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.
Autoimmune diseases happen when the immune system – your body’s defence team- mistakes your own tissues for a threat.
What is autoimmunity?
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A healthy immune system maintains immune tolerance – the ability to tell “me” from “not me.”
In autoimmune conditions, tolerance breaks down.
When your own proteins appear at the same time as “danger” signals – for example during an infection, after tissue injury, or in ongoing inflammation – the immune system can misread them and start an attack it shouldn’t.
That misplaced attack creates inflammation and the symptoms you feel.
Same process, different targets:
The underlying problem is similar, but the tissues targeted are different. That’s why conditions look different:
- Thyroid: Hashimoto’s or Graves’ disease
- Joints: Rheumatoid arthritis
- Gut lining: Crohn’s disease or ulcerative colitis
- Multi-system: Systemic lupus erythematosus (joints, skin, organs)
Autoimmune conditions are more common in women (roughly twice as common as in men) – some studies show that 6.4% of women are affected by autoimmune conditions but only 2.7% of men are.
Autoimmune conditions frequently begin between the mid-teens and mid-40’s.
Genetics can raise susceptibility (some conditions run in families or are more frequent in certain groups), and rates appear to be rising over time.
Environment and lifestyle also matter – things like infections, smoking, certain medications, chronic stress, nutrient gaps, and gut barrier changes can all add “danger” signals that keep the fire going.
Our role at Coho is to be clinical detectives:
- Identify what’s undermining tolerance in your case (e.g., ongoing inflammation, chronic infections, environmental chemicals and biotoxins, gut barrier issues, nutrient status, sleep, stress..)
- Build a step by step Coho you=1 functional medicine plan to calm those drivers and support a return toward better immune tolerance
- Work alongside your medical team. Medicines like steroids, DMARDs, or biologics have an important place; over time, a personalised plan may help some people reduce reliance on them - only when appropriate and agreed with their clinician. If you haven't yet started on any medications - then our approach has helped many clients over the years, avoid the need for starting on immune-suppressing drugs
- Work alongside your medical team. Medicines like steroids, DMARDs, or biologics have an important place; over time, a personalised plan may help some people reduce reliance on them - only when appropriate and agreed with their clinician. If you haven't yet started on any medications - then our approach has helped many clients over the years, avoid the need for starting on immune-suppressing drugs
- Our aim is remission and improved quality of life
Book your free 15 minute Discovery Call with Dee Brereton-Patel now
Diagnosed, undiagnosed, or family history?
Many people who come to our Functional Medicine clinic already have a diagnosis and want to improve their quality of life – fewer flares, more stable energy – and want to explore whether they can safely reduce reliance on medications over time and with their doctors guidance.
Others have no diagnosis yet. They’re dealing unexplained symptoms, which might be fatigue, joint or muscle pain, rashes, gut issues, brain fog – and want a clear plan.
Sometimes, a family history of autoimmunity prompts people to seek support early, because some autoimmune conditions do run in families.
Our approach is personalised and evidence-based.
We start by mapping what’s driving your loss of immune tolerance, what are the possible triggers and root causes, and identifying priority nutrition and lifestyle factors that require optimisation.
We use advanced testing to help accurately identify imbalances and likely root causes, so we can work together to design a precise and effective plan forward.
We’re happy to collaborate with your medical team for a seamless, joined-up approach to your care.
Signs and symptoms you may have an autoimmune disease
Common signs and symptoms of autoimmunity we see in clinic are listed below.
In our almost 30 years of combined clinical experience, we know that clients don’t usually have all of these symptoms at once – symptoms vary and can flare and settle over time. Any new symptoms should always be discussed with your GP/consultant.
- Muscle or joint pain, joint swelling
- Fatigue
- Bloating, diarrhoea, constipation
- Dry eyes, dry mouth, dry skin
- Skin rashes, patches of lost pigment on your skin
- Brain fog or poor memory
- Multiple miscarriages
- Abdominal pain or digestive issues
- Feeling cold when others aren’t
- Weight gain
- Recurring fever
- Dizziness
- Hair loss
- Tingling sensations or numbness in your hands or feet
- and many, many more...
Symptoms vary by condition and by which cells or tissues the immune system is attacking.
Common autoimmune diseases (and how they're grouped)
There are over 80 autoimmune diseases (2). Below, we’ve grouped common autoimmune conditions by body system. Many of these can overlap and affect multiple systems:
– 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’s possible to have more than one autoimmune disease. If you have one condition, your risk of developing a second – or even a third – can be higher (3).
To better 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 (in-built) 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:
- Protective barriers (skin, the mucosal lining of the gut, lungs, sinuses)
- First-responder cells such as neutrophils, macrophages, dendritic cells, and natural killer (NK) cells. They act quickly, clear debris, and call for backup
The Adaptive (acquired) immune system
The acquired immune system is your specialist. Slower to respond than the innate immunity, but more precise. It uses:
- B cells (which make antibodies)
- T cells (which coordinate responses and can directly kill infected cells)
- Humoral. B cells turn into plasma cells that release antibodies into fluids like blood, mucus and saliva. They include IgG (found in blood and lymph), IgA - the main 'mucosal' antibody (tears, mucus, saliva, breast milk) and IgE, IgD, IgM (more about these later)
- Cell mediated. The cell mediated aspect of the acquired immune system involves T cells; Helper T cells - the conductors (organise and focus the response), Cytotoxic (killer) T cells (remove infected or damaged cells), and Regulatory T cells (help maintain tolerance)
A healthy immune system protects you and tolerates your own tissues.
In autoimmunity, tolerance breaks down.
When your own proteins show up at the same time as danger signals – from an infection, tissue damage, or ongoing inflammation – the immune system can misread self as a threat and attack, driving inflammation and symptoms.
Is autoimmunity curable?
Some illnesses (like many infections) resolve once you remove the cause.
Autoimmune diseases don’t work that way.
They reflect an ongoing tendency of the immune system to react to self. So rather than a once-and-done “cure,” the realistic goal is control and remission – fewer flares, milder symptoms, and better day-to-day function (quality of life).
So autoimmunity is not curable in that sense.
But autoimmune disease can be put into remission.
Remission doesn’t mean the immune system is “switched off.” It means the condition is quiet: minimal symptoms, low inflammation, and stable markers, ideally with the least medication necessary (as agreed with your clinician).
One of the goals in a Functional Medicine approach to autoimmunity, is to rebuild immune tolerance and reduce ‘danger signals’ that keep the immune system on high alert.
In practice, that means:
- Calming chronic inflammation (e.g. nutrition, sleep, stress, movement, targeted nutrients)
- Supporting the gut barrier and microbiome (because they strongly influence immune tone)
- Identifying and addressing personal triggers (e.g. chronic or high stress, infections, biotoxins, chemicals, lifestyle)
- Nudging the immune system toward balance, including support for regulatory T cells (T-regs). They act as the 'brakes' and help regulate other immune cells
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.
At Coho, we’d look to support natural T regulatory cells that have a ‘modulating’ effect on the immune system, but immunosuppressive medications act by ‘turning off’ the immune system.
And turning the immune system off (or reducing its function) can have some undesirable side effects, as, at the same time 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 the associated 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 with a personalised, evidence-based, step-by-step plan, inflammation can be reduced and immune tolerance restored, meaning longer periods of remission and more good days.
And some of our clients have achieved remission for many, many years, without needing to go back on to medications like DMARDs and Biologics.
What’s the conventional medicine approach to autoimmunity?
Conventional treatments for autoimmune disease aim to control immune-driven inflammation and the symptoms it causes.
Options include corticosteroids to quickly reduce inflammation and pain, and immune-suppressing medicines (such as DMARDs and biologics) to calm an overactive immune response over time.
As with many medications, there is a right time and place for its use and these immune-suppressive medications are important in some cases – but they do carry (often significant) side effects.
With that in mind, here’s an overview of the main medication options.
Drugs to manage autoimmune disease symptoms
NSAIDs
Many people with autoimmune disease experience pain (6), often managed with non-steroidal anti-inflammatory drugs (NSAIDs).
These medicines reduce pain by inhibiting cyclo-oxygenase (COX) enzymes, lowering prostaglandin production.
While that helps with pain and inflammation, prostaglandins also protect the stomach and intestinal lining, so NSAIDs can cause gastrointestinal side effects such as nausea, dyspepsia, and diarrhoea.
They may also increase intestinal permeability (‘leaky gut’) (7), which can further aggravate autoimmune activity.
Common examples include ibuprofen, diclofenac, and naproxen.
Steroids
Corticosteroids (glucocorticoids) are medicines related to hormones your adrenal glands naturally produce (like cortisol).
In autoimmune flares, prescribed steroids such as prednisolone can rapidly dampen inflammation and relieve pain. Because they act broadly on the immune system, they’re usually used at the lowest effective dose for the shortest possible time. Potential side effects include:
- Fatigue
- Mood changes
- Weight gain
- Diabetes
- Osteoporosis
- and increased risk of infection due to its immunosuppressive effects (8)
Prednisolone is one of the most common steroid medications used.
Opioids
Opioids are often used to treat chronic pain despite this class of drug having many side effects, such as:
- Constipation
- Hormone dysregulation
- Depression (9)
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:
- Rheumatoid Arthritis (RA)
- Ankylosing Spondylitis (AS)
as well as for management of other connective tissue diseases such as:
- Systemic Lupus Erythematosus (SLE)
- Inflammatory Bowel Disease (Crohn’s disease)
- and some cancers (for instance non-Hodgkin's lymphoma)
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:
- Nausea
- Loss of appetite
- Vomiting
- Diarrhoea
- Mouth ulcers
- Skin rash
- Liver dysfunction
- Changes to white blood cells and platelet numbers
- Headaches
- Mild hair loss
- Fever
- Symptoms of infection
- Bruising
- Bleeding
- Shortness of breath
- Troublesome cough causing pneumonitis (inflammation in the lungs)
- Photosensitivity
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:
- Gastrointestinal distress (nausea, abdominal pain, diarrhoea)
- Rash / allergic reaction
- Bone marrow suppression
- Alopecia
- Hepatotoxicity
- Interstitial lung disease
- and cirrhosis of the liver, which means some patients need to stop treatment
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
Some people are born with genes that make autoimmunity more likely. These genes can influence how susceptible you are, which auto-antibodies you might form, and which tissues are most at risk (14).
A key set of genes here are the HLA genes (part of your immune “ID card”) – certain HLA types (e.g., HLA-DR, HLA-DQ variants) are linked with many autoimmune conditions.
We also see this pattern clinically and in families: autoimmunity can cluster in relatives.
Important note: genes aren’t destiny – they set the stage, but triggers and environment determine whether the play begins.
2. Environmental triggers
Genes load the spring; triggers pull it.
Triggers add “danger” signals or increase exposure to antigens, tipping a susceptible immune system toward an autoimmune flare.
Not everyone reacts to the same things – this is about your personal load and tolerance.
And we don’t assume every item is a trigger for everyone. Instead, we map your health timeline, test where useful, and then start by reducing the most problematic triggers – so the immune system sees fewer danger signals and tolerance has a better chance to recover.
Common triggers:
- Lifestyle - Poor sleep, chronic psychological stress, low daily movement (or excessive training) all can amplify inflammatory signalling and reduce immune tolerance
- Dietary proteins - Individual food triggers vary - e.g., gluten, dairy proteins, eggs, or, for some, nightshades or higher-lectin foods
- Antigens - virus, bacteria, parasites, fungus, mould, persistent dysbiosis/overgrowth - these can provide strong “danger” signals
- Chemicals - Air pollution, solvents, pesticide residues, heavy metals, and damp/mouldy indoor environments, plastics (phthalates) - can add inflammatory load in susceptible people
- Nutrition - Insufficient vitamin D, omega-3s, iron, zinc, selenium, B vitamins, magnesium, etc., may affect immune balance and impair tissue repair
- Major life events & trauma - a life event or experience that has had significant emotional (or sub-conscious) impact, can act as triggers via neuro-immune and stress-hormone pathways.
- and a whole host of additional factors that can trigger autoimmunity in those with a genetic predisposition
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.
Your gut lining is a selective barrier: it lets nutrients through while keeping most microbes and large food particles out.
Problems arise when this barrier becomes too permeable (‘leaky’).
More fragments slip across, which can stimulate the immune system and add “danger” signals.
Our article on increased intestinal permeability / leaky gut goes into more detail.
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:
Figure from https://pubmed.ncbi.nlm.nih.gov/33968085/
Genetics (wooden log)
+
Trigger/s (fuel + match)
+
Leaky gut (Oxygen)
=
Autoimmunity
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, could include the use of:
- Healing nutrients such as curcumin
- Omega 3 essential fatty acids & specialised pro-resolving mediators (SPMs)
- Green tea
- Boswellia
Pain reduction can also be targeted through investigating and addressing imbalances in
- Cell energy functions (mitochondrial and ATP function)
- Oxidative stress
- Intestinal barrier function
- Detoxification capacity
- Inflammation
- Environmental toxins
An experienced Functional Medicine practitioner will take time to hear your story, map your health timeline, and test where useful – so you can identify your specific triggers and support better function across body systems.
Alongside genes, triggers and gut barrier integrity, one factor matters in every case: the microbiome.
The balance of microbes in your gut strongly shapes immune tone and tolerance.
Apply for your free 15 minute Discovery Call with Dee Brereton-Patel now
A Functional Medicine approach to autoimmunity: the microbiome
In Functional Medicine, two gut factors consistently shape immune balance:
- The microbiome (the community of microbes that live with us)
- Intestinal permeability (“leaky gut”)
Let’s start with the microbiome.
Your body – inside and out – is home to trillions of microbes.
Most live along the gut lining. Together (and along with their genes), they’re called the microbiome. This community includes mainly bacteria, plus archaea, fungi, and viruses.
A well-balanced microbiome helps train and calm the immune system.
Dysbiosis – an imbalance or overgrowth of less helpful microbes – can tilt the body toward inflammation and is linked with autoimmune activity (16).
The gut and the innate immune system talk to each other constantly; when one is disrupted, the other often follows suit (17).
Too many pathobionts (microbes that can cause trouble when overgrown) can fire up an inflammatory cascade – a chain reaction where more and more immune signals are recruited to “solve” the problem. Once rolling, that cascade can be hard to switch off, undermining both immune function and tolerance (18).
The gut’s two big jobs:
Your gastrointestinal (GI) tract is an interface with the outside world. Everything you eat and drink must pass this checkpoint before entering your bloodstream.
- Digest & absorb nutrients - breaking food down so vitamins, minerals, fats, proteins, and carbohydrates can reach your cells
- Defend against intruders - limiting the entry of harmful microbes and toxins
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.
Having 80% of your immune system living in your gut helps to protect you from foreign invaders entering our body and blood stream.
These immune cells are constantly sampling what comes through and deciding what to tolerate – and what to fight.
Two things strongly influence that decision-making:
- Barrier integrity (permeability): A healthy gut lining is a smart filter - nutrients in, bigger “wrong-size” fragments out. When it becomes too permeable, more immune-provoking fragments cross the barrier, adding “danger” signals
- Microbiome balance: Helpful species tend to support a calm, tolerant immune tone; imbalances increase background alarm
With a Functional Medicine approach, we can – where appropriate – test for dysbiosis and potential gut pathogens/overgrowths, and then create a plan to:
- Reduce identified overgrowths or pathogens
- Rebuild the barrier (nutrition, targeted nutrients, lifestyle, and sleep)
- Rebalance the microbiome (dietary pattern, prebiotic fibres, and - in selected cases - probiotics)
Lower the inflammatory load, so the immune system is better supported.
Can fixing your intestinal permeability slow autoimmune progression?
The short answer is: yes.
For many people, strengthening the gut barrier can calm immune activation and reduce flares. It isn’t a “cure,” but it’s a meaningful lever.
The body is remarkably resilient.
It can tolerate a lot – chemical exposures, ongoing stress, nutrient gaps, and irritating foods – before the gut barrier becomes too permeable (“leaky”).
If that barrier is already compromised and the same triggers keep showing up (problem foods, chronic stress, sleep loss, nutrient insufficiency), healing may stall.
We know that increased intestinal permeability is common in autoimmune disease.
What’s still being clarified is direction: does leaky gut drive autoimmunity, or does autoimmunity drive leakiness?
In practice, it’s often a two-way street – a leakier barrier adds “danger” signals to the immune system and can skew the microbiome; inflammation from autoimmunity can, in turn, worsen barrier integrity.
It’s not only “bad bugs” that cause trouble. When the barrier is leaky, even commensal (normally helpful) microbes can cross the line, provoking inflammation. That keeps the “inflammatory cascade” rolling and makes immune tolerance harder to maintain.
The good news: with a Functional Medicine approach, we can use targeted nutrition and lifestyle strategies to support barrier repair and calm the immune load.
Some common nutrients that are considered include:
- Glutamine and butyrate
- Omega 3's and Polyphenols
- Vitamin D and Zinc Carnosine
- Vitamin A
- Colostrum and Probiotics
- Collagen and N-acetyl-glucosamine
There is increasing evidence that diet can contribute to systemic inflammation (19).
Identifying and removing foods that you may be mounting an immune response to can help lower inflammatory activity. And as you’ll have gathered, inflammation is the enemy in autoimmune conditions.
Food intolerances, food sensitivities, and food allergies can be challenging to diagnose, and testing varies in sensitivity and specificity. Because of this, many researchers consider elimination diets the gold standard for identifying food reactions (20).
Guided by your Coho Functional Medicine practitioner, an individually designed elimination diet can help determine which foods you’re reacting to and which may be driving inflammation.
Often, clients don’t notice obvious food reactions, which makes problem foods harder to spot. However, subtle reactions – sometimes called “hidden intolerances” – can still add fuel to inflammatory processes and are important to uncover and address.
Optimising nutrition and removing problem foods can bring meaningful 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:
- Sleep
– 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).
- Fatigue
– physiological processes known to be involved in fatigue include oxygen / nutrient supply, mood, sleep, metabolism and motivation, all of which are affected by inflammation.
- Exercise
- Stress
– 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:
- Genetics
- Environmental triggers
- Intestinal permeability
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:
- Heavy metals
- Mycotoxins (produced by mould)
- Industrial chemicals
- Phthalates
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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