Introduction to Autoimmunity PDF

Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 Introduction to Autoimmunity Historical aspect of autoimmunity Autoimmune diseases are the pandemic of this century. They have been increasing since the second World War, and we can say...

Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 Introduction to Autoimmunity Historical aspect of autoimmunity Autoimmune diseases are the pandemic of this century. They have been increasing since the second World War, and we can say that they are numerous autoimmune diseases. We make diagnoses every 4 hours of autoimmune diseases in Italy. If the immune system is educated and trained by the environment, then certainly in evolutionary terms what has happened is that all the environment we live in is cleaned up and the challenge for the immune system has decreased dramatically. After the second World War 70% of the Italian population was living in the farms, in contact with animals- they had different lifestyles, whereas now it's the opposite. That result in the antigenic challenge has made the aberration of the immune system way more common. An example: most of us never had parasites which are common. There is a devoted part of the immune system where it was responsible to fight worms,however it has no job now. The image on the right is a very dynamic scheme of a proper immune response against the pathogen or an autoimmune response. We always have somewhere in our body there is something like an antigen presenting cell which is a part of the immune system. They are in the tissues, they can derive macrophages and many cells in our body have the ability to present antigens. How can we initiate an immune response ? We have 2 types of MHC molecules, they are surface molecules (meaning that they are molecules that can be found on the surface of the cell) that will digest each and every protein from the cell or virus. What the cell does is take a sample of each and every protein and cut it in pieces mount them on MHC type 1 molecules and put them on their surface They are specialized cells that are bridging between innate and adaptive and are called NK cells (natural killer cells). They kill every cell they see that either has a MHC (Major Hystochombability complex) molecule which is not autologous or even if they don’t have MHC. This is fantastic because, for example, in tumor cells we may not have MHC 1. MHC class 1 almost every cell in the body has it. However class 2 is specialized, there are guardians in tissues and they present proteins outside of the cell. For example APC (antigen presenting cells ) take bacteria, cut them in pieces and present them to class 2. As we said, MHC class 2 are specialized so a restricted number of cells can express this class and those cells are called antigen presenting cells. These are the 2 ways we can initiate an immune response Sofia Ferretti, Panagiotis Kotsopoulos 1 Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 In any part of our body it will present an antigen presenting cell either the class 1 or class 2 on there surface When we have a lesion for example some dirt and bacteria get in and we have some antigens presenting cells like Langerhans that will digest these bacteria and put them on the surface. What's the other element that is necessary to initiate the immune response ? Except the antigen and the antigen presenting cell we also need a danger signal. The immune system cannot distinguish between self and nonself, however it can distinguish between danger and not danger situations What happens when APC in a tissue sees an antigen and takes it on the surface there is a danger signal ? It changes phenotype and becomes mature and it will require migration ability which means lymphatics. Lymphatics are the most relevant highway for the APC to initiate an immune response. They will travel to lymphatic nodes where there you have cells from the adaptive immune system and APC can meet with B or T cells. How do the B or T cells communicate with the APC cells? APC are able to present both class 1 and class 2 MHC to the B or T cells Student question: Could you please repeat which cells have class 1 MHC and which cells have type 2? Answer: Class 1 is present in all molecules with a few exceptions like neurons, brain cells and astrocytes dont present but they do when it's needed. Why are they not killed by NK cells? Because they have inhibitory molecule that will make NK cells not to kill them. What are B and T cell receptors ? Why can the immune system produce diverse responses? B and T cells receptors are so diverse and this is done thanks to recombination. When the antigen presenting cell gets to the lymph node they will find the T cells and see if there is a match. If it finds the T cell which is the perfect match nothing will happen because of its signal 1, the only thing that might happen is energy deletion and this T cell (self reactivity) is eliminated or shut off. However if we signal 2 the situation is different: it is elicited by inflammation. At this point the T cells are activated and it takes 40-60 mins of constant interaction to really start the adaptive immunity response because it wants to be sure the reaction Is going through because the wrong response can lead to autoimmunity. The T cells now proliferate, make the clonal expansion and finally get to a maturation state where it can travel and get out of the lymph node into the bloodstream. At the bloodstream the activated T cell searches for the target when it Sofia Ferretti, Panagiotis Kotsopoulos 2 Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 arrives on the target tissue. In the case of a virus let's say the T cell can't see the virus but only it can see the only piece of protein that has been shown to him. So we need a second antigen presenting cell which re-activates the T cell in locally following the same system before, otherwise the T cell will either die or shut off and cause autoimmunity. If for example in a mechanism called molecular mimicry the specificity is super specific and the recognition from PCR is degenerated. So you might have a PCR that has been selected on a virus but it also recognizes a piece of your body. If he sees the same epitope on a different protein which is a self protein it will be presented in a normal environment and the specificity will be eliminated not to cause autoimmunity. Only if the inflammation is represented by the APC locally will finally license the T cell to become effector. T cells are subdivided into CD4 and CD8 T cells. CD4 T cells recognize antigens on MHC class 2 whereas CD8 recognizes antigen on MHC class 1. CD8 are extraordinary elements to fight viral infections because viruses behave like cellular parasites therefore the antigens for parasites are taken from inside the cell and present mostly on class 1. While CD4 is more relevant for other types of infections for example parasites and bacteria. There are many checkpoints to avoid an autoimmune reaction so how is it possible despite these checkpoints and all the possibilities for the immune system to recognize this is a self antigen and we should shut down this autoreactive T or B cell, why does it occur? If the APC in the tissue licenses the T cell to kill the pathogen, you will have tissue distribution and presentation of numerous of self-antigens in inflammatory conditions So why doesn't any inflammatory trigger autoimmunity ? This is because of the checkpoints For example, several autoimmune diseases which are self-limiting. I'm thinking in the neurology field, for example, about the Guillain-Barré syndrome,which is caused by, as I was saying, molecular mimicry. You have a trivial gut infection, Campylobacter jejuni, and some of us, because they have some predisposing genes or they have a certain MHC class 1 and 2 haplotype,they more likely mount a cross-reactivity between the Campylobacter jejuni and a certain ganglioside, GM1 or GM2, which is on peripheral myelin. These persons develop a neurological disease because they start to have an immune reaction that fights the bacterium, but at the same time destroys myelin on peripheral nerves. It's a very severe disease, but it's self- limiting.You have an invasion time, and then you have fought the bacterium, which has disappeared, the stimulus is not there anymore, and, correctly, then the neurological disease fades away with self-limiting mechanisms. The picture on the right is a graphic recap. We see the MHC molecule and the receptor on T lymphocytes. If there is not the signal 2 on CD8 which is the corresponding Sofia Ferretti, Panagiotis Kotsopoulos 3 Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 receptor on T lymphocytes nothing happens. If it's there we have the generation of effector T lymphocytes and also memory. It is very relevant that we develop memory. Vaccines work through developing memory because usually, just to give you the timing. An adaptive immune response takes 15 days to develop and to become effective. Reason why so many people have died during COVID, it took them 15 days to develop a specific response. Meanwhile, the bilateral pneumonia was killing many of them, making them so miserable to end up in the Intensive Care Unit. What happens if the signal II is missing? Either they become anergic and even suppressive. There are T lymphocytes that are antigen-specific, but instead of activating, they suppress all the responses against antigens. Becoming regulatory T cells or you can be simply deleted (killed). Question: How do we get to tolerance when we do not have signal II? Answer: T lymphocytes instead of being deleted or becoming simply anergic, can become T regulatory cells. It is a T cell that is able to suppress immune reactions in the lymph nodes and in the tissues. It has several effector mechanisms, it can suppress proliferation by competing for IL-2, which is the most relevant trophic growth factor for T cells. Because they have a high affinity for IL-2 receptors, so they will be scavengers of IL-2. But they are also able to hydrolyse ATP. Extracellular ATP is one of the most trivial and powerful dangerous systems that you can have. Because ATP is the fuel of cells, it is perceived by others cells as danger. The fact that there are purinergic receptors all over the cell to activate. So, for example, the T regulatory cells have ectoenzymes, which are enzymes on the surface of the cell. These enzymes are able to hydrolyze ATP to reduce it to AMP. This shuts off or cuts off danger signals. How are autoimmune response possible? There are several hypothesis. The starting point very often may be molecular mimicry. One of the possibilities is that there is a genetic predisposition. We have cases where families have numerous autoimmune diseases. Although Sofia Ferretti, Panagiotis Kotsopoulos 4 Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 the incidence (weight of genetic predisposition) is relatively low. Autoimmunity is a lottery that we all have tickets for, at any age. The environment is largely predominating. Nevertheless, genetics and genes have their role. Genes that are predisposed to autoimmunity There is a non-ending list of alleles that will predispose you to autoimmunity, but we are going to talk about just the important ones. Eg: FoxPT. It is a nuclear transcription factor, which is considered the master gene for the differentiation of T regulatory cells, fundamental to ensure peripheral tolerance. There is a central tolerance which is obtained in the thymus. T cells are selected and mature in the thymus (reason why they are called T cells). What happens in the thymus? The stroma of the thymus has antigen presenting capabilities. It will present a large number of antigens. It expresses so many different antigens and autoantigens. The stroma of the thymus expresses proteins that have nothing to do with the stroma. It has been an evolutionary mechanism to select T cells. The T cells that get through the stroma, will be selected. What is the general rule for selection? All the T lymphocytes that have a T cell receptor and recognizes antigens in the stroma of the thymus with a very high affinity, are eliminated, because they are clearly dangerous. These are potentially autoreactive and we don't want them in our repertoire. We do not want them to circulate as those have a very high affinity for antigens that we have in the body. The thymus is not infected, has no bacteria, so we don’t want them. If a TCR has a very low affinity, it will be eliminated. Because most likely these TCRs are not working. So in the thymus, all the TCRs that have intermediate affinity are selected, and are by definition autoreactive. But being of intermediate affinity the recognition has been largely degenerated. So they will have a lot of different specificities. ***Going back to FoxPT:*** A genetic defect in FOXP3 can lead to a condition known as IPEX (Immune dysregulation, Polyendocrinopathy, Enteropathy, X-linked syndrome). This human disease can present with varying degrees of severity, depending on how much the Sofia Ferretti, Panagiotis Kotsopoulos 5 Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 FOXP3 protein is affected. In cases where the protein is severely impaired or even deleted, the severity of the condition increases. In the most severe instances of IPEX, individuals may experience a complete loss of immunity to certain diseases, such as polio, and develop multiple autoimmune disorders, leading to significant health complications and, in some cases, death. T-regulatory cells are clearly crucial for maintaining immune balance. They play a significant role in preventing autoimmunity, and variations in genes related to these cells can predispose individuals to autoimmune diseases. However, if genetic factors are not the only consideration, it's important to note that we all have the potential to lose functionality in T-regulatory cells. When T-reg cells fail to function properly, peripheral tolerance is compromised, leading to an increased risk of autoimmune responses. In addition to T-reg cells, there are other regulatory cells within the immune system. Recent discoveries have identified suppressive myeloid cells, contributing to our understanding of immune regulation. While there are various types of suppressor cells, T-reg cells remain of paramount importance. The absence of functioning T- regulatory cells means that the immune system lacks the necessary suppression mechanisms, which can lead to conditions such as impaired immunity to diseases like polio. Mechanisms of autoimmunity diseases Autoimmunity can manifest in various ways, leading to conditions such as lupus, arthritis, and Crohn's disease simultaneously. This complexity suggests that multiple mechanisms may contribute to the onset of autoimmune diseases. One mechanism is bystander activation. For an immune response to occur, we typically need a danger signal, which is often absent when an autoantigen is presented. However, if a danger signal arises for another reason, it can lead to bystander activation. In this scenario, the danger signal acts as an innocent bystander that inadvertently activates the immune response against the autoantigen. Another important mechanism involved in the initiation of autoimmunity is molecular mimicry. This phenomenon has been demonstrated in many autoimmune diseases. For example, in Guillain-Barré syndrome, the immune system may mount a response against a pathogen, such as a virus or bacterium, that inadvertently cross-reacts with the body's own tissues. This cross-reactivity can lead to autoimmune responses, where the immune system attacks its own cells instead of just targeting the pathogen. Paraneoplastic disorders Sofia Ferretti, Panagiotis Kotsopoulos 6 Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 One aberrant example of immune response. In these cases, the immune system mounts a vigorous reaction against a tumor, but this response can inadvertently trigger an autoimmune reaction.This situation creates a dilemma for physicians. On one hand, the immune system's activity is crucial for fighting a tumor that may be difficult to eradicate through surgery or chemotherapy. On the other hand, this same immune response can lead to severe neurological diseases. Healthcare providers often find themselves puzzled in such scenarios, facing the challenge of balancing the need to harness the immune system's power against the tumor while managing the potentially harmful autoimmune effects. For instance, several ovarian tumors and pulmonary tumors have been associated with these paraneoplastic syndromes. In situations involving paraneoplastic syndromes, the immune system can be doing both good and bad simultaneously. This creates a challenge for intervention, as we currently lack the ability to selectively shut off one of the two conflicting reactions. Paraneoplastic syndromes encompass a wide range of diseases, highlighting their complexity. These conditions are not solely immune-mediated; rather, they can arise from various mechanisms depending on the type of tumor involved. As a result, there are many different paraneoplastic diseases. While some of these conditions are mediated by the immune system, others may operate through different pathways, further complicating the clinical picture. Development of autoimmune disease Many years ago, we proposed the idea that the development of an autoimmune disease, particularly in the brain, may be influenced by a combination of genetic predisposition and various environmental factors. Essentially, for an autoimmune response to occur, there must be a situation in the periphery where a T-cell with inappropriate reactivity—specifically, auto-reactivity— has the opportunity to develop, proliferate, and become activated. Simultaneously, within the brain, some degree of micro-inflammation is necessary. Without this micro- inflammation, there would be no antigen-presenting cells capable of interacting with these aberrant T-cells, thereby initiating the autoimmune reaction. Sofia Ferretti, Panagiotis Kotsopoulos 7 Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 Dual signal hypothesis There must be at least two aberrant situations for autoimmune reactions to occur. 1. The first is in the periphery, where a reactivity develops that is undesirable. 2. The second is in the target organ, where a dangerous signal—one that shouldn't be present—is needed to initiate the autoimmune reaction. Without these two conditions, the occurrence of autoimmunity would be impossible. According to this hypothesis, two signals are necessary, making the onset of autoimmunity seem both unlikely and mysterious, especially given the increasing rates of these conditions. Despite this rise, autoimmune diseases still affect only a minority of the population. However, a significant number of individuals will experience an autoimmune disease at some point in their lives. The situation is quite complex, involving a dialogue between the brain and the deep cervical lymph nodes, which are responsible for draining the brain. Basis of autoimmune neuroinflammation - Multiple Sclerosis The first descriptions of multiple sclerosis date back to the second half of the 19th century. Babinski was truly a remarkable figure in the study of multiple sclerosis (MS). While Charcot and Cuvier provided the first clinical descriptions of some of the disease's features, Babinski made the first pathological description. He identified MS as an inflammatory disease, illustrating this with a central vein surrounded by an inflammatory infiltrate, represented by black dots, which are lymphocytes. Notably, in MS, the majority of these lymphocytes are CD8 positive. For years, researchers have speculated about a possible viral trigger for MS. As I mentioned previously, CD8 cells are primarily involved in responses to viral infections. Therefore, viruses may be one of the triggers for this demyelinating disease, where the target is myelin. To Sofia Ferretti, Panagiotis Kotsopoulos 8 Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 illustrate this, I present a Sudan black staining of a human spinal cord, highlighting the demyelination characteristic of MS. The image appears entirely black because it represents white matter. Sudan black stains lipids, and since myelin is primarily composed of lipids, this demonstrates a demyelinating plaque where myelin has disappeared. The consequence of losing myelin is the exposure of naked axons. If this condition persists, the axons can degenerate and die, as shown by the transected axons in the illustration. Thus, multiple sclerosis is an immune-mediated demyelinating disease that ultimately affects nerve fibers and axons. It can affect virtually any area of the brain and spinal cord, resulting in lesions throughout. Consequently, symptoms can be incredibly diverse, ranging from focal neurological symptoms like vision loss, seizures, and even psychiatric onset, to numbness in a limb or paralysis. One common pattern is relapsing- remitting courses, where an individual experiences an attack followed by a period of recovery, which can be almost complete or, at times, complete. During these periods, the clinical score may return to baseline before subsequent attacks occur months later. After 10 to 15 years of the disease, the course can change to a secondary progressive form. In this stage, inflammatory activity diminishes, and while attacks cease, there is a gradual degeneration of neurological functions. Additionally, primary progressive forms exist, where the relapsing-remitting phase is absent. In these cases, the onset of symptoms occurs, on average, 10 to 15 years later, leading directly to a progressive decline in neurological functions. Multiple Sclerosis - Treatments I have been involved in the field of MS since 1989, so I feel I have some experience to share. At that time, treatment options were extremely limited. We primarily administered steroids during acute attacks, but chronic steroid use did not alter the disease course, leaving us with very few options for management. As of 2024, we have over 20 effective treatment molecules for multiple sclerosis, each offering unique benefits. With the opportunity for early diagnosis and appropriate intervention at the onset of Sofia Ferretti, Panagiotis Kotsopoulos 9 Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 the disease, our target is referred to as NIDA (No Evidence of Disease Activity). Remarkably, we can maintain NIDA for 90-95% of patients over a span of 25 years, marking a significant improvement in the management of MS. That said, MS remains a potentially dangerous and disabling disease if diagnosed late, treated improperly, or if individuals are not fortunate enough to have access to treatments, particularly in Western countries. Unfortunately, MS is increasingly spreading to regions such as North Africa, the Middle East, Iran, Iraq, and parts of South America, including Venezuela, Nicaragua, and Uruguay. Some nations struggle to afford the very expensive treatments for multiple sclerosis, which are primarily biological therapies. However, it's important to note that the landscape of MS management has changed significantly. Myelin and its importance in MRIs A myelinated axon has a conduction velocity of around 100 meters per second, while an unmyelinated axon has a conduction velocity of roughly one meter per second. This difference is crucial, as it significantly impacts your ability to process reactions, movements, and other functions. The aberrant signal on MRI can vary depending on the sequence used. In this case, we are looking at a T1 sequence with contrast, which reveals the so-called "Dawson’s fingers." These areas take up contrast and appear hyper-intense, meaning they show up as white on the MRI. This finding illustrates that the lesions are typically located around veins. The process occurs outside the vessels and leads to the formation of demyelinating plaques. In contrast, the third picture is a T2 sequence, which presents a completely different appearance. Here, we observe a pseudo-tumoral presentation. Although this type of lesion is visually impressive on the MRI, the prognosis for these lesions is generally not bad. The challenge with diagnosing lesions on an MRI lies in the ambiguity of the findings. When you first encounter such a presentation, it can be difficult to determine whether it is a glioblastoma, which is a very different and aggressive situation that may result in only a few weeks or months of survival. Alternatively, it could be a primitive CNS lymphoma, which has a much better prognosis, or a pseudo-tumoral presentation of multiple sclerosis. In this case, we are looking at a pseudo-tumoral presentation of MS. While MRI is essential for making a diagnosis, it is clear that additional elements are needed for a definitive conclusion. Sofia Ferretti, Panagiotis Kotsopoulos 10 Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 Other examples of autoimmune diseases and their targets: Hashimoto's thyroiditis, its target is thyroglobulin. In myasthenia gravis, the target is the acetylcholine receptor. However, when it comes to multiple sclerosis (MS), the situation is more complex. Extensive research over the past 30 years has sought to identify the specific antigen responsible for the autoimmune reaction in MS. While we know that myelin is involved, the precise protein, epitope, or molecular target remains elusive. Current thinking suggests that there may not be a single target; rather, each individual with MS has their own unique auto-reactivity, which we refer to as "private" autoimmunity—not shared among patients. How do we know that MS is immune-mediated? How do we know it’s autoimmune? Many researchers, over 20 years ago, explored the possibility that MS might be an inside-out mechanism. If the disease was purely autoimmune, it would follow an outside-in mechanism, where tissue reactivity is generated in the periphery, allowing it to enter the brain and cause damage. But what if it is an inside-out mechanism? In this scenario, oligodendrocytes might die for some reason, leading to secondary inflammatory responses that are merely epiphenomenal. Clearly, when cells are dying, inflammatory cells will enter to clear up the damage. So, why do we believe it’s an outside-in process? Couldn’t it be an inside-out mechanism? As scientists, we need to postulate hypotheses and then seek answers to these questions. The hypothesis here is that if MS is immune-mediated, then inhibiting the immune system should lead to improvement in the condition. Bringing us to the concept of bone marrow transplantation First, let’s clarify what a bone marrow transplant involves. In a bone marrow transplant, the first step is to mobilize the stem cells from your blood. This is typically done using a drug like cyclophosphamide. After mobilization, CD34 positive cells, which are the stem cells capable of generating all the various blood cells, are collected. While this can also be done through a biopsy of the bone marrow, it is now more commonly performed by collecting stem cells from peripheral blood, which is a less invasive procedure. Once a sufficient quantity of CD34 stem cells is collected, they are frozen for later use. The next step is called conditioning. This involves using chemotherapeutic agents to eliminate the existing bone marrow cells. A combination of very toxic drugs, often used in oncology, is employed for this purpose. There are different conditioning regimens available depending on the specific needs of the patient. The most effective treatments for autoimmune diseases, particularly multiple sclerosis (MS), are those that are myeloablative. This means the goal is to completely wipe out the existing immune system. The third step in this process is transplantation. After the immune system has been thoroughly ablated, the previously collected stem cells are taken from storage Sofia Ferretti, Panagiotis Kotsopoulos 11 Basic Mechanisms of Diseases Prof. Roberto Furlan 11/10/2024 and infused back into the patient. The general concept here is to reset the immune system completely. By eliminating the previous immune system, the infused stem cells can repopulate and generate a new immune system. If the hypothesis is correct, this should result in the resolution of the autoimmune disease. Does this approach work for MS? Absolutely. We now have individuals who underwent transplantation 17 to 20 years ago and remain free of the disease without any further therapy. While we are hesitant to label them as "healed," this caution is likely a matter of prudence and understatement. Why aren’t we transplanting every patient with an autoimmune disease? The answer lies in the risks associated with bone marrow transplantation. The procedure leaves patients without an immune system for 6 to 8 weeks, during which time they are highly vulnerable to infections and other complications. Consequently, there is a procedure-related mortality rate that varies depending on the statistics and specific patient series. The procedure-related mortality for bone marrow transplantation can be around 1 to 2%, which is significant. When patients rush into my clinic insisting they want to be transplanted, I have to explain that we cannot proceed with such a request. Ethically, we can only select patients who are not responding to conventional treatments or those who have a very severe condition, and we must ensure they understand all the associated risks. In fact, our statistics show a much lower procedure-related lethality, around 0.2% to 0.3%. Additionally, we have very effective medications available for managing other aspects of their condition. Therefore, it is ethically incorrect to propose a transplant for every patient. However, the transplant process clearly demonstrates that substituting the existing immune system with a new one can lead to the resolution of the disease. This supports the notion that the condition is immune-mediated. Importantly, all memory cells in the immune system are wiped out during this process. When the immune system is re-established after a bone marrow transplant, patients must receive all their vaccinations again. This also highlights the danger of the procedure: even a trivial infection can become life-threatening during the recovery phase, as patients lack immunity. That said, the outcomes of these transplants provide compelling evidence that MS is an immune-mediated disease. There is no oligo dystrophic mechanism or hidden virus destroying oligodendrocytes; rather, the inflammation is a direct consequence of immune activity. When the immune system is wiped out, the disease resolves, demonstrating that it is indeed immune-mediated. Sofia Ferretti, Panagiotis Kotsopoulos 12