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How the Immune System Works and What Goes Wrong!

by | Jun 16, 2018 | Autoimmune, Autoimmune Disease

How the Immune System Works and What Goes Wrong!

In this second video describing what autoimmunity is all about, we delve into what a healthy immune system does, and what goes wrong when you have autoimmune disease. Watch the first video describing what autoimmunity is here.

Welcome to the second video in my series on autoimmune disease. I’m Robin Puglia, I’m a clinical nutritionist and functional medicine practitioner in the UK. I’m also a working mom of two little girls with an autoimmune disease myself. For more information on my story, my background or the work that I do please see my website So this video is really delving into the immune system and what changes away from healthy balanced function when you have autoimmunity. Immunology is pretty technical but I’m going to try to do my best to make it easy to understand because I think it’s really important to know how your immune system works and what the basic component parts of it are if you have or are working with autoimmunity.

Autoimmunity does not happen overnight

So before I get into the nitty gritty of immunology. First, I actually think that this concept is critical, autoimmunity does not happen overnight. You don’t go to sleep healthy one night and wake up the following morning with an auto immune disease. There is a spectrum of function that starts with healthy optimal function and progressively changes over time until you get to serious defamation and degradation of tissue, which is often when diagnosis occurs. So if we look here at this image, we see illustrated the phases of development of autoimmunity. So on the left we have healthy function and after healthy function we have a triggering event or set of triggers. In functional medicine, we recognize that before the triggering event that needs to be a set of variables that predispose us to developing autoimmunity so that when that trigger occurs, that cascade is set in place.

You know, the trigger alone is not enough. If you have a healthy body and a good genetic background, just for example. But I’ll be discussing those at length in other videos in this series. And today we’re really going to keep it simple in this way. So we start with the trigger. And from that moment on, the immune system no longer works in a healthy, balanced, tolerant way. It is now overreactive and proinflammatory and we have a cascade of inflammation and events in the body that is like a snowball rolling down a hill and unless we recognize that there’s a problem early on and we intervene, then we will go on to develop more and more unhealthy function in the body characterized by inappropriate immune and inflammatory responses and that can happen for a little while below the surface without really having any symptoms, and certainly without coming to our attention, without there being a tangible awareness.

Immune dysregulation

The body has a really great capacity for compensation, it will work really hard to continue with all of the normal processes that we need to get from A to Z during the day. Eventually given enough time, as that snowball continues to roll down the hill then we start to have some symptoms related to inflammation or related to immune dysregulation. Those symptoms might not actually be obviously related to the auto immune disease that we go on to develop. It might be something like a serious hayfever, environmental allergies, Eczema, hypersensitive red skinned that’s reacting to cosmetic products. It might be that we don’t heal very well from injury or from surgery, or you might actually have gut symptoms such as pain, bloating, diarrhea, or constipation. Over time we developed more symptoms, those symptoms might go on to include something like fatigue or brain fog and eventually we will start to exhibit symptoms that indicate the disease we are developing, such as dry eyes and inadequate saliva if your developing sjogren’s or you might end up with joint pain for rheumatoid arthritis, etc. And when those are bad enough when the antibodies to that tissue are high enough and when our compensatory mechanisms overwhelmed, eventually we hopefully will end up with a diagnosis.

But the reality is that I think a lot of people know that there is something wrong a long time before it gets to that end stage. You can have a lot of symptoms and a significant reduction in quality of life before you get to the point where diagnosis is possible and in some diseases it’s actually pretty difficult to get a diagnosis. It can take a really long time even beyond the point where your symptoms are kind of overwhelming your life.

The message here really is that you have been developing a chronic illness below the surface for usually years and sometimes even decades before it’s actually recognized. My other message alongside that is actually also that you don’t need a diagnosis to start making changes that can improve your health. The earlier that you recognize that there’s a problem, which might actually just be as simple as simple as identifying your symptoms as being clues instead of just thinking of them as being normal triggers that everybody has, the sooner you start recognizing that your body’s trying to tell you something and you start interventions, the better off you have the potential to be. With autoimmunity some diseases are easier to develop than others.

The autoimmune response

The autoimmune response, if we refer back to the previous image, starts at that yellow band right after the trigger for the autoimmune disease doesn’t actually come until much later. So you have your immune system has an active autoimmune mechanism at a certain point before you have anything that is actually diagnosable or recognizable as autoimmune disease. Those two things are actually a separate to each other but once that mechanism is activated, that autoimmune mechanism, then your immune system is having deranged responses and is hyper reactive. One study found that about 25% of people with a single autoimmune disease went onto develop secondary and tertiary autoimmune diseases. Once a patient has at least three autoimmune diseases this is defined as multiple autoimmune syndrome which is increasing in frequency.

That brings me to the question, how does your immune system actually work? I think that before we really start looking at what goes wrong we need to start to understand how things work when they’re working correctly. This is an introduction to your immune system. Our very first line of defense is actually our physical barriers and they are basically like about outside of a nightclub they are there to stop pathogens from getting into our body in the first place, pathogens, toxins, and our environments. So much like the nightclub and the bouncer our barriers are actually there to allow some things. But to keep troublemakers out so the skin is obvious because it’s immediately visible. But actually our mucous membranes are far larger barrier and a far larger perimeter to the body.

The skin and mucus membrane

So our skin is two square meters but our mucus membranes, which are our respiratory tracks and reproductive tract are 400 square meters. A very significantly greater surface area and because of the food that we eat and the bacteria that we take in without food and also the bacteria that we host in our guts (bacteria and other microbes). The GI tract is actually the area of the largest interaction between our immune systems in our environment. It’s fairly common knowledge these days that the gut is of central importance when it comes to autoimmune disease. We consider that a leaky gut, for example, or inappropriate intestinal permeability and microbial imbalances in the gut are almost a prerequisite to developing an autoimmune disease in the first place. But actually if you take it a step back from that our gut is a prime location of healthy immune function as well. That’s because it is the number one place where our immune system interacts with our environment. So any invader that manages to make it past the barriers is immediately greeted by our innate immune system. So all animals have an innate immune system and some of the weapons used by the innate immune system are very old estimated to be up to 500 million years old.

The innate immune system

So the innate immune system has specific cells such as macrophages, as seen here in this image on this slide. The job of a macrophage is to basically gobble up bacterial invaders or invaders that it finds. Macro means big and phage means to eat. These are the big eating cells in our body and that is how they provide us with immune defense. That’s part of our immune defenses that they gobble up anything that appears to be problematic. I’m going to use the example of a splinter to demonstrate how our innate immune system works. When a splinter breaches the barrier, and it can do that because it’s pointy and sharp and it physically forces its way through it transports a dirt, bacteria and other microbes and potentially toxins with it Trojan horse style.

You will know from having a splinter in the past that the skin around the spleen gets red and swollen in the area of the intrusion. That is because your immune system starts to work almost immediately that barrier is breached and your innate immune system has special cells that are present and floating around in your immune system all the time. It is capable of launching a very fast response. As soon as that barrier is broken and that splinter that goes into your skin the cells in that area start to respond, they have sensors and you can see. In fact that the microphone and the image has a protuberance and there are lots of cells in the immune system that are actually capable sensing using for want of a better term, arms and legs to understand when there’s a problem in the general vicinity.

Once they’ve identified that there’s an issue two things happen, they immediately spring into action. So the resident macrophage in that area or the resident dendritic cell in that area (let’s just say microphage) springs into action. It starts working, so it’s triggering enzymes and other weapons of microbial destruction. But the second thing that macrophage will do, apart from physically taking action itself is it going to start signaling like crazy to the other branches of the immune system and immune cells in the vicinity, but also in the central body. So it’s sending out chemical messengers of inflammation, which we call cytokines to let everybody know that there’s a party and where that party is so that your immune system can send the appropriate cells to come and defend this, the breach in barrier basically. What also happens from an immune system perspective is that you start to work to repair that bridge so that more bacteria and and invaders aren’t coming in through that hole in the skin, so that’s the innate immune system. And then a third level of defense is actually called the adaptive immune system.

The adaptive immune system

The adaptive immune system has a couple of different branches,  the T cells and the B cells, and adaptive as is clued up by the name actually helps us to adapt to defend against specific invaders. The innate immune system has a very general, nonspecific mode of attack and defense, whereas the adaptive immune system is trained to identify and respond in a very specific way only to a very specific invader. It’s more choosy about what it will respond to and what it wont. I’m going to be talking about B cells and antibodies and how that works, and also about T cells. B cells and antibodies primarily respond to invaders that are outside the cell. T cells are designed to be responding to invaders that are inside the cell. All antibodies are produced by B cells as a receptor on the cell surface, but the B cell can actually release them into circulation so that they can roam around the body and do their jobs independent of the cell. If you’d like to know more about what an antibody actually is specifically, I do define antibody in presentation number one of this video series, but we also have a little bit more information on antibodies here.

So our immune system is akin to the defense force of a country. Then think about the antibodies as the different branches of that defense force. So if a country has army, navy, air force, etc. Each of these branches of the defense force actually have a common goal and similarities, but each also has their own specific job. You can’t send a submarine to do a job that you need a black hawk helicopter for and vice versa, and then immune system is actually the same. It works in a very similar way. We have different branches, each with a common goal, but each also with unique characteristics and jobs that it does. So we have five different antibody classes and IgM which has five arms of chains that you can see on the slide is the big mama antibody classically considered to be a first responder with the rapid aggressive inflammatory response to an invader to try and deal quickly with the problem.


When IgM isn’t capable of completely and effectively keeping the pace. Then we see the other smaller antibodies rise up to provide support and defense. So IgE antibody, pictured blue, is the antibody that’s associated with true allergy. So we see this antibody elevated when people are having an allergic reaction to food such as peanuts or to environmental allergens such as pollen, dust mites and dental. If you’ve had a skin prick test that can be assessing IgE reactions and if you have an anaphylactic reaction to food that’s IgE mediated. IgD is actually slightly mysterious. You know we don’t know a lot about what this guy does, so I guess you can consider him to be a sort of a secret service. You know, our bodies don’t ever do anything for no reason, so he must have a really important role to play in the immune system, but to date, while some observations around the function of IgD have been there, it’s still immunologically considered to be a little bit of a puzzle. Now IgG is interesting because it makes up about 75 percent of the antibodies in the blood. It is very small and is often associated with past exposures to viruses or foods for example. But we also see IgG coming back up to support IgM and IgA. So IgG can certainly can indicate a current and immune reactions.

However, IgG is 75 percent of the antibodies in the blood, but actually around 60 to 80 percent of the active immune cells in the body are found in the gut and those are a very specific type of IgA antibody called secretory IgA. So IgA antibodies are found in high numbers on the mucosal barrier surfaces, which makes up our largest barrier and in the blood are more associated with autoimmune reactions. So with celiac disease, for example, the medical test is looking for IgA antibodies to gluten and also to specific tissues in the gut.

Bacteria vs. Viruses

So the unfortunate big floor in the B cell and antibody defense is that it doesn’t deal particularly well with viruses, but it’s great with bacteria. Viruses by comparison to bacteria are tiny, really minuscule. It is actually much easier for a virus to escape past our first two to three lines of defense if you consider B cells in there and to get inside the cell. Once the virus has managed to get inside the cell, then antibodies can’t get to it. Because the antibodies and B cells are for defense against things that are inside the body, but outside the cells, once it’s in the cell, the virus is then able to make thousands of copies of itself into replica, which can be very problematic for the body. So in response to this intracellular invasion, we have this T cell response which is designed to deal uniquely with problems that are occurring inside the cell.

T cells

They are about 1 trillion T cells in the human body and interestingly it is actually very difficult to distinguish between a B cell and the T cell underneath a microscope even by immunologists. So when a T cell receptor binds to a specific antigen, an antigen is a protein or a molecule that creates an immune response. So for example, viruses and antigen or a food can be an antigen. When the specific T cell attaches to a specific antigen, specific T cell receptor attaches to the specific antigen, then that cell produces an army of clones to fight that specific antigen. But this clonal expansion, which is needed to fight the fight, can actually take up to a week to occur, which is why if you think about when you had chicken pox as a child you were sick for a week or two weeks and that is actually because it took a little while for your body to make enough cells because chicken pox is from a virus. First the virus had to get past your immune defense, your first two lines of immune defense and then into the cell. And then it started causing problems inside the cell, at which point it was the T cells problem. Your t-cell take about a week to kick into action and then it probably took another week to overcome the virus because the virus had a week to run relatively free. You were probably sick for a couple of weeks, that’s pretty normal for chicken pox. But the interesting thing is you may have come into contact with chicken pox multiple times during your life.

And that first time you got very, very sick. But the second, third, fourth, and fifth time you caught chicken pox, you didn’t even know that you had it. That is also because of a T cell response. And we’ll talk about that a little bit later in this video. So the other unique thing that’s important to understand about T cells is that T cells only recognize antigens as a problem if it has been properly presented to the T cell. There are a bunch of mechanisms in place in the body and in the immune system just using chicken pox is that same example that would have shown the T cell this exact virus chicken pox virus, this is a problem you need to go and get this. And if it wasn’t presented in the right way, almost think about it. Like if somebody is showing you a label, I’m trying to find a label, somebody showing you a label on a bottle so that you can go out and buy that exact product.

Antigen presentation

If I was to show you the label that way around, that would not be helpful for you because there’s not enough information there. But if I show you the label appropriately, then I am giving you the information that you need to take action, and that’s exactly how your T cells work. The information has to be shown to it in, in a certain way so that it can act appropriately. This is called antigen presentation and it is a very important part of how the immune system works. It’s also a very important part of what goes wrong with the immune system especially with viruses.

There are three types of T cell. We have cytotoxic T cells or killer cells or ninja cells, according to this little cartoon, we have T helper cells who sounded pretty friendly frankly with the whole helper cell label but in fact are also kind of weaponry related. These cells cytokine factories, and you’ll remember that cytokines are those messages, chemical messengers of inflammation. There are multiple different kinds of T helper cell. So we have Th1, Th2, Th3 and Th17. I’m not going to go too much into detail about all of the different T helper cells that there are because it does get a bit complicated and I think that’s probably, I’m branching away from a keeping things simple, but it’s important to know that there are different kinds of T helper cells and T helper cells communicate with B cells.

They intercommunicate with each other so that our immune system can work properly. There is a constant back and forth of communication between B cells and T cells so that there is good balance and an appropriate response in the immune system. The third possibly most important to understand type of T cell for auto immune disease is the T Regulatory cells also abbreviated to T-regs. The T-regs are required for balance in the immune system and for tolerance.  They are involved in helping us to understand when an immune reaction is required and important and also finished, but also when we shouldn’t be reacting in the first place and taught that, not reaction, that’s called tolerance and is possibly the most important thing that your immune system does in any given day.

Antigen presentation

So how does the antigen presentation work? So special cells basically present pieces of a protein from a bacteria or a virus, and those special cells are called MHC cells. T cells have receptors on this surface that can view these proteins when they’re properly displayed or presented. So like I was showing you the bottle on the webcam. It’s also a little bit like a billboard on the surface of the cell in your mother tongue. If you are traveling in another country and you’re going past billboards that are in a language that you don’t understand, you can’t read that message and therefore you don’t know if you should buy that insurance or stay in that hotel for example. But if the billboard is displayed in your mother tongue, it’s displayed in a language that you understand, then you are able to read the information and act appropriately and you can see in this cartoon that’s when the T cell is being presented with a protein or a message that is inappropriate, that’s not being presented correctly. It’s saying, sorry I don’t recognize that I’m not going to take any action.

There are two different class classes of MHC antigen presentation selves. So class 1 MHC cells tell killer T cells that there is a problem inside the cell so that the cell can just straight up be destroyed. Class 2 MHC molecules on antigen presenting cells, tell the T helper cells that a problem exists outside the cell and they trigger cytokine production, which is inflammation and need signaling. Two different kinds of MHC cells instruct two different kinds of T cell for different activity. It is of course a little bit more complicated than that, and I hope that I have explained that in a way that’s easy enough to understand. I feel like that’s probably in as much detail as I should go with so that it doesn’t get confusing, but just to back it up a little bit and do a little revision. An antigen needs to be presented properly to a T cell for that T cell to be able to take action.  Antigen presentation is done via an MHC cell or an MHC molecule. There are two different kinds of MHC. MHC class 1 instructs killer cells so that an entire cell can be destroyed because it’s infected with the virus.  Class 2 instructs T helper cells to trigger cytokine inflammatory reactions.

Your lymphatic system

Now I’m not sure how many of you have ever really thought about the role that your lymph system or your lymphatic system plays in your immune system. So what exactly even is your lymphatic system, It’s your secondary circulatory system, second of course to your heart and your blood vessels. Whereas your heart pumps blood around your body your lymphatic system is actually passive, it doesn’t have a pump. So lymph is moved around the body by the contraction of our muscles when move. As it moves around the body it passes through these stations which are known as lymph nodes or lymph glands. Without the lymphatic system our tissues would actually fill up with fluid, we would be a bit like a water balloon. Lymph nodes are actually secondary lymph organs, we have thousands of lymph nodes in the body and some of our lymph nodes are very tiny and some are actually as large as the brussel sprouts.

So how does that relate exactly to our immune system? Bacteria, viruses and immune cells are transported around our body in lymph and the nodes actually act like a meeting place for the antigen and the immune system. It’s a little bit like a singles bar where they go to meet their destiny. T cells and B cells and antigen presenting cells and antigens or congregate together there, and this increases the probability of efficient function of all of these interactions. It’s kind of a way that we can guarantee that the appropriate part of the immune system is going to meet the appropriate antigen as opposed to having all of this just floating around in the body and operating willy nilly.

Memory cells

When I talked about you getting chicken pox multiple times in your life or coming into contact multiple times throughout your life, and once you’ve had it the first time and you get sick when you get it the second, third, fourth, and fifth time, you don’t even know you’ve had it. That is because of this mechanism called immunological memory. After the initial battle between good and evil or chicken pox and body most of our B cells and T cells will actually die off. But a small number of experienced cells persist, and this is so that we don’t have to start that process from scratch the next time we encounter the antigen. These cells are called memory cells and memory cells are much easier to activate than the inexperienced cells from before the exposure. This is so that the adaptive immune system can spring into action when they’re exposed to the same immune trigger again in the future. It’s a very important part of the way that the immune system works to protect us from invading microbes.

Just to kind of summarize again, I’m going to compare the innate and the adaptive immune systems. The innate immune system is present in tissue all the time, it detects the most common troublemakers. it uses macrophages to eat bacteria and other antigens. It produces enzymes and other weapons of microbial destruction. It triggers chemical messengers of inflammation and other immune cells to come out and help us to help protect us and it communicates with the adaptive immune system to create the plan of action for the immune response. Even when it’s not directly involved in the battle, because it’s not a B cell or T cell, the innate immune response is still kind of overseeing what’s going on with those specific battles, it’s the one creating the plan of action that the adaptive immune response immune system is responding to. The adaptive immune system is talking about T cells and B cells they produce inflammatory cytokines and antibodies. T cells are composed of T helper cells, cytotoxic or killer T cells which is different than natural killer cells. Just in case anybody is getting a little bit confused about that, so killer T cells and natural killer cells are separate than each other, the difference. So we also have T regulatory cells which are critically important for immune balance and for dampening down inflammation, and from a B cell  perspective, we’ve got five classes of antibody which is IgM, IgA, IgG, IgD, and IgE.

Putting it together

Just to use an analogy in case all of that has gotten a bit too technical. Imagine that you’re in the center of town and somebody steals your shoes, so you need to buy a new pair of shoes in order to get home and you see two shops across the street from each other. First we have Charlotte’s custom shoes and they have shoes of every size and every style that you might ever need, but they are custom fit to your exact feet, so it takes a week or two to have prepared for you. That’s not exactly going to help you get home within the next hour. Across the road you see Fiona’s fast fit, this shop only has a few styles and in the common sizes that will fit. Most people write Shaquille O’Neal or a world class ballerina wouldn’t be able to shop here because of size or specificity of function but they have something that you can wear immediately to get home.

That is pretty much exactly how the immune works from an innate or adaptive perspective. In many circumstances the innate response is so efficient that the adaptive response is not needed at all. But at other times the adaptive response will need to be mobilized and that can take a little while because the B cells and the T cells, that can deal with a very large number of almost any invader, but their weapons need to be custom made. That can take a little while to get up to one number that is appropriate for the kind of defense that is required in that situation. In the meantime the innate response kind of does its best until the adaptive response can take over.

The Nuts and Bolts

That’s the nuts and bolts of the component parts of your immune system. Another thing that I think it’s important to understand about a healthy immune system is that actual antibodies or auto-antibodies are produced fairly frequently. However, production in a healthy body is curbed by a immature B cell, basically have to pass a special test before they’re released into the bloodstream. If they don’t pass that test because remember its B cells that make antibodies. Any B cell that is making antibodies inappropriately or in an unhealthy way because the B cell itself is defective, won’t pass that test before it’s released into our central circulation. Our thymus gland which is an endocrine and immune regulatory gland in the center of our body will actually weed out  auto reactive T cells again before they’re released into circulation and faulty B cells and T cells are both killed. And lastly, any auto reactive cells that do escape into our blood or into our limbs are taken care of by our T regulatory cells. Auto antibodies are produced as part of frequently in a healthy body. But we have these mechanisms in place to stomp on that production and auto immune responses early before they become problematic so in a healthy body that is taken care of.

Immune tolerance

The next thing that’s incredibly important to understand about the immune system when it comes to autoimmunity is this concept of immune tolerance. Immune tolerance is health, to be healthy, you must have a tolerant body. Immune tolerance is basically the ability to suppress reactions to foreign molecules that are not harmful to the body. It is also the ability to mount affective reactions to invaders. This thing that the immune system does is to identify what is self from what your stranger and then when it’s identified a stranger it has to be able to differentiate between a harmless stranger and a dangerous stranger. Because really pollen is not going to kill you, pollen is not a dangerous stranger so we should be tolerating pollen but certainly viruses and bacteria do have the ability to kill you. Particularly certain strains so identifying that virus or that bacteria is potentially deadly. We need to mount a response to that, it is very important part of not just how our immune system works with regards to autoimmunity but how our immune system keeps us alive.

Most of the time most of our energy in the immune system is actually given to not responding to things. The immune systems job really is to only respond when it’s appropriate which is a small amount of the time. Most of the things that we come into contact with on a daily basis from an environmental perspective are actually things that we need to not respond to. That’s not a passive thing our body doesn’t just automatically not respond. We have to decide not to respond, a that decision is something that is called immune tolerance and related to our T regulatory cells.

A loss of tolerance

Autoimmunity or auto immune disease is defined as loss of tolerance. It is a broken immune tolerance mechanism against the tissues in our cells. Taking a step back, it’s that inability to identify what his body and what is foreign. It is a response to a part of the body which is not supposed to happen. Immune tolerance is actually a fairly difficult state to achieve and maintain and when it’s broken, and I think that this is important, there is no single magic bullet in order to repair tolerance. It actually requires a collective holistic approach to restore it because there will be multiple mechanisms that have gone into breaking your tolerance mechanisms in the first place and they will be multiple things that need to be repaired and rebalanced in order to restore tolerance.

I debated whether or not to share this or not because it’s just sort of an inside joke of mine and I feel like everybody is probably familiar with the serenity prayer. Grant me the serenity to accept the things I cannot change, to change things I can and the wisdom to know the difference. Whenever I’m writing about immune tolerance, I have this little thing playing in my head, which is lord grant me the immunity to suppress the reactions to things I need not fear to mount affective reactions to invaders and the cellular wisdom to know the difference. And I think for me that sums up immune balance.

3 Kinds of Tolerance

There are three different kinds of tolerance in the body. So the first and possibly one of the most important ones to understand is actually oral tolerance. It is pretty much exactly what it sounds like, it is tolerance to things that are coming in through your mouth. So what are those things? Those things are food and bacteria usually. Central tolerance is the mechanism by which we eliminate defective B cells and T cells before they’re released back into the circulation. Then peripheral tolerance, this is developed after the T cells and the B cells and mature and into the circulation. It includes suppression of auto reactive cells by T regulatory cells. In autoimmunity we have a broken tolerance to self, a broken tolerance mechanism to self, and that is really involving our peripheral tolerance. It’s gone past central tolerance at that point, but it’s often preceded by an associated with broken oral tolerance.

Depending on the mechanism and what the triggers were that preceded your autoimmunity in the first place broken oral tolerance might’ve been the first problem with your immune system or the first problem with tolerance that led to you developing immunity in the first place, that broken oral tolerance lid after a little while to broken central or peripheral tolerance and reactions to self tissue. When we’re trying to restore tolerance which are to promote healthy tolerance restoration in the body, you need to have a oral tolerance in place for that to come back again. Immune homeostasis is when we have a balanced and healthy function in the immune system. It’s not static. Your immune system is designed to be reacting to things on a daily basis, so it’s not a constant state of peace, but it a constant bringing back into balance. When we’re having an inappropriate reaction, we are also having inappropriate termination of that reaction at the end of its life cycle. When there is immune homeostasis and the actions of the auto reactive T cells are counted by regulatory T cells, they’ve got an off switch. But in an inflammatory body, one of the disordered functions that occurs is the generation of T regulatory cells that are unable to suppress the autoreactive T cells. We’re now really looking at what goes wrong with the immune system. When we develop autoimmune disease. Tight control of autoreactive T cells by T regulatory cells is necessary to suppress the development of autoimmune disease in the beginning stages.


In order to induce long lasting remission of immune mediated disease two important factors need to be in place. We need to have some control over the inflammatory environment, which means we need to understand what are the factors in your diet and in your life and possibly in your body that are promoting inflammation. So we need to basically identify and remove triggers, immune triggers, inflammatory triggers, or anything that’s perturbing normal immune function in your body. And we need to boost the frequency and the function of regulatory T cells. Those are two extremely important factors, in understanding and addressing health in somebody who has the autoimmune mechanism present or auto immune disease. Here is an image for those of you that like a little bit more technical detail. So in all autoimmune disease there is an imbalance between the T cells that are capable of causing problems and contributing to auto immune disease. So these includes a Th1 one a which produce interferon gamma, the T follicular cells which produce interleukin 21, and Th17 which produce interleukin 17 and 22.  These interleukins, when I’ve talked about inflammatory chemicals, inflammatory messengers, these are some of the specific ones. There is an imbalance between the T cells that cause inflammation and autoimmunity and T regulatory cells. So there needs to be a balance between the T regs and the T cells. Some of the things that essentially knock the balance or have a negative effect on healthy T regulatory cells or an unhealthy stimulatory effect on T cells include, our genetic background we may be predisposed towards having unhealthy immune reactions. They certainly include environmental factors, that might include something like smoking or low levels of vitamin d. It can include exposures to toxins having a poor quality or inflammatory diets or having inappropriate reactions to even healthy foods in your diet.

It can certainly include infection, in my opinion, most often does. A lot of the research around autoimmune diseases, very focused on bacteria and viruses, even though it is a little bit more complex than that. It can includes a history of antibiotic use and it can also include imbalances in the microbial ecology in the gut, so unhealthy populations of bacteria and viruses present in the body. These are some of the things that predispose  or promotes inappropriate, aggressive inflammatory responses from the T cells a and the B cells, and also promote an imbalance between the T regulatory cells and the pro inflammatory T cells. They can in fact set up a cycle where T regulatory cells us suppressed by some of the chemical messengers that are produced by the immune system. Or it can just create what is essentially a forest fire that gets out of control. There is so much inflammation present after a little while because there is so much stimulation of inflammation by these environmental factors that the regulatory part of the immune system is overwhelmed and unable to respond to appropriately.

One of the, I think important points of course is that each autoimmune disease is distinct and separate and by each disease I don’t mean each of the 80 diseases or 156 diseases, I mean each individual person with the disease. You with celiac and me with celiac, even though we have two very different experiences of celiac disease, but also mechanisms that play in the body, me with celiac and you with rheumatoid arthritis or me with celiac and you with ankylosing spondylitis, any of the auto immune diseases. We have very, very different presentations of illness, but may with celiac or you with celiac, or me with celiac and you with rheumatoid arthritis, there are very specific or overlapping mechanisms that are common to all of us. That is the reason that I think it’s really important to understand these basic mechanisms of immunology.

  1. How does The immune system work?
  2. What goes wrong in the immune system that helps us or lead us to developing autoimmune disease in the first place?
  3. Why does that happen? I’ve touched on a couple of the factors about why does that happen here, but of course I’m going to be talking about that in more depth and in my next video I’m going to be talking about genetic predisposition and the genetics that are involved in ordering. So that’s a wrap on the basics of the immune system and what goes wrong when you have autoimmunity. I hope you’ve enjoyed this video. Thanks for watching and stay tuned for video three.

If you’re suffering from autoimmunity and feeling ready to beat your stress and trauma, and also to improve your health, check out my course The Foundations of Health.

If you would like to get in touch to organise nutrient deficiency testing or discuss how to address your on-going issues, please drop me a line here.

And be sure to sign up for my newsletter for monthly information from me including clinic updates, recommendations for podcasts and books that I have enjoyed each month and more.

Robyn is a Clinical Nutritionist with a specialised interest in the Functional Medicine approach to health. Robyn is very involved with the field of Coeliac Disease, Gluten-Reactive Disorders and Autoimmune Disease. Her passion for the healing power of food, has led her to work with complex cases, involving multiple diagnoses, and chronic health issues such as ME, auto-immune diseases and fibromyalgia. She also has a passion for working with the growing tide of chronic, lifestyle mediated illness; diabetes, cardiovascular disease and obesity, and runs a lifestyle intervention clinic for these issues. Robyn works with patients to nutritionally support their bodies, so that they can heal. She has successfully helped many people around the world improve their health and increase their quality of life. Robyn sees clients in London, Tokyo and New York, and has a virtual practice that allows her to work with people all over the world.

Robyn Puglia

My mission in life is to share my knowledge in order to help people heal. I love to unravel the health stories and the biochemistry to get to the heart of the problem, and to help support nutritional and lifestyle changes that have the ability to transform people’s health. I have seen incredible changes in the health of my clients, and I hope to do the same for you.

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