have exploded in the last 30 years.

Part of this is due to a better understanding of the over 80 autoimmune diseases in general and their symptoms. Which, up until recently, were too often labeled as mental health, stress-related, or “just hormonal issues” (and sadly, this still happens a lot).

But there is more to the story than that.

And if you’ve been diagnosed with an autoimmune condition like Hashimoto’s, Celiac disease, inflammatory bowel disease, lupus, multiple sclerosis, rheumatoid arthritis, psoriasis, etc. you know how frustrating it is to be told: “You’ll have this disease forever. There’s nothing we can do but try to manage your symptoms with these very expensive and powerful drugs.”

You want to know why you developed an autoimmune condition in the first place.

Especially if you receive a diagnosis when you’re supposed to be in the prime of your life, have just become a parent, or are finally starting to enjoy your retirement.

Yet, many doctors are unaware of the new research about the autoimmune triad: the three common causal factors behind most autoimmune disease. And if you don’t know what’s causing a disease, you have very limited treatment options to offer.

In this article, you’ll discover the facts and latest science on autoimmune disease. Including: what it really is, what causes it (“the triad”), why women are affected more than men, and what you can do to treat it and get your life back.

If you’ve been told there’s no hope but drug-based symptom management, I’m here to tell you—as an autoimmune patient and functional medicine physician—that’s simply not true.

So let’s dive in and get to the root cause behind autoimmunity and how to address it.

What is autoimmunity?

In the simplest terms, autoimmunity is a chronic condition in which your immune system attacks healthy tissue such as your thyroid, skin, joints, etc.

As we touched on in the introduction, autoimmune disease has become a gigantic issue in the last few decades. With varying kinds now affecting an estimated 1 in 5 (20%) Americans…and that’s just in the United States! 1

There are over 100 known autoimmune conditions as of this writing. 2, 3

Some of the most common include: 4, 5

  • Type 1 Diabetes
  • Psoriasis/Psoriatic Arthritis
  • Hashimoto’s Thyroiditis
  • Lupus
  • Inflammatory Bowel Disease (Crohn’s, Ulcerative Colitis)
  • Rheumatoid Arthritis
  • Multiple Sclerosis
  • Celiac Disease
  • Addison’s Disease
  • Grave’s Disease
  • Sjögren’s syndrome

Despite the growing number of cases, it’s still very difficult for autoimmune sufferers to get an accurate diagnosis and typically takes years and lots of doctor’s visits.

This is largely because the symptoms vary person to person, are non-specific, may come and go in frequency and intensity, and can mimic those of other conditions.

Plus, not all practicing physicians are equally skilled or trained to recognize them and run the appropriate diagnostics. This isn’t your doctor’s fault, but most of us just weren’t taught about this at-length in medical school. Various specialists have additional training in autoimmune diseases – such as rheumatologists.

To make it more difficult, there isn’t one single catch-all diagnostic test. For example, if autoimmunity is suspected, the standard first course of action is to order antinuclear antibodies (ANA). And although a positive result coupled with symptoms indicates the need for further testing, a negative result doesn’t necessarily mean you don’t have an autoimmune condition. Regardless, additional tests are usually warranted.

Bottom line: it takes a lot of additional skill, knowledge, and experience to get good at autoimmune diagnosis.

Now, if you’re thinking: “Wait a minute, my immune system is supposed to protect me. Why would it betray me?” Then bravo! You’re already on the right critical thinking path to understanding autoimmune disease.

It’s true that if you have an autoimmune condition your body is damaging its own tissue. This is what causes the unpleasant symptoms like fatigue, rash, achy joints, weight gain, etc.

However, your body has not betrayed you. Nor is it out to get you. On the contrary, it’s trying to protect you.

The problem is that somewhere along the way, your immune system became confused, its signals got scrambled, and now your healthy tissue is caught in the cytokine crossfire.

Why and how did your body get confused in the first place? And why didn’t our parents and grandparents seem to have these same problems in their youth?

Conventional medicine says, “We don’t know why this happens in some people and not others. It may be genetic and/or environmental”.

However, the evidence is clear that a specific combination of factors contribute to the formation of autoimmune disease.

In other words: autoimmune disease isn’t random, or even entirely genetic or lifestyle-driven. It results from a combination of root causes that affect people differently.

What causes autoimmune disease?

Speaking from first-hand experience as a person with an autoimmune disease and a doctor who treats it extensively, I can tell you it’s a really difficult disease to live with.

It can also be invisible. Meaning, even when you don’t feel well, you may look well, which can lead some people (and doctors) to dismiss symptoms.

The symptoms can range from mild but annoying, to incessantly irritating, to completely debilitating. Plus, like I mentioned before, getting an accurate diagnosis can be almost a full-time job.

Then, once you finally have a diagnosis, your treatment options can be scarier than the disease itself in terms of dangerous side effects, quality of life, and financial burden.

The conventional approach to autoimmunity is to suppress the overall immune response using powerful immune-suppressive drugs.

This kind of makes sense in terms of managing symptoms in a short-term one-size-fits-all approach (and there is a time and place for this sometimes).

However, this approach fails to address what’s actually causing the immune response in the first place. Not to mention (but I will) how it increases your risk of other health issues by partially shutting down your immune system.

When it comes to any medical decision making, I’m all about risk vs. benefit. And if the risks outweigh the benefits, it’s time to keep looking for better solutions.

So, what’s causing this rise in autoimmune disease?

Earlier I hinted at the role of genetics and environment, but we now know they’re only part of the autoimmune triad.

In the vast majority of cases, it takes three underlying causes to create a full-blown autoimmune disease:

#1: Genetics

#2: Environment

#3: Intestinal hyperpermeability (aka gut health)

We’ve known about the role genetics play in autoimmunity for some time. 6

And if you and your mother or grandmother all have rheumatoid arthritis or Hashimoto’s, for example, you’re aware of this connection too.

However, since not everyone with a family history always develops autoimmunity, we knew this wasn’t a blanket cause. There had to be other factors at play.

Thankfully, new research has surfaced about the roles of environment/epigenetics (the way environment affects gene expression) and gut health in autoimmune risk. 7, 8, 9

With regards to environment, there’s a saying in functional medicine: “Genes load the gun, and environment pulls the trigger.” In other words, just because you have a genetic predisposition to a disease or disorder, doesn’t mean it will manifest…unless something triggers it.

Environmental triggers for autoimmune disease are different for everyone and may include: mold/mycotoxin exposure, trauma of any kind, heavy metals, toxic body burden, radiation, chronic stress, medications, a food sensitivity, chemical exposure, sleep deprivation, undiagnosed infections, breast implants, smoking, or a combination thereof.

Then there’s the “missing link” known as gut health. 

Up until recently, genetics and environment were the main two recognized causes of autoimmunity. But they didn’t explain the entire picture.

Then, about ten years ago physician and researcher Dr. Alessio Fasano showed that intestinal barrier function plays an important role in autoimmunity. 10

He proved that when intestinal barrier function is compromised (aka: Intestinal Permeability, informally known as “Leaky Gut Syndrome”), the body’s ability to regulate the immune response becomes imbalanced which can be a causal factor in autoimmune disease.

In his research, Dr. Fasano identified a protein called zonulin, which is released in the presence of small intestinal exposure to bacteria (SIBO) and gluten, among other environmental triggers. 11

Zonulin has been shown to influence the tight junctions in the gut—thus causing an increase in intestinal permeability and autoimmune disease in genetically susceptible individuals.

This discovery was a game-changer, because it brought all the pieces together in the autoimmune-etiology-puzzle.

And once we understood this triad of causal factors, we could develop targeted strategies to address the disease at its root vs. just treating the symptoms.

Why are women more affected by autoimmunity than men?

Great question! The answer is: we don’t know for sure, but we do have some clues.

About 84% of people living with autoimmune disorders 12 are typically women of childbearing age.

Some theories behind this are:

  • Gender differences in immunity—science has shown that the female immune system is more sophisticated than a man’s 13 , which makes sense given that women are able to carry babies. Women naturally have stronger inflammatory responses than men when their immune systems are triggered, and inflammation plays a key role in many autoimmune diseases.
  • Sex hormones—many autoimmune diseases tend to improve and flare along with female hormonal fluctuations. This suggests that hormones and hormonal events such as the menstrual cycle, pregnancy, birth, lactation, postpartum, perimenopause, premenopuase, menopause, and post-menopause may play a role. 14
  • Genetic susceptibility—there is some evidence that variations in the X chromosome may be related to susceptibility to certain autoimmune diseases. 15

But, as you just learned, genetics alone are not a reliable predictor of risk.

This may be due to those hormonal fluctuations we just discussed or the stress and sleep deprivation that accompanies childbirth and adjusting to the life change. New research has also shown a link to microchimeric fetal cells with the onset of autoimmunity after pregnancy. 17

  • Th cell immunity—T helper (Th) cells play an important role in the immune response, especially during pregnancy. These incredible cells help modulate the mother’s maternal immune response, keeping both you and your baby as protected as possible from pathogens. However, these changes in Th cell immune response can also drive the progression of certain autoimmune conditions, resulting in flare-ups or first-time diagnosis postpartum. 18

The science is far from settled on why women are at higher risk of autoimmune disease than men (especially postpartum).

But now that we understand the three causal factors (genetics, environment, and gut health), coupled with the additional points just outlined, you can see why women are more susceptible.

What is the functional medicine approach to autoimmunity?

In functional medicine our goal is always to treat the individual root cause(s) of disease.

Thus, the treatment strategy for autoimmune conditions is to address the causal factors that we can influence: environment and gut health. And these will be different for everyone.

As a functional medicine doctor, environmental toxins are always of particular interest to me.

We know that medical conditions linked to toxic chemicals include: obesity, metabolic syndrome, diabetes, cardiovascular disease, Alzheimer’s, Parkinson’s, cancers, fibromyalgia, multiple chemical sensitivities—and as mentioned, autoimmunity.

But we really aren’t taught a lot about this—including how to avoid toxins—in medical school.

So, how do we address the environmental causes?

This is all about avoidance, avoidance, avoidance.

If needed we can use labs and other diagnostic techniques to identify which toxins are causing trouble. Some examples include: heavy metals, mold/mycotoxins, plastics, pesticides and phthalates.

In addition, we almost always run specific tests to check for gut infections and intestinal permeability. Because the environmental causes and gut health issues typically coexist (although both issues vary person to person).

Once we have that data, we put together a strategy to help address toxins and begin healing your gut.

This strategy will look different for everyone based on their unique health history, environmental triggers, specific gut health issues, autoimmune symptoms, co-infections, symptoms, food sensitivities, goals, timeline etc.

However, there are some universal healing principles that can generally benefit anyone with autoimmune disease:

  • Eliminate gluten and other trigger foods—this varies for every person, but I consistently recommend eliminating gluten because of Dr. Fasano’s research mentioned above, which shows the connection between gluten, zonulin, and autoimmunity.
  • Eat a nutrient-dense diet—think whole, unprocessed foods, and healthy fats (like olive oil, avocado oil, olives, nuts, seeds, and omega-3-fats from wild-caught fish like salmon and sardines). Cut back or eliminate refined carbs, refined sugar, artificial sweeteners, and alcohol.
  • Reduce stress—this is imperative because stress can cause autoimmune symptoms to get worse and/or re-surface and it’s been shown to increase intestinal permeability.
  • Get enough sleep—that’s 7-9 hours per night for adults. If you struggle to sleep, ask your doctor about natural supplements such as passionflower, chamomile, melatonin, and magnesium.
  • Remove heavy metals from your life—these may come in the form of food sources (such as large fish like tuna), mercury dental amalgams, or other sources. If you have dental amalgams (silver fillings) be sure these are removed safely by an IAOMT certified dentist (otherwise just leave them alone).
  • Eliminate as many chemicals from your environment as possible—It’s kind of crazy how many toxins are hiding in cleaning products, cosmetics, foods, plastics, laundry detergent, air fresheners, etc. And this is one area we can absolutely control! I have a whole free download on 12 Ways to Detox Your Home you can grab here.
  • Exercise daily—about 30 minutes a day is optimal for most people, but listen to your body and adjust accordingly based on your level of health and fitness. Not everyone benefits from high intensity workouts, but we all need to move.
  • Talk to your doctor about supplements that support a healthy inflammatory response—some to look into include: omega 3s, curcumin, boswellia, vitamin D, magnesium, ashwagandha, and a high-quality multivitamin.
  • Talk to your doctor about Low Dose Naltrexone (LDN)—this is an off-label compounded medication that may help modulate the immune system in a positive way, with minimal risks/side effects.19, 20, 21, 22

Is autoimmune disease reversible?

Autoimmune disease is not reversible. However, we can put it into remission.

Successful remission depends on the severity of the condition, the amount of damage that’s been done, the skill of the physician in diagnosing and treating autoimmune disease—along with other causal or contributing factors, and at what level the patient is willing or able to make (and stick to) the changes necessary to heal.

Treatment is all about reducing your symptoms and improving your quality of life. This might look like having enough energy to enjoy your life again, finally losing weight, falling asleep easily and sleeping through the night, having clearer skin, getting pregnant, or finally getting rid of the brain fog that’s been plaguing you for years.

The point is, even if you are unable to technically “reverse” your condition, you can still feel like yourself again.

I also have some patients who whip their condition into remission, only to have it return years later due to a very stressful life event… This is disheartening, but it’s something to be aware of with a major life event.

The good news is, when you know your triggers, you have the tools to get back on track. That’s the empowerment that comes from educating yourself and addressing the root cause.

Interested in exploring a functional medicine approach to autoimmunity?

My team and I are all personally and professionally highly experienced in helping people overcome autoimmunity (you can read all about our own journeys to health here).

Click here to learn more about functional medicine consultations (available for residents of Michigan, Colorado, and Texas), or apply to be a patient to tell us about your specific case.

And whether you contact us for help or go elsewhere (hopefully to a functional medicine practice), do not give up on yourself. Despite what you may have been told, autoimmunity doesn’t have to ruin your life. We know the causes and there are solutions…you just have to find the right support.

Not in our tri-state area? I’d still love to keep in touch (as I will likely broaden my scope of practice in the future). Click here to join the mailing list and/or join the fun on Instagram @drchristinemaren and 



About Dr. Maren

Christine Maren D.O., IFMCP is a board-certified physician and the founder of a virtual functional medicine practice in Colorado, Michigan, and Texas.  She is best know for her work in thyroid, gut and reproductive/ preconception health. Dr. Maren is board-certified by the American Board of Family Medicine and is an Institute for Functional Medicine Certified Practitioner (IFMCP)

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