Can You Improve Your Autoimmune Condition with Functional Medicine?

Discover how a Functional Medicine approach to autoimmunity can help you feel better...

Autoimmune disease affects hundreds of millions of people worldwide, and rates are increasing (1).

There are four million people in the UK known to be living with at least one autoimmune disease.

And about 25% of those with one autoimmune condition will develop more than one autoimmune condition.

What is autoimmunity?

Functional medicine approach to autoimmunity - picture of woman in purple light

Autoimmune diseases are conditions that occur when your immune system attacks your body.

The immune system is a natural defence mechanism that is designed to attack and destroy foreign substances or antigens.

When your immune system senses a foreign invader, it produces and deploys special cells to destroy the threat.

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In autoimmune diseases, the immune system mistakenly attacks healthy cells or tissues.

The immune system is composed of a complex network of cells that, when they work correctly, are able to distinguish between what is ‘self’ (your own cells) and what are foreign invaders – such as germs – that need to be destroyed.

Autoimmune conditions happen when the immune cells can’t tell the difference between your own cells, and foreign invaders that need to be destroyed.

When this happens, the immune system mistakenly produces a response, destroying normal, healthy cells and tissues.

The type of tissue the immune system attacks will determine which autoimmune condition manifests.

If the immune system attacks the thyroid gland, then either Graves or Hashimoto’s disease may develop.

If the immune response is focused on the joints, then Rheumatoid Arthritis may develop.

If the immune response attacks the gut lining, then Crohn’s or colitis can develop, or as seen in SLE (Lupus) many parts of the body may be affected; joints, skin and internal organs. 

Autoimmune conditions affect women more than men, with women being affected at a rate of 2:1 compared to men (6.4% of women are affected by autoimmune conditions but only 2.7% of men are).

Autoimmune conditions can begin anytime from the mid-teens to the mid-40’s.

Susceptibility to autoimmune conditions also seems to show some genetic link, with some conditions running in families, and others being more prevalent in specific ethnic groups.

Studies suggest that the number of people with autoimmune conditions is increasing over time.

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Do you suspect you have an autoimmune condition?

Many people who attend our Functional Medicine clinic come to us because they have been diagnosed with an autoimmune disease, and want to improve their quality of life by reducing their ‘flare ups’, or by reducing their medications.

Some clients have no diagnosis but come to us searching for answers to the array of unexplained symptoms they are experiencing, and those symptoms turn out to be autoimmune related.

Or sometimes people come to our Functional Medicine clinic because a family member has autoimmunity, and they want to prevent acquiring an autoimmune condition themselves, as they’ve heard that autoimmunity can run in families.

Using a Functional Medicine approach to autoimmunity enables our team to establish the root cause of your symptoms and to get you on the path to recovery again. 

Signs and symptoms you may have an autoimmune disease

Some common signs and symptoms of autoimmune disease are:

Symptoms of autoimmune disease vary depending on the disease, and exactly which tissues in the body are being attacked by the body’s own immune system.

What autoimmune diseases are there?

There are over 80 different types of autoimmune diseases (2) but below are some of the common systems affected, together with the related autoimmune condition.

Many of these conditions can overlap, affecting multiple systems in the body:

 Brain: multiple sclerosis, Guillain Barre syndrome, autism

Thyroid: thyroiditis, Hasimoto’s, Graves’ disease

Bones / joints: rheumatoid arthritis, ankylosing spondylitis, polymyalgia rheumatica

Muscle: muscular dystrophy, fibromyalgia

Skin: psoriasis, vitiligo, eczema, scleroderma

Lungs: fibromyalgia, lupus

Nerves: peripheral neuropathy, diabetic neuropathy

GI tract: coeliac disease, Crohn’s disease, ulcerative colitis, diabetes type 1

Blood: lupus erythematosus, haemolytic dysglycaemia

It is possible to have more than one autoimmune disease, and when you have one autoimmune condition, there’s a chance you’ll develop a second or even third autoimmune condition (3). 

To understand autoimmunity, let’s first look at how the immune system works

What is immunity? 

The immune system has two aspects to it – the innate (born with) and the acquired (learnt). 

The innate immune system

The innate immune system is both a detective, scanning the body for potentially threatening invaders, and a first responder, destroying pathogens and prompting repair (4).

The innate immune system is the gatekeeper for coordinating the body’s entire immune response, and its simple defence strategies rely chiefly on: 

The acquired immune system

The acquired immune system features:

that recognise billions of different molecules, with even higher specificity and memory than the innate immune system, but it is slower to respond.

There are two parts to the acquired system:

Central to the immune system’s ability to mobilise a response to an invading pathogen, toxin or allergen is the ability to distinguish self from non-self (5).

The ability of the immune system to tell the difference between what is the self, and what is an invader, is the key to autoimmune conditions, and this is what goes wrong in autoimmunity.  

Is autoimmunity curable?

Other diseases, for instance infections, can be cured by killing the bacteria or virus that causes the infection.

Autoimmunity isn’t like that.

Autoimmunity can’t be cured, because once it’s ‘switched on’, your immune system can’t simply be switched off.

So autoimmunity is not curable in that sense.

But autoimmune disease is manageable, and it can be put into remission, especially with a Functional Medicine approach to autoimmunity.

One of the goals in a Functional Medicine approach to autoimmunity, is to promote immune tolerance to self-tissue in order to help reduce the amount, duration and intensity of autoimmune flares.

Supporting T regulatory cells is key to this approach.

T regulatory cells are a type of cell that helps to dampen down the immune response that is attacking ‘self’.

And that’s really important in autoimmunity.

While we’re talking about helping the immune system, there’s also an important distinction to be made between this Functional Medicine approach to autoimmunity, and the medication route.

While we’d look to support natural T regulatory cells that have a ‘modulating’ effect on the immune system, immunosuppressive medications act by ‘turning off’ the immune system.

Turning off the immune system can have some undesirable side effects, as, at the same time as you’re stopping the immune system attacking your own tissues, you’re also lowering your defences to other harmful pathogens.

While we’ll cover the Functional Medicine approach to autoimmunity more in a minute, implementing an approach where inflammation is reduced is really helpful.

If we can reduce the inflammation associated with autoimmune diseases, our clinical experience is that this can help people to feel better, have improved quality of life, and be less reliant on medications.

So while autoimmune conditions aren’t curable, our experience is that there are strategies that can significantly reduce, or put into remission, the processes that are causing the undesirable symptoms.

What’s the conventional medicine approach to autoimmunity?

Most conventional medical treatments for autoimmune conditions focus on suppressing the symptoms caused by the autoimmune response.

This can include immunosuppressive drugs to suppress the immune system, or corticosteroids, which are suppress inflammation and help reduce pain.

As with most if not all conventional medical treatments, there’s a time and place for them, despite the side effects.

With that in mind, let’s cover some of the medication options.

Drugs to manage autoimmune disease symptoms


Many clients with autoimmunity suffer with pain (6) which is often managed with Non-Steroidal Anti-Inflammatory Drugs (NSAIDs).

These are excellent at managing pain, and work by affecting prostaglandin production, which is responsible for the pain.

Unfortunately, these prostaglandins also support the mucosal layer in our digestive tract, and so NSAIDs can cause gastrointestinal related side effects such as nausea and diarrhoea.

NSAIDs can also increase intestinal permeability (leaky gut) (7) which as we explain below, can further exacerbate autoimmune disease.

Examples of these medications are Ibuprofen, Diclofenac, and Naproxen. 


Steroids, also known as corticosteroids or glucocorticoids, are used to help control many forms of inflammatory conditions.

These steroids occur naturally in the body, and are produced by the adrenal glands.

But when given as medication, they work quickly and powerfully to reduce the symptoms of inflammation and pain.

However, steroids tend to be used sparingly because of the many side effects, which include:

Prednisolone is one of the  most common steroid medications used.


Opioids are often used to treat chronic pain despite this class of drug having many side effects, such as:

Examples of commonly used opioids are Codeine and Tramadol.

Drugs to manage autoimmune disease

Disease-modifying antirheumatic drugs (DMARDs)

Disease-modifying antirheumatic drugs (DMARDs) are a class of medication that are indicated for the treatment of several inflammatory autoimmune diseases that affect the musculoskeletal system, including:

as well as for management of other connective tissue diseases such as:

This class of medication can work well, but unfortunately, they can take anywhere from 12-weeks to 6 months to provide benefits.

They also come with individual side effects, including:

Examples of DMARD medications are methotrexate, leflunomide, hydroxychloroquine, Azathioprine, Cyclosporine and sulfasalazine. 

Biological drugs

Biological drugs were introduced in the early 1990s, and are usually prescribed when conventional DMARD therapy has failed, where there is ongoing disease activity, or where there is clinical or radiographic disease progression.

Biological drugs are highly specific drugs, that are also called monoclonal fusion antibodies, and their aim is to block the production or biological activity of cytokines.

Cytokines are a group of important signalling molecules (protein mediators) produced by the immune system. 

They help to control the immune system, inflammatory processes, and fight disease.

Dysregulation of these cytokines plays a major role in the disease process of autoimmunity (10).

There are more than 100 cytokines in the body, but only a few are linked to autoimmunity.

One type of cytokine that you may have heard of is TNF-alpha (which plays a role in the inflammatory process in Rheumatoid Arthritis).

Biological drugs can be used on their own, but higher efficacy can be achieved when combined with Methotrexate (11).

Examples of biological drugs are Etanercept, Infliximab, Adalimumab, Rituximab, Abatacept, Tocilizumab.

JAK inhibitors

JAK Inhibitors, like biologic drugs, are ‘targeted’ therapies, which work by influencing the immune response and inhibiting cytokines.

Unlike the biologics, they can be taken in tablet form.

Examples of JAK Inhibitors include Tofacitinib and Baricitinib. 

Biosimilar medicine

Biosimilar medicine is a biological medicine manufactured to be similar to existing, licensed biological drugs.

There are no meaningful differences from the original biological medicine in terms of quality, safety or efficacy.

Biosimilar medicines represent very good value, since they are often much less costly than the original medicine, although the same side effects can still occur as with the original biological drugs. 

Adverse effect from these drugs include:

Despite new advances in these biological and DMARD drugs, which can improve patient outcomes, many conditions do not achieve remission (13).

We also have to remember that these forms of treatment do not cure the disease, and clinical symptoms can unfortunately recur after treatment is stopped.

How can a Functional Medicine approach to autoimmunity help?

To help understand how a Functional Medicine approach to autoimmunity can help, we need to first explore how autoimmune diseases develop (the pathogenesis of autoimmune disease). 

The development of autoimmune diseases is complex and highly individual, however they are all influenced by the following triad of factors:

1. Genetic predispositions to autoimmunity

Different genetic factors are linked to the susceptibility of developing autoimmune disease, which specific auto-antibodies one is likely to produce, and the type of autoimmune disease that could manifest (14). 

One gene which is significantly associated with many autoimmune conditions is the HLA gene. 

We see this both in reported statistics, and in our clinical experience, that autoimmunity often runs in families.

2. Environmental triggers

Our modern day environment is often full of hidden toxins – chemicals that put a strain on our immune system and that affect our ability to detoxify normally.

There are many environmental triggers for autoimmunity, such as:

3. Increased intestinal permeability (commonly referred to as ‘Leaky Gut’)

Normal intestinal permeability exists to help absorb nutrients from the intestinal system into the blood, so nutrients can be transported to our cells.

However, issues arise when the intestinal barrier is more permeable than it should be i.e. increased intestinal permeability / leaky gut.

This physical state is strongly implicated in the onset and progression of autoimmune conditions (15).

Or for a more specific, in depth version of how a leaky gut / increased intestinal permeability can cause autoimmune conditions, take a look at the graphic below:

An unhealthy, leaky gut barrier leads to over activation of the immune system.

Think of this triad like the triad needed to fuel a fire –

Genetics (wooden log)


Trigger/s (fuel + match)


Leaky gut (Oxygen)



Without oxygen (leaky gut) the fire won’t ignite, but with oxygen the fire keeps burning.

A Functional Medicine approach to autoimmunity and controlling the associated pain, without driving undesirable side effects such as increased intestinal permeability (commonly referred to as a ‘leaky gut’), could include the use of:

Pain reduction can also be targeted through investigating and addressing imbalances in

Experienced Functional Medicine practitioners who work closely with you and listen carefully to your health history, can help you to identify your individual triggers, and help to restore optimal function across the body systems.

In addition to the above three factors, what is also of importance in every case, is the microbiome.

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A Functional Medicine approach to autoimmunity: the microbiome

In thinking about the Functional Medicine approach to immunity and the role of the intestinal system, there are two main areas we want to focus on:

– the microbiome

intestinal permeability (leaky gut)

So let’s start by taking a look at the microbiome.

The human body, inside and out, is covered in microbes, with the bulk of them lining the walls of the intestinal system.

The microbiome consists of trillions of microorganisms from thousands of different species. These include bacteria, fungi, parasites and viruses, and their genes.

Imbalances among the gut microbiota can drive inflammatory conditions, including autoimmunity (16).

The gut microbiota and the innate immune system have a reciprocal relationship, with any microbial disruption (dysbiosis) potentially altering the innate immune response and vice versa (17). 

For example, too many pathogenic (‘bad’) microbes in the microbiome likely contributes to the ‘inflammatory cascade’.

This is a complex sequence of inflammatory responses that take place, where the immune system recruits more and more inflammatory molecules to try and ‘fix’ the problem. 

An inflammatory cascade can, in some cases, become difficult to ‘switch off’.

This negatively impacts immune system function and immune system tolerance (18).

To understand more about how the microbiome impacts autoimmunity, let’s take a deeper dive into the digestive tract…

The gastrointestinal tract has two main functions:

1/ Digestion and assimilation of nutrients

2/ Protection against pathogens

The main function of the digestive system is to break down and absorb nutrients from food.

This is probably an obvious function of the gastrointestinal system, but less well known, is its role in protection and immunity – yet this is a crucial role.

The gastrointestinal tract is an interface between what is on the outside (the external environment of the body), and what enters the body.

Basically, everything you eat or drink has to pass through the gastrointestinal system to get into your blood stream, and from your blood stream to your tissues and cells.

As well as the good stuff – nutrients, water, and so on, it also includes the bad stuff; germs, bacteria, viruses, and toxins.

Having 80% of your immune system living in your gut helps to protect you from foreign invaders entering our body and blood stream.

This is greatly affected by intestinal permeability and dysbiosis (imbalance of bacteria).

Using a Functional Medicine approach, we can specifically test for many of these invaders, and then support the elimination of them, while helping to restore optimal function and structural integrity of the digestive tract.

Can fixing your intestinal permeability arrest your progression of autoimmunity?

The short answer is: yes.

The human body is phenomenal, and can tolerate many exposures to things like toxic chemicals, heavy metals, stress, and foods that irritate the gastrointestinal system, before the development of a pathogenic ‘leaky gut’.  

If someone has a ‘leaky gut’ and has repeated exposures to the same offending foods, lifestyle choices, or lack of nutrients to support the gut lining and immune system, then the intestinal barrier may fail to heal.

We know that many people with autoimmune disease have increased intestinal permeability.

But what we don’t know yet, is whether the increased intestinal permeability causes the autoimmunity, or does the autoimmunity cause the increased intestinal permeability?

As we mentioned earlier, if we have increased intestinal permeability, then this can go on to affect our immune system, and also our microbiome.

And it’s not only the bad bugs in the intestinal system that cause problems.

When there is a ‘leaky gut’ even the commensal (good) bacteria can escape the intestinal lumen and cause inflammation.

The resulting ‘leaky gut’ then acts as the gateway to inflammation, and this can cause further immune system dysregulation.

However, using a Functional Medicine approach, there are effective tools available to help restore optimal function to the intestinal lining.

Some common nutrients that are considered include:

There is increasing evidence that diet can contribute to systemic inflammation (19).

So identifying and removing foods that you may be producing an immune response to can help reduce inflammatory responses.

And as you’ll have gathered by now, inflammation is the enemy when it comes to autoimmune conditions.

Food intolerances, food sensitivities, and food allergies can be challenging to diagnose, and testing for these reactions is variable in terms of sensitivity and specificity.

Because of this, many researchers believe that elimination diets are the gold standard for the diagnosis of food reactions (20).

Guided by your Coho functional medicine practitioner, an individually designed elimination diet can help determine which food (or foods) you are reacting to and are driving inflammation.

Often, clients don’t have any obvious signs or reactions to foods which makes it difficult to pinpoint foods that might actually be causing an issue. 

However, it is possible to still be reacting to foods in a subtle way that is not obvious.

These subtle reactions (some people call them hidden food intolerances) are still very important to understand and address, as they can be adding more fuel to inflammatory processes.

Optimising nutrition and eliminating food reactions can bring significant benefits in autoimmune conditions.

Autoimmunity & Functional Medicine in practice

Functional Medicine doesn’t just help manage the symptoms of autoimmune disease, such as pain or fatigue, but also considers the antecedents, triggers and meditators of disease.

Antecedents are pre-disposing factors i.e. factors that have pre-disposed the development of disease, such as family history or genetics.

Triggers are factors that have initiated the immune dysfunction, such as trauma or a chronic viral infection.

Mediators are factors that continue to drive the imbalances, such as food reactions or ongoing stress.  

The antecedents, triggers and meditators are unique to each person and their autoimmune condition.

For example, if we have ten clients, all with psoriasis, then their antecedents, triggers and mediators are unique in each case.

It is for this reason, that each case has an individually designed protocol to optimise health.

This comprehensive approach enables us to enhance the conventional medical care you may be receiving, and is not necessarily an alternative to your medical treatment.

However, in our clinical experience, we find that our clients generally have longer remission phases, are less dependant on medication to manage their symptoms and have a better quality of life than they did before their Functional Medicine journey.

Functional Medicine allows us to dig deeper into your specific triggers, the functioning of each body system, and to design personalised protocols to help optimise your health.

The Functional Medicine Assessment

An essential part in identifying your triggers/stressors is to listen carefully to your story and map out key events in chronological order.

This is called the Functional Medicine Timeline.

The Functional Medicine Timeline is unique to each person, as it is their personal health timeline, and allows us to understand if previous illnesses, medications, stressors, or life events have potentially shaped how their health is currently.

Autoimmunity does not develop overnight, and there will often have been a sequence of events that would have put strain on the immune system over the years.

Identifying all of these factors is essential in order to effectively plan the path back to optimal health.

The Functional Medicine assessment also involves a comprehensive understanding of antecedence, for example birth history.

Factors like the method of birth can impact the development of the microbiome and in turn the immune system.

The Functional Medicine assessment also includes gaining an understanding of family history, as autoimmunity does have a genetic component.

A nutritional analysis is also performed to help your practitioner understand if there are any nutritional deficiencies, excesses, food triggers or sensitivities involved in.

Additionally, a physical examination observing for signs that can point to autoimmunity is performed.

The Coho Functional Medicine plan

As part of the Functional Medicine approach to autoimmunity, lifestyle related suggestions are made.

These are a hugely important element of the protocol, and an area often missed in conventional nutrition and medicine approaches, despite lifestyle interventions having a tremendous capacity to restore health in autoimmunity (22, 23, 24, 25, 26).

In Functional Medicine, emphasis is given to identifying and improving modifiable lifestyle factors such as:

– plays a restorative role for the immune system (27) and sleep disturbance has been linked with affecting the Hypothalamus-Pituitary-Adrenal Axis (HPA) and the development of autoimmune disease (28).

– physiological processes known to be involved in fatigue include oxygen / nutrient supply, mood, sleep, metabolism and motivation, all of which are affected by inflammation.

– generally, low-to-moderate exercise is beneficial for patients with autoimmune conditions (29, 30), more specifically in MS (31) psoriasis (32); lupus (33); RA (34) and Type 1 Diabetes (35).

– can be a trigger to the development of autoimmunity (36), perhaps due to stress hormones like cortisol altering cytokine production which can result in immune system dysregulation (37).

Not only can stress cause autoimmunity, but having an autoimmune condition can also cause more stress.

Relaxation can improve HPA axis dysfunction and thereby improve its effect on the immune system.

Mindfulness and improving vagal tone (that supports the parasympathetic nervous system – the ‘rest and digest’ state) with techniques such as deep breathing and meditation, have been documented to improve immune function (38)

All – or any – of these factors can trigger, or mediate, autoimmune disease.

Since everyone has unique triggers and mediators for their autoimmune condition, a 100% bespoke nutritional and lifestyle medicine plan that addresses these factors, for each person, can result in life-changing benefits that go way beyond what can be achieved by the  standard regimen of medication alone. 

This root-cause, personalised approach takes into account the uniqueness of each person and their disease, over the ‘one pill for all’ approach of conventional medicine.

You, your symptoms, your journey, the treatment you have already had, are all unique to you – so your plan needs to be unique too. 

What tests are useful in a Functional Medicine approach to autoimmunity?

Despite the prevalence of autoimmune conditions, many people remain undiagnosed.

People can be suffering from an array of symptoms which may instead be attributed to other non-autoimmune conditions.

Conventional testing

Your GP will likely do a full blood count, look at markers of inflammation – CRP, ESR, white blood cells, and perhaps your Hb1Ac (a blood sugar marker), plus some autoimmune antibodies.

Scans may also be performed.

Functional testing

So what can a functional medicine test tell you that your GP can’t? 

Your GP may test for some autoimmune antibodies – but there are many that are not tested.

These can be further explored using advanced testing such as the Cyrex Array 5 test (Systemic Autoimmune Reactivity Screen).

The Cyrex Array 5 test can identify a range of auto-antibodies over and above those tested in conventional medicine.

And with this kind of testing, autoimmune antibodies can be detected years before you have symptoms.

Advanced testing in our Functional Medicine approach to autoimmunity can potentially detect autoimmune issues in those whose symptoms have yet to begin.

As we’ll explore further below, functional testing helps us to pinpoint the root cause of your symptoms, enabling Coho practitioners to personalise your dietary, lifestyle and supplement schedule to get you effective results, fast.

So, let’s think back to the ‘triad’ of factors that influence the development of autoimmune diseases:

that are involved in the pathogenesis (development) of autoimmunity and some of the functional tests we routinely perform at Coho Health. 

1. Genetic predispositions to autoimmunity

Nutrigenomic Testing focuses on identifying genetic variants called Single Nucleotide Polymorphism (SNPs), which may make us more or less vulnerable to certain health conditions.

Nutrigenomics is the scientific study of the effect of food and nutrients on gene expression, and how certain nutrients have been shown to upregulate or downregulate specific genetic pathways. 

While understanding genetic polymorphisms is helpful, health outcomes are likely to be a result of genetic predispositions combined with lifestyle choices and individual triggers.

As the saying goes:

“Genetics are the loaded gun, but the environment pulls the trigger”

2. Environmental triggers

Food Intolerance testing:  Understanding which foods in your diet are inappropriately activating your immune system is incredibly important.

As practitioners, it allows us to prescribe the right therapy, and as we’ve mentioned previously, food intolerances can be addressed using an elimination diet.

However, we may also suggest specific food sensitivity testing such as the Cyrex Array 10 X 90 or Wheat/Gluten Array 3X test to identify and measure IgG antibodies related to food reactions. 

Other tests may be recommended that measure IgE (allergy) antibodies, IgG, IgG4 antibodies (intolerances), and C3d levels (inflammation) in response to foods.

Toxins: toxins that are not detoxified from the body can attach themselves to normal molecules, making them then appear as a foreign substance and therefore causing an immune response.

This immune involvement can further perpetuate an autoimmune process.

We use a variety of functional medicine tests to identify certain toxins like:

that may be contributing to autoimmunity. 

Chronic infection testing: infections, particularly certain viral infections, are known triggers for autoantibodies (39).

Viral infections can increase susceptibility to autoimmunity, and, at the same time, autoimmunity may increase susceptibility to viruses (and viral re-activation flares) in the future.

Viruses can cause genetic modifications that could be responsible for a dysregulated immune system, as was reported with Epstein-Barr virus (EBV) (40).  

Epstein-Barr virus has been linked to the development of Hashimoto’s disease, and Human Papillomavirus (HPV) has been associated with Lupus (SLE). 

Tests that assess for chronic viral infections can help to understand if viruses may be part of the picture in the development of autoimmunity. 

Appropriate immune and anti-viral support could be helpful to reduce the viral ‘load’.

Oxidative stress is a state where there are more ‘reactive oxygen species’ (reactive molecules in the body) than antioxidants (that help reduce reactive oxygen species). In this state, there are more damaging molecules that can drive inflammation and exacerbate autoimmune diseases.

8- OHdG and lipid peroxides are two examples of markers of oxidative stress that can be measured and which may be elevated in chronic diseases.  

A high level of oxidative stress warrants immediate action, with efforts made to find the source(s) of oxidative stress and to eliminate them, whilst ensuring that antioxidant status is improved. 

Nutrient deficiency testing: Nutritional status affects, and is affected by, autoimmune conditions.

Assessing the macronutrients protein, fat and carbohydrate, and also fibre, is critical to the establishment and maintenance of a healthy, diverse microbiome and mucosal tissue. (41, 42, 43, 44).  

Clients are often surprised at the level of nutrient density required to provide the optimal intake of key nutrients.

This is vastly different to the Standard American Diet or Western diet, where frequently there are numerous nutrient insufficiencies.

People with autoimmunity are often deficient in basic nutrients that are anti-inflammatory, or which have a role in modulating the immune system, such as Vitamin D, Omega 3 and glutathione.

A functional test called the Organic Acids Test (OAT) offers a comprehensive metabolic snapshot of overall health with over 70 markers.

Insulin testing

Chronically high levels of insulin are a common driver of inflammation in almost all chronic diseases. 

Issues with insulin arise when the body is having to produce more insulin than is ideal, usually to help regular blood sugar levels after consuming a high amount of carbohydrates or sugars.

Insulin is a driver of systemic inflammation.

And as we’ve already discussed, inflammation is not your friend in autoimmune conditions, so it follows that insulin surges aren’t, either.

Insulin surges over a period of time can be problematic for the immune system (even when there is no diagnosis of diabetes). 

Hypothalamus-Pituitary-Adrenal (HPA) axis imbalance testing

Chronic stress leads to chronic inflammation and immune upregulation, especially when the adrenal glands can no longer adapt to all the stress our bodies encounter on a daily basis.

Here is an example of how we can identify your stress response by measuring your cortisol levels throughout the day. 

Oestrogen testing

Hormones are the chemicals that tell our bodies what to do, and hormone imbalances lead to the wrong signals being sent out, and so cells end up receiving the wrong instructions.

For example, excess oestrogen is inflammatory and impacts the immune system.

Using urine samples, we can measure hormone levels (and many other additional markers) which can affect inflammation, such as melatonin (sleep hormone) and B vitamins (involved in detoxification). 

3. Intestinal permeability and gastrointestinal function

Comprehensive gastrointestinal function testing is the cornerstone of optimising health in any chronic disease, and this is also true in a Functional Medicine approach to autoimmunity.

Gastrointestinal imbalances have a knock on effect on every system in the body, so it’s a great place to start making improvements.

Comprehensive testing includes immune markers (to identify gut inflammation), and a thorough breakdown of gut bacteria levels, parasitic infections and yeast levels, helps to identify pathogens that could be driving inflammation. 

As with viruses, there are known bacterial and parasitic autoimmune triggers too.

Zonulin is a protein that can be measured in stool samples, which is just one indicator of increased intestinal permeability (there are also other tests to assess for a ‘leaky gut’).

Understanding gut bacteria levels can be very insightful and helps us to better understand how the gut is functioning.

For example, low levels of Faecalibacterium are associated with lower levels of butyrate.

Butyrate has anti-inflammatory effects, which is potentially very helpful in a range of health conditions, including autoimmune conditions.

And an overgrowth of Proteobacteria and Actinobacteria is associated with increased inflammation – potentially not so useful.

A comprehensive stool test also includes a markers call Secretory IgA (SIgA).

SIgA is considered the ‘first line of defence’ of the intestinal immune system.

A very low SIgA level suggests long term infections or loss of immune tolerance, whereas a high SIgA is associated with an inflammatory response to a bacterial or yeast infection (or food reactions).

These are just a few of the very useful markers that functional digestive system testing can give us.

4. Predictive autoimmunity testing

Many autoimmune diseases do not develop spontaneously, but instead evolve over time before they become clinically evident – and by ‘clinically evident’ we mean when you start to experience symptoms.

This suggests that environmental factors may dampen – or amplify – the autoimmune process over time.

One indicator of predictive autoimmunity testing is a positive ANA test (commonly run as a first line test for autoimmunity) many years prior to the development of symptoms.

Advanced autoimmune testing e.g. via Cyrex Labs can help predict autoimmune disease years prior to a diagnosis by detecting the presense of auto-antibodies.

Stages of autoimmunity

The following three stages exist in the development and resolution of autoimmunity;

Initiation – ‘lighting the match’

The initiation phase of the disease, where you may be unaware of any clinical symptoms (subclinical) but you may already have detectable levels of antibodies, sometimes referred to as silent autoimmunity.

Propagation – ‘fuelling the fire or fanning the flames’
The propagation phase is characterised by progressive inflammation and tissue damage due to cytokine production and T regulatory cell imbalances.

The ongoing elevated antibodies may mean you have symptoms and measurable tissue destruction.

Remission – ‘putting the fire out’

Remission is when there is resolution of autoimmunity (the T-reg cells in particular) play an important role in establishing control of the autoimmune responses.

However, other mechanisms also exist that have been proposed to limit autoimmune reactions.

Prevention is always better than a cure, and science and functional medicine are working towards preventing the match from ever being lit!

In this hugely evolving field, researchers and practitioners are working towards increasing the options available to effectively improve immune tolerance, and to prevent and help patients recover faster from autoimmune flares.

Book your free 15 minute Discovery Call with Dee Brereton-Patel now

The wrap

Because we’ve worked with so many clients who are suffering from autoimmune conditions, we understand just how frustrating and life changing and kind of autoimmune disease can be.

Sometimes you can just feel so helpless and hopeless. With all of autoimmune clients, our aim is to help you take back control of your health, and put your autoimmune condition into remission.

We hope this article has been useful and has helped you to gain a better understanding of autoimmunity, as well as the advanced testing options treatment pathways available to you.

Through a functional medicine approach to autoimmunity, we can help to pinpoint factors that can be disturbing immune function.

Then we can help to reduce episodes of autoimmune flares, and ultimately help those with autoimmune conditions to move into the remission / recovery phase.

If you think the Coho Functional Medicine approach to autoimmunity can help you, you can book a free 15 minute discovery call with us here.

We offer Functional Medicine consultations in the UK, in Mallorca, and to clients around the World through our virtual Functional Medicine clinic.

To your optimised, healthy future,

Lulu & the Coho Health team

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