Autoimmune Diseases and Genetic Markers


develops in genetically predisposed individuals under the influence of environmental factors. It’s a spectrum that can manifest as a variety of diseases, most of which are commonly diagnosed only after a significant degree of tissue damage has taken place. Because auto-reactive T and B cells persist in the body for as long as we live, we say that autoimmunity is incurable. This means that ongoing holistic support is needed for autoimmune patients to keep their conditions dormant. In this article, we briefly discuss some of the most important concepts regarding autoimmunity, including genetic predispositions, environmental triggers, immune mechanisms involved, and clinical solutions.

Genes are not your destiny!  

By now, we all know that our genes do not determine our destiny and that it’s the epigenetic influences that shape our current state of health and our future. This is great news because it means that we can redefine who we are simply by modifying our environment or, to be more specific, the environment our cells are in. 

Keeping that in mind, it can be massively useful to know our genetic makeup so that we can be proactive and implement strategies that negate the potentially harmful effects of the genetic SNPs we were born with and thus prevent the onset or the progression of disease. 

Genes do not determine our destiny. It’s the epigenetic influences that shape our current state of health and our future.

Numerous genetic polymorphisms are thought to be autoimmunity antecedents. One simple example you are probably familiar with (perhaps not in this context) is the MTHFR gene, which determines how well the methylation pathway works. The methylation cycle needs to run smoothly to ensure immune self-tolerance, which is lost in all types of autoimmunity. That’s one reason to make sure your intake of green leafy veg is up, especially if you’ve got a slow MTHFR. And that’s one reason why protocols such as the Wahls protocol for MS feature copious amounts of leafy greens. 

A high intake of leafy greens ensures the methylation cycle runs smoothly, which is crucial for maintaining self-tolerance. 

As chronic inflammation is both the contributor to and the result of autoimmunity, genes controlling the inflammatory pathways, such as the NF-κB have been studied in relation to a number of conditions. For instance, several SNPs within the NF-κB signalling cascade have been identified in MS and ulcerative colitis (1). High intake of dietary antioxidants from brightly coloured fruit and veg may help dampen the negative consequences of this SNP.

A high intake of dietary antioxidants from brightly coloured fruit and veg helps to dampen the negative consequences of NF-κB SNP.

SNPs in genes responsible for the making of our antioxidant enzymes, such as GST & GSX, which determine how well our glutathione mediated detox works, are also relevant in autoimmunity. Increased toxic burden resulting from impaired GST & GSX function is a predisposing factor to chronic disease beyond autoimmunity. Limiting your daily exposure to chemicals (household cleaning products, personal care products, pesticides, etc.) is a must if your GST & GSX are slow. 

Limiting your daily exposure to chemicals is a must if your GST & GSX are slow.

Other examples of genetic predisposition, this time to a specific type of autoimmunity, would be the famous HLA-DQ2 and HLA-DQ8 genes linked to Coeliac disease and type 1 diabetes as well as autoimmune thyroid disease. We keep learning more and more about the genes directly or indirectly linked to autoimmunity but the one crucial thing we’ve learned so far is that having a particular genotype does not sentence the carrier to developing a disease. We can shape our destiny! 

Your (cell) environment 

The composition of the biochemical soup washing over our cells (blood, interstitial fluid) determines how well they perform, which translates into how well our tissues, organs, and organ systems function, and thus how well our bodies function. It depends on our diet (abundance or lack of nutrients), environmental exposures (toxins), pathogens (inflammatory molecules, LPS), as well as psychological factors and our social environment (stress hormones). All these factors have the potential to act as triggers for autoimmunity and identifying and removing the triggers is the first step to managing/reversing autoimmune conditions. Taking a detailed case history allows the practitioner to spot these, so, if you’re a practitioner, keep your ears pricked up for any major events and changes in your client’s circumstances prior to the onset of their symptoms, and if you’re a client, don’t hold anything back – the more you share, the better. 

Common autoimmunity triggers include diet, environmental toxins, pathogens, psychological factors, and our social environment.

Downstream effects 

When we talk about finding and removing the root cause of the problem, it’s important to remember we might also need to deal with its downstream effects. If, for instance, high sugar consumption is the root cause, simply removing sugar may not be enough to reverse the downstream effect of prolonged excess sugar consumption, such as metabolic syndrome or diabetes. On top of removing the offender, it’s crucial to implement strategies to restore insulin sensitivity and signalling, leptin signalling, etc. 

After removing the triggers, deal with their downstream effects.

Many autoimmune conditions cause significant tissue damage (Coeliac, ulcerative colitis, MS, RA, etc.) and strategies to support tissue regeneration are a crucial part of the therapy. Intestinal hyper-permeability is a common feature in autoimmune conditions and repairing the gut lining with agents such as glutamine helps to prevent immune hyper-reactivity. As gluten naturally increases gut permeability (via zonulin release) (2), removing all its sources from your diet is one way of preserving gut integrity. 

Mistaken identities

While we’re on the topic of gluten, it seems appropriate to mention cross-reactivity and molecular mimicry. The cells of our immune system decide what is what in the body by reading special labels on molecules or on cell membranes. Based on what they think they see, they decide whether to raise the alarm or do nothing. It’s a great system and it works most of the time but sometimes when the labels are very similar, things get confused. 

All of the cells of our body have special recognition receptors on their surface so that the immune system can distinguish self from non-self. Sometimes microbial patterns get confused with self patterns and when the immune system launches an attack on the microbe, it also destroys the host tissue. This mechanism has been termed molecular mimicry and has been implicated in the development of various autoimmune conditions, such as autoimmune thyroid disease (3). (The microbes to blame here include Yersinia Enterocolica, Helicobacter Pylori, Borrelia Burgdorferi as well as viruses such as HCV, Herpes Simplex and Epstein-Barr.) 

Antibodies made in response to food proteins (eg. gluten & dairy) can cross-react with our own tissues. For instance, antibodies to bovine milk protein (butyrophilin) cross-react with myelin oligodendrocyte glycoprotein (MOG) and exposure to this common dietary protein can influence the course of multiple sclerosis (4). Dairy proteins and gluten exhibit molecular pattern similarity, which is why people who need to avoid one are often told to avoid the other.

Antibodies to bovine milk protein (butyrophilin) cross-react with myelin oligodendrocyte glycoprotein (MOG) and exposure to this common dietary protein can influence the course of MS.

This identity confusion is most likely to happen in conditions of chronic inflammation when the immune system is under a great deal of strain. When I try to explain this to my autoimmune clients I often tell them to imagine the cells of their immune system as border workers who have been overworked and underpaid (poor nutrient supply) for a long period of time. Being tired and undernourished, they are just more likely to make mistakes. They still want to do their job well, so to avoid the risk of missing an invader they go after anything that resembles one. 

Apart from molecular mimicry, pathogens contribute to the development of autoimmunity via other mechanisms, such as epitope spreading and cryptic antigens. Pathogen independent mechanisms involve the escape of autoreactive T cells and impaired function or lack of regulatory Ts. 

Mechanisms involved in the development of autoimmunity include molecular mimicry, epitope spreading, cryptic antigens, escape of autoreactive T cells, and impaired function or lack of regulatory Ts.

What can we do about it?

Although it’s important to know as much as possible about the genetic predispositions and the mechanism involved in autoimmunity, the most important question is what can we do about it all. I’ve already mentioned a few things to consider while developing a treatment plan, such as green leafy veg for methylation, dietary antioxidants from brightly coloured fruit and veg, limiting chemical exposure and eliminating trigger foods, such as gluten and dairy. 

In terms of supporting detox mechanisms, brassica and onion family vegetables are massively useful. They also support female sex hormone balance (by upregulating CYP1A1, which promotes the protective form of oestrogen) and blood sugar balance due to their high fibre content. The fibre from all of the above is also crucial for the health of our microbiome, which in turn promotes a healthy regulatory T cell population. Vitamin D is also supportive of Tregs and immune self-tolerance, as well as gut integrity, and regular sun exposure can help promote immune health. If you’re lucky and live somewhere sunny. If like me, you live in the UK, supplementing vitamin D may be a better option.  

Blood sugar balance is a big thing for most autoimmune clients and I tend to give this a priority in the initial phase. First of all, in order for the body to be able to start fixing itself, the energy supply (ATP) needs to be abundant. Second of all, blood sugar drops stimulate the stress response and by preventing them we decrease the overall stress burden. Blood sugar spikes, on the other hand, lead to the formation of AGEs (advanced glycation end-products), which bind to RAGE receptors (another great name!) and trigger off inflammation. Apart from high amounts of fibre, blood sugar balancing diet limits carbohydrates and includes sufficient amounts of quality protein and healthy fats. 

To keep autoimmunity dormant: 

  • Promote self-tolerance

  • Support methylation

  • Support antioxidant status

  • Eliminate environmental toxins

  • Support detox

  • Eliminate dietary triggers 

  • Support gut health

  • Support blood sugar balance

Lots more can be said about what to include/exclude on an autoimmunity treatment plan but perhaps the most important thing to remember is to always treat the patient, not the disease and that food really is powerful medicine. To cite Dr Wahls, who’s a great inspiration to me (both as a patient with an autoimmune disease and as a practitioner) – “Food is a disease-modifying drug and if you stop taking it you should expect the disease to flare”.  




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