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Exploring the Relationship Between Autoimmune Diseases and Chronic Conditions: Testing & An Integrative Approach to Treatment

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Exploring the Relationship Between Autoimmune Diseases and Chronic Conditions: Testing & An Integrative Approach to Treatment

It’s estimated that autoimmune diseases affect up to 24 million Americans, and there are an additional 8 million who could be at risk. While autoimmunity still isn’t well-understood, it has been well-established that people with autoimmune diseases tend to be at higher risk of developing other chronic diseases like cardiovascular disease, cancer, and type 2 diabetes. This connection is thought to be related, at least in part, to the chronic, low-grade inflammation that underlies both autoimmunity and chronic diseases. 

If you have the symptoms of or have been diagnosed with an autoimmune disease, it’s important to not only understand the connection with these other conditions but also to learn the foundational strategies you can use to keep your inflammation levels in check. In this article, we’ll explore why autoimmune diseases and other chronic conditions often go hand-in-hand, shared risk factors and how to address them, and testing that may be helpful.


What Are Autoimmune Diseases?

The immune system is designed to protect your body from illness and infection. However, in people with autoimmunity, the body begins to see its own cells, tissues, and organs as invaders. When the body mounts this misguided defense, pro-inflammatory mediators are released, and if this inflammatory process can’t be quelled, tissue destruction results, leading to dysfunction and long-term damage.

There are at least 80 identified autoimmune diseases that affect various body parts and systems. Some of the most commonly known are type 1 diabetes, rheumatoid arthritis, inflammatory bowel disease (IBD), psoriasis, multiple sclerosis (MS), and scleroderma. 

While autoimmune diseases still aren’t well-understood, it’s thought that the interplay between genetic and environmental triggers, including gut dysfunction, culminates in triggering a loss of self-tolerance, which leads to the inflammatory cascade and hallmarks of autoimmunity. 

Symptoms of autoimmune diseases include:

  • Chronic fatigue
  • Unexplained fever
  • Muscle and joint pain
  • Muscle and joint swelling
  • Skin problems
  • Digestive distress
  • Swollen lymph nodes

Autoimmune Diseases and Chronic Conditions: How Are They Connected?

Autoimmune diseases are associated with a variety of other chronic conditions, and this may be related to uncontrolled, low-grade inflammation. When the misguided immune-inflammatory response goes unabated, tissues and organs can be damaged. This damage can increase the risk of chronic diseases like cardiovascular disease, cancer, and type 2 diabetes but also increases the likelihood of developing other autoimmune diseases.

In addition, having a chronic disease like obesity may increase the risk of developing an autoimmune disease. Obesity studies have found that pro-inflammatory immune cells replace anti-inflammatory cells in visceral adipose tissue (VAT), which may correlate with systemic inflammation and insulin resistance. This process in the VAT may partly explain the link between metabolic dysfunction and autoimmunity, as well as other chronic diseases. 

The Autoimmune Disease-Cardiovascular Disease Link

Cardiovascular disease (CVD) is the number one killer of Americans. Diabetes is a known significant risk factor for CVD, but people with autoimmune diseases have been found to have a similar risk. For example, people with diabetes have a 12.4% risk of CVD, and people with RA have a 12.9% CVD risk. In addition, people with systemic lupus erythematosus (SLE) have a 4 to 8-time greater risk of developing CVD when compared to healthy controls.

CVD development is related to a chronic inflammatory process, and since autoimmunity often begins in people who are younger, they may experience the negative effects of inflammation for a longer duration. People with autoimmunity can develop vascular lesions and the production of inflammatory mediators in the vascular regions early on. Excess production of CRP, fibrinogen, and cytokines favors endothelial dysfunction, which increases arterial stiffness and increases arteriosclerosis and the risk of CVD events. Pro-inflammatory mediators also increase the production of low-density lipoproteins (LDL) and contribute to plaque instability.

The Autoimmune Disease-Type 2 Diabetes Link

While type 1 diabetes has traditionally been considered the autoimmune form of diabetes, current research suggests that an autoimmune process may also be involved in the pathogenesis of type 2 DM. While many factors culminate to ultimately create type 2 diabetes, losing beta-cell function is a hallmark of both type 1 and type 2. 

For obese patients, there’s an upregulation of pro-inflammatory immune mediators, which creates antigen-driven continual systemic inflammation. While it’s not completely understood, it appears that islet-specific T-cell autoimmunity may increase the loss of pancreatic beta-cell function contributing to the development of type 2 diabetes, at least in some cases.

The Autoimmune Disease-Cancer Link

Evidence suggests that autoimmune diseases increase the risk of cancer. Patients with RA, scleroderma, Sjogren’s syndrome, SLE, and systemic vasculitis have all been shown to have greater cancer risk. And patients with IBD are 4-7 times more likely to develop colorectal cancer.  

Chronic inflammation is a likely culprit in the increased cancer risk. The increased levels of inflammatory mediators found in autoimmunity can lead to DNA damage and increase the genetic instability of cells. 

Shared Risk Factors in Autoimmune Diseases and Chronic Conditions

While genetics likely play a role in the development of both autoimmune and other chronic diseases, it’s the low-grade inflammation over time that may tip the scale in favor of disease development. Inflammation is at the core of both autoimmune and other chronic diseases. While acute inflammation is a natural, healthy, sometimes life-saving process, chronic inflammation signals the body to send out pro-inflammatory mediators on an ongoing basis. This process can be triggered by a variety of lifestyle and environmental factors like poor sleep, unmanaged stress, inflammatory diet, physical inactivity, toxins, medication use, and food sensitivities.  

Leaky Gut

Research suggests that increased intestinal permeability, or leaky gut, is a common denominator in autoimmune diseases and other chronic conditions. Leaky gut occurs when zonulin, a family of proteins that regulate intestinal permeability, is upregulated either via gliadin (a protein in gluten-containing grains) or dysbiosis (an imbalanced gut microbiome). 

Essentially, the delicate intestinal lining is compromised and becomes more permeable than it should be, which allows the contents of the GI tract to seep over into the systemic circulation triggering inflammation and upregulating the immune system response. This process can set the stage for autoimmunity, but also other chronic diseases. 

A great example of this leaky gut-autoimmune connection involves antigen-stimulated pro-inflammatory immune cells, like TH17 cells, which are associated with autoimmunity. Through leaky gut, these TH17 cells can leave the gut and travel through the circulation to other organs and joints and have been found to create autoimmune arthritis.

Common causes of dysbiosis that can trigger leaky gut include the standard Western diet, chronic stress, food sensitivities, medication use, poor sleep, and environmental toxins like pesticides, endocrine-disrupting chemicals, heavy metals, and mycotoxins.

Hormonal Imbalances

There seems to be a bidirectional relationship between chronic diseases (including autoimmunity) and hormones. Meaning hormonal imbalances may contribute to the development of chronic diseases, but they may also be the result of the disease process. The same factors that contribute to leaky gut (chronic inflammation, environmental toxins, and gut microbiome imbalances) can also disrupt hormone balance. 

Patients with Hashimoto’s thyroiditis (an autoimmune condition) have a higher risk of developing hypothyroidism, which results in the insufficient production of thyroid hormone. And altered estrogen levels may increase the risk of some types of autoimmune diseases in women. In addition, insulin dysregulation (a hormone that regulates blood sugar) increases the risk of developing type 2 diabetes and cardiovascular complications.

Functional Medicine Labs to Test For The Root Cause of Autoimmune Diseases and Chronic Conditions

Since autoimmune diseases and chronic conditions tend to have similar root causes, there are several functional medicine tests to consider for early detection.

Comprehensive Stool Test + Zonulin

The GI-MAP with Zonulin from Diagnostic Solutions detects microbial imbalances, microbes contributing to illness, and indicators of digestion, absorption, inflammation, and immune function- all important factors in autoimmune disease. This test also includes zonulin, a leaky gut marker.

BostonHeart Diagnostics

BostonHeart Diagnostics offers several helpful labs, including a basic lipid panel (LDL, HDL, triglycerides), a high-sensitivity CRP (hs-CRP), and two unique tests called the HDL Map Test and the Cholesterol Balance Test. These panels go beyond the basics to provide multiple markers of cardiac risk, as well as a unique analysis of cholesterol synthesis and HDL particle size. Together, these allow practitioners to better understand their patient's cardiac risk in order to personalize their recommendations.

Food Sensitivity Testing

The Array-10 Multiple Food Immune Reactivity Screen by Cyrex Laboratories is a food sensitivity test that measures the body’s immune response to various foods. This test analyzes blood samples for IgG and IgA antibodies against common food proteins. Food sensitivities may be one driver of inflammation, which is a root cause of autoimmunity and other chronic diseases. Identifying food sensitivities in an individual will help practitioners tailor meal plan recommendations.

Micronutrient Testing

The SpectraCell Micronutrient Test analyzes 31 vitamins, minerals, and other nutrients to determine nutritional deficiencies, but it also analyzes the performance and functional micronutrient deficiencies. Poor nutrient status can increase the risk of inflammation and insulin resistance. Practitioners can use this test to determine which nutrients a patient needs to highlight in their meal plan.  

Comprehensive Thyroid Panel

A Thyroid Panel (with TPO and Tg antibodies) measures thyroid peroxidase (TPO) and anti-thyroglobulin (TG) antibodies and can be used to diagnose Hashimoto’s thyroiditis and Graves’ disease, two autoimmune diseases that affect the thyroid gland.


This test assesses for a comprehensive array of sex and adrenal hormones to determine imbalances. This test also measures cortisol, the main stress hormone produced by the adrenals. Finally, the DUTCH Plus measures a number of organic acids (hormone metabolites measured in the urine) that have important roles in the metabolism and function of enzymes required for hormonal health.

Additional Lab Tests 

Anti-Nuclear Antibodies (ANA): A positive ANA test means autoantibodies are present, but this isn’t diagnostic, so additional testing will need to be completed. 

C-Reactive Protein (CRP): A high CRP, usually above 3.0, can indicate inflammation and immune activity and may help screen for autoimmune disorders.

Erythrocyte Sedimentation Rate (ESR): A high ESR can indicate an immune disorder.

Extractable Nuclear Antibodies (ENA): The ENA panel is ordered as a follow-up after a positive ANA test if a person also has signs of an autoimmune disease. This blood test looks for several different proteins and helps to distinguish between autoimmune disorders.  


Integrative Treatment for Autoimmune Diseases and Chronic Conditions

Conventional treatments for autoimmune diseases are often lacking because they aren’t specific to the autoimmune disease. For example, immunosuppressive drugs, the most common medications used for autoimmunity, work by reducing the response of the immune system. They don’t, and can’t, specifically target the dysfunctional segment of the autoimmune system only. These types of drugs have serious side effects, like increasing the likelihood of life-threatening infections and cancer. 

An integrative approach that targets the root causes of chronic inflammation, like poor gut health, can provide much symptom relief and may help to reverse the development of autoimmune and chronic diseases. Since diet is a main risk factor for gut dysfunction and inflammation, it’s a great first place to start.

Nutrition Guidelines for Autoimmune Diseases and Chronic Conditions

The nutrition plan will ideally be personalized to address any specific food sensitivities since they’re a trigger for leaky gut. But in general, people with autoimmunity and other chronic conditions can benefit from starting with an anti-inflammatory diet. The Mediterranean diet is a great initial option that’s been well-researched, but any diet that eliminates ultra-processed foods, sweets, sugary beverages, inflammatory fats, refined grains, and alcohol will help to quiet inflammation. 

However, targeting inflammation isn’t just about removing certain foods. It’s also about bringing in nourishing, anti-inflammatory foods like fruits, vegetables, beans, nuts, seeds, whole grains, herbs and spices, tea, fish, and healthy fats. If the diet is already pretty healthy and symptoms aren’t well-controlled, then a more restrictive elimination diet, like the autoimmune protocol diet, may be necessary.

Supplements & Herbs for Autoimmune Diseases and Chronic Conditions

While an anti-inflammatory diet is foundational for addressing the root causes of autoimmune diseases and other chronic conditions, several spices and supplements have been shown to improve gut health and inflammation.


Ginger has multiple bioactive compounds, such as gingerols, shogaols, paradols, and zingerone, which are responsible for its medicinal and anti-inflammatory effects. It has been shown that ginger can modulate the immune system response and limit inflammatory pathways, and it has anti-inflammatory effects similar to non-steroidal anti-inflammatory drugs. Ginger also targets gut health by inhibiting pro-inflammatory responses in the large intestine.


Curcumin, the active compound found in turmeric, can down-regulate pro-inflammatory mediators in a variety of chronic diseases and may be helpful for lowering inflammation in the gut. Bioavailability can be improved when curcumin is combined with piperine (black pepper).

Omega-3 Fatty Acids

Omega-3 fatty acids found in fatty fish, including eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), have been found to significantly lower inflammation in the body, and they may act as prebiotics for healthy gut bacteria. Since the body can’t make these essential fatty acids, they must be obtained in the diet or from dietary supplements. An anti-inflammatory diet will include at least two servings per week of fatty fish (salmon, mackerel, herring, trout, and sardines). Omega-3 fatty acid supplements are also an option.


Probiotics provide an anti-inflammatory benefit in the gut and beyond. Not only do they help reestablish balance in the gut microbiome, but they also help to protect the tight junctions of the small intestine, helping to prevent leaky gut. They can produce short-chain fatty acids to reduce inflammation in the colon, and they upregulate polypeptides that lower inflammation. In addition, probiotics help to decrease the translocation of lipopolysaccharides (LPS – bacterial endotoxins) from the gut into the systemic circulation. This serves to reduce the immune system burden and lower inflammation outside the gut.

Complementary and Integrative Medicine Treatment Options

While diet and supplements can be very effective, there are other valuable complementary and integrative treatments for autoimmune diseases and other chronic conditions.

Lifestyle Strategies for Managing Autoimmune Diseases and Chronic Conditions

Unmanaged, chronic stress can significantly impact gut and immune system function. Stress increases inflammation and dysbiosis, which increase the risk of leaky gut and the cascade of inflammatory events that lead to autoimmunity and chronic disease development. Practicing a daily stress-management technique may help to reverse this process. 


Yoga may provide a variety of benefits for those with autoimmunity and other chronic diseases by reducing the levels of inflammatory mediators and improving immune system function. In a study of people with RA, yoga improved mental health, as well as physical symptoms like pain and range of motion. In addition, yoga can help promote higher heart rate variability (HRV), a measure of autonomic nervous system health, and may improve a variety of cardiovascular risk factors like hypertension.


Meditation reduces the levels of stress hormones and perceived stress, and it can reduce inflammatory markers like CRP.

Deep Breathing

Intentional, deep breathing techniques can lower stress levels and help shift the body from the sympathetic nervous system to the parasympathetic nervous system. HRV improved in people with RA and SLE after 30 minutes of deep breathing practice. 


Healthy amounts of exercise have been shown to help rebalance the nervous system, but exercise may also help to modulate the gut microbiome and reduce chronic disease risk factors like high blood pressure and insulin resistance.



Autoimmune diseases occur when the body can no longer determine friend from foe. Instead of attacking bacteria, viruses, and toxins, the immune system begins to attack the body's own tissues and organs, leading to damage. The misguided immune system response and resulting chronic inflammation in people with autoimmune diseases increases the likelihood that they’ll develop other chronic conditions like cardiovascular disease, type 2 diabetes, and cancer. Likewise, having a chronic condition like obesity may also increase the risk of developing an autoimmune disease.

Chronic inflammation is a common feature of both autoimmune diseases and other chronic conditions, so it’s a great target for integrative providers. By addressing the root causes of inflammation like poor gut health, unmanaged stress, and hormonal imbalances with nutrition, supplements, and lifestyle, it’s possible to significantly improve quality of life and disease parameters.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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