welcome back to week nine of applied immunology the first lecture for this week centered on allergic reactions which encompass several types of detrimental adaptive immune responses that are activated in response to harmless environmental antigens and we call these allergens we will build on that theme with today's lecture 9b where we will look at another set of immune pathologies resulting from undesirable activation of inflammatory responses against self-antigens using the greek prefix auto which means self we collectively refer to these as autoimmune disorders today we will discuss the ways in which genetic and environmental factors promote a breakdown in immunological tolerance we will also talk about the effector cells and tissue types that can be affected based on patterns of antigen expression and then end by summarizing the mechanism of action of several autoimmune pathologies autoimmunity encompasses a wide variety of diseases that attack healthy self-tissues through several different underlying mechanisms this table summarizes some of the most common autoimmune disorders many of which we will learn about in depth today these all vary with respect to the mechanism of disease pathogenesis which since these are mounted in an antigen specific manner against self tissue these require adaptive immune activation through either autoreactive t cells or the production of auto antibodies by autoreactive b cells for some of these specific autoantigens have been defined while others may be driven by a mixture of autoantigens these diseases also vary with respect to the consequences or symptoms of immune activation which largely depends on where autoantigen is expressed in the body lastly the prevalence of each disorder varies although it's thought that roughly five percent of the population in western countries is affected by autoimmune disease a recurring theme in this course is that inflammatory immune responses must be deployed against pathogens while remaining non-reactive to healthy self-tissues which is the concept of immunological tolerance to self-antigens we've learned that there are numerous mechanisms through which tolerance is established and maintained in lymphocytes and that these mechanisms must be functional in order to avoid autoimmune diseases like the ones listed above in order to learn more about how tolerance is broken in autoimmunity let's first recap the mechanisms through which tolerance is established in the healthy patient we can start with central tolerance and primary lymphoid organs which refers to selection mechanisms that occur at different checkpoints during either b-cell development in the bone marrow or t-cell development in the thymus these checkpoints serve to either delete or edit lymphocyte antigen receptors that bind strongly to self-antigens or they recognize self-antigens one important mechanism of central tolerance during t cell development is something that we haven't talked about yet which is the expression of a transcription factor called autoimmune regulator or air now selection in the thymus is based on expression of the majority of self-antigens within the thymus but there are still some self antigens that are only expressed in specific organs or tissues that would not otherwise be expressed in an organ like the thymus these are called tissue specific antigens or tsas and these include things like insulin which is expressed in the pancreas myelin proteins that are found in the brain and some retinol proteins that are expressed in the retina of the eye air is a transcription factor activated in thymic epithelial cells and thymic dendritic cells that actually turns on expression of these tsas in different apc subsets and this allows the apcs to present these antigens to developing thymocytes in order to establish central tolerance against peripherally expressed self antigens central tolerance therefore should remove autoreactive t-cell clones that recognize either thymic antigens or peripheral tsas if central tolerance functions perfectly then the end result is that only non-autoreactive lymphocyte clones are allowed to develop into a mature naive state and these cells are the only ones that are found in the pool of lymphocytes that circulate through tissues and populate the secondary lymphoid organs there are also several mechanisms for establishing peripheral tolerance or tolerance exerted on lymphocytes once they finish development in the primary lymphoid organs we haven't covered all of these extensively except for our lecture 5a on b-cell development where we learned about energy and again this is a state where b cells become unresponsive to cognate antigen there are other mechanisms of peripheral tolerance including the physical segregation of antigen either intracellularly where lymphocytes can't access it or within organs that are not surveyed by lymphocytes which are called immune privileged organs and these include places like the eye brain and reproductive organs lymphocytes can also undergo activation-induced cell death which is a form of apoptosis that occurs following repeated antigen stimulation and this is meant to remove inflammatory activated lymphocytes from the body after they've presumably had enough time to exert effector functions to remove pathogens functional deviation is another thing that refers to the differentiation of t cells towards alternative or less inflammatory phenotypes such as th2s in some contexts or t regulatory t cells lastly t regs are extremely important in establishing and maintaining peripheral tolerance their immunosuppressive activities often override inflammatory signals from neighboring t cells as the secretion of cytokines like il-10 and tgf-beta inhibit effector t-cells including those that may be self-reactive t-regs can also kill effector t cells either directly through cytotoxic mechanisms or indirectly by starving them for nutrients or survival cytokines like il-2 t-regs can also inhibit apcs through expression of regulatory ligands like ctla-4 lag-3 and ido collectively the activities of t-regs make them a potent inhibitor of potentially auto-reactive inflammatory responses in the periphery and it's worth noting that many mechanisms of t-reg mediated immune suppression are actually co-opted in the context of tumor suppression of the immune response which we will learn more about next week in week 10 lectures on tumor immunology we can think of all of these mechanisms used to establish and maintain both central and peripheral tolerance as a sort of gauntlet or succession of checkpoints and each of these checkpoints work together to prevent either the development or activation of autoreactive lymphocytes and any individual checkpoint can catch any potentially dangerous autoreactive clones that slipped through a fault in an upstream checkpoint and this works the majority of the time in healthy individuals so what types of defects in these mechanisms actually occur in the patients that present with autoimmune disorders much like allergy autoimmune disorders can be controlled by both genetic and environmental factors let's start by looking at genetic factors so genetic mutations that affect the presence or function of certain genes involved in immune regulation understandably influence the phenotype of certain immune cells which could enable autoimmune disease through a number of mechanisms depending on the mutation and the tissue that it affects these mutations may affect the survival of certain cell types or key aspects of their function that are needed to maintain tolerance and this leads to a variety of pathologies depending again on the cell type as well as the tissues that are involved there are a handful of rare autoimmune disorders that are driven by mutations or deletion of a single gene and we call these monogenic disorders these are quite rare and are often inherited in either x-linked or autosomal recessive fashion this includes air deficiency or mutation which again is required for tissue-specific antigen expression in the thymus so without air people develop a severe autoimmune disorder called ape-said which attacks peripheral organs ctla4 mutations are associated with graves disease type 1 diabetes and others due to decreased regulation of effector t cells fox p3 mutations can lead to a lack of functional t-regs and this results in a severe autoimmune disease called ipex where patients die at a fairly young age other monogenic diseases include fast mutations which render tnb cells more resistant to fast ligand mediated killing this results in a lymphoproliferative disorder called alps these types of monogenic disorders make sense since they involve genes that are directly required for the cells and mechanisms of central or peripheral tolerance which we just talked about in the last slide however the majority of autoimmune disorders are thought to be polygenic and that they result from numerous defects in multiple immune pathways that are required for either immune tolerance or the regulation of inflammatory responses understanding how different gene products interact with one another and polygenic disorders is complicated but let's look at two genetic factors that are often implicated in autoimmunity the first of these is quite straightforward since it is biological sex this graph shows incidence of diabetes in a mouse model of type 1 diabetes called nod where you can see that female mice in red have earlier onset and higher penetrance of type 1 diabetes compared to male mice of the exact same genotype in the blue line so again these are genetically identical individuals except for their difference in sex this is obviously an example from a preclinical animal model used in research but it's worth noting that autoimmune disorders in general tend to occur at higher rates in women than men this is an example of sexual dimorphism this is particularly true for systemic lupus erythematosus or sle as well as multiple sclerosis or ms the mechanisms underlying why this happens are still unclear but sex-dependent mechanisms of autoimmunity are a major area of ongoing research hoa haplotypes are another genetic factor that is associated with susceptibility with some autoimmune disorders this table lists mhc alleles that are strongly associated with particular autoimmune diseases presumably because these mhc alleles exhibit especially strong binding to an epitope of self-antigen that's involved in that autoimmune disease alternatively certain mhc alleles may influence the tcr repertoire during establishment of central tolerance in a way that sort of allows for maturation of more autoreactive t cell clones as would be the case of mhc bound weekly to some self antigens expressed in the thymus and therefore didn't exert sufficient negative selection on thymocytes the exact mechanism underlying these types of associations likely depends on the specific disease context but nevertheless hla haplotype is a recurring genetic locus that is associated with susceptibility towards autoimmune pathologies the second type of factor implicated in autoimmune disease development are environmental stimuli such as infections or injuries that induce an inflammatory state in the body there are interesting correlations in patients where a bad inflammatory event preceded the onset of autoimmune pathology and there are a few different proposed mechanisms for this the first is that self-antigens presented during homeostasis will not stimulate t cell activation because these only consist of signal one of tcr activation without any co-stimulatory marker expression or cytokines that are needed to fully activate t cells however self-antigen that's presented by some apcs that are also activated by a concurrent inflammatory reaction could mistakenly lead to the activation of autoreactive t cells which are unable to differentiate between inflammatory cues that are associated with pathogen-derived antigens versus self-antigen that is presented in a sort of coincidentally inflammatory context in individuals with successful immune tolerance mechanisms this would be a rare event because it would involve the encounter with one of only a few autoreactive t or b cell clones but in a genetically susceptible individual this may occur more frequently the second mechanism has to do with infection or injury that induces tissue damage which releases self-antigens that haven't been used to establish immune tolerance this could involve antigens that are either sequestered intracellularly and so they're not usually available to lymphocytes or entire organs containing antigens that aren't usually surveyed by lymphocytes and the latter example involves what we call immune privileged sites that aren't typically surveyed by lymphocytes at least not to the same extent as other tissues these include organs like the brain eye ovaries and testes an example of this type of injury is something called sympathetic ophthalmia where injury to one eye leads to retinal antigen drainage to the lymph node and this primes t cell responses that can then traffic to the other uninjured eye to attack antigen-expressing cells over there lastly there are some pathogens whose antigens closely resemble certain self-antigens this is a case called molecular mimicry where the immune system is mounting a response to foreign antigen but the t cell receptor or b cell receptor just happens to be cross-reactive with self-antigen an example of this is rheumatic fever which can occur following infection with streptococcus bacteria in this case an epitope in the streptococcal bacterial cell wall is structurally similar to antigens that are expressed in the valves of the heart so these anti-streptococcus antibodies cross-react with the heart valves and cause inflammatory tissue damage in the heart there's no actual breakdown intolerance or immune recognition here it's just a unfortunate coincidence that antibacterial antibodies happen to cross-react with self-antigen the exact mechanism of autoimmune initiation depends on the specific patient in the specific autoimmune disease so as scientists and clinicians we try to attribute a disease etiology to a clearly defined root cause or root causes but this just may not be possible for most types of autoimmune disease in most patients autoimmunity is likely caused by some combination of both predisposing genetic factors as well as inflammatory environmental triggers like infection or injury regardless of the underlying causes all autoimmune pathologies are characterized by some degree of immune dysregulation that leads to the pathological activation of immune responses against self-antigens before we get into the specific mechanisms of action of several autoimmune disorders i want to touch on the fact that these pathologies often involve multiple components of an immune response this table summarizes how autoreactive t cells b cells and secreted antibodies all play a role in the pathogenesis of common autoimmune disorders like sle type 1 diabetes myasthenia gravis and multiple sclerosis each of which we will discuss later on on in today's talk although the specific underlying mechanisms may vary most autoimmune diseases involve a breakdown of immunological tolerance of both t and b cells for b cells this is characterized by presentation of self antigens to t cells and or the generation of auto antibodies for t cells this can be mediated through direct cytotoxic effects of th ones or cytotoxic t lymphocytes or cd8 t cells as well as t cell help to b cells to promote class switch recombination and tailoring of auto antibody responses so although we tend to categorize some autoimmune disorders due to the primary effector functions that drive autoimmunity keep in mind that for most of these diseases autoimmunity is quite comprehensive in that it involves a loss of tolerance by multiple lymphocyte populations with that being said most autoimmune disorders can be grouped according to the predominant mechanism that drives autoimmunity this chart organizes several autoimmune diseases according to whether the pathology is primarily exerted by auto antibodies that are bound to surface antigens antibody antigen complexes that form aggregates responsible for driving inflammation or t-cell mediated autoimmune diseases note that for some disorders like rheumatoid arthritis multiple immune mechanisms are implicated in parallel which is why it is categorized as both an immune complex and t-cell-mediated disease the consequence or pathological characteristics of each disorder is described in the far right column of this chart much like allergy autoimmune diseases present with a wide variety of clinical symptoms that depend on the tissues where autoimmune responses are activated it's also interesting to note that many autoimmune disorders usually present as cycles of flare-ups called relapses that are separated by periods of reduced disease symptoms called remissions and these are called relapsing remitting courses of disease that may continue in this cycle for months or years or even decades although both the stimuli that induce symptom relapse and the regulatory mechanisms that induce symptom remission even when autoantigen is still present both of these are largely unknown in many cases these diseases are treated with anti-inflammatory medications such as monoclonal antibodies against tnf alpha or integrins involved in lymphocyte trafficking although these immunosuppressive therapies understandably lead to off-target effects that increase patient susceptibility to certain types of infections since classical autoimmune disorders occur in an antigen specific manner because they're mediated by lymphocytes the organs where autoimmune pathology is concentrated unsurprisingly depends on where autoantigen is expressed some diseases are driven by a tissue-specific antigen that is not expressed widely throughout the body so not surprisingly autoimmune pathology is limited to the tissue or organ where that autoantigen is expressed examples of these would be type 1 diabetes which specifically targets antigens expressed by beta cells in the pancreas another example of this would be hashimoto's disease which attacks the thyroid due to self-reactivity against thyroid peroxidase which is an enzyme that's only expressed in the thyroid other autoimmune diseases are spread across tissues throughout the body and so they are referred to as systemic autoimmune diseases antigens that drive systemic pathologies are usually things that are more ubiquitously expressed by many cell types in sle patients this includes autoantibodies against chromatin or other nuclear proteins and since these are expressed in many tissues sle pathology affects diverse organ systems including the skin as well as the kidneys for the remainder of this lecture we will drill down into understanding a bit more about some of these individual autoimmune pathologies one by one the first example we will look at is something called myasthenia gravis which is a autoimmune disorder that affects peripheral nerve signals that act on muscles this disease involves both autoreactive t cells and b cells though the primary pathological effector are the b cells which produce antibodies specific for acetylcholine receptor and this is expressed on muscles the t cells are primarily cd4s that provide t cell help to the acetylcholine specific b cell clones the auto antibodies function by binding to acetylcholine receptors on muscle cells this leads to the internalization and degradation of the receptor muscle cells therefore cannot respond to the neurotransmitter acetylcholine which is released by peripheral nerves that enervate skeletal muscle and acetylcholine is a key signal involved in inducing sodium ion influx to mediate muscle contraction patients with this autoimmune disease exhibit muscle weakness that gets progressively worse and can be potentially fatal myosthenia gravis is a disorder that is characterized by auto antibodies that bind to a cell surface antigen in this case a receptor expressed in muscle tissue and this blocks its function and leads to disease symptoms specifically within skeletal muscle another disorder that's primarily driven by auto antibodies is systemic lupus arithmetosis or sle sle is caused by auto antibodies that recognize broadly expressed antigens these are oftentimes nuclear antigens such as self nucleic acids chromatin or other nuclear proteins these become exposed when dying cells aren't cleared properly by phagocytes and are allowed to sort of fall apart or dissociate in tissues and release their contents and this kind of demonstrates how important the tolerogenic signals associated with apoptotic cell clearance are for suppressing inflammatory autoimmune responses this diagram considers sle where the auto antibodies recognize self rna and self dna in this case antibodies are bound to a certain type of dendritic cell called a plasmacytoid dc or pdc these are particularly good at mediating antiviral responses since they produce a lot of type 1 interferon in sle however pdcs can phagocytose antibody antigen complexes through fc receptor binding and once these complexes are transported into endosomes the nucleic acids that are bound to the antibody can activate endosomal tlr's that recognize nucleic acids including tlr7 and tlr9 tlr activation by these cells triggers type 1 interferon production that can then act on other cells note that this entire process is abnormal since in healthy individuals dying cells are cleared quickly enough to not be found extracellularly and these ligands don't usually find their way into pdcs without the presence of anti-nucleic acid autoantibodies type 1 interferon produced by pdcs can then stimulate neighboring myeloid cells to produce baf which is a survival ligand for b cells in this way type 1 interferon indirectly supports the survival of autoreactive plasma cells that are located in inflamed tissue this results in a feed forward loop of auto antibody production because the nuclear antigens and sle are ubiquitously expressed they form many small immune complexes that are not cleared by phagocytes instead these immune complexes circulate throughout the blood and they get deposited in small capillary walls joints and this is really important but they also tend to stick in the glomeruli of kidneys and once they're located here these immune complexes interfere with renal function and induce inflammation this tissue section from a sle patient shows an affected glomerulus where immune complexes have triggered the thickening of the basement membrane and this is shown as the thickened sort of clear areas surrounding the glomerulus at the center of the slide sle patients therefore show systemic symptoms including skin inflammation but the impaired function of the kidneys is a serious concern that can lead to renal failure in these patients the next few autoimmune disorders that we will look at are those driven by pathologically activated t cells this includes type 1 diabetes mellitus which is caused by autoreactive cd8 t cells whose tcr recognize autoantigens that are expressed by beta cells and beta cells are found in the pancreatic eyelids of longer on beta cells produce insulin so when ctls recognize and kill beta cells the pancreas no longer makes insulin and this is what leads to the symptoms of diabetes in mouse models of type 1 diabetes insulin itself can serve as the auto antigen that's recognized by ctls although other beta cell antigens may be recognized in humans as well the destruction of beta cells is obvious in these tissue sections on the bottom here which compare a healthy mouse pancreas on the left to a diabetic mouse pancreas on the right the brown cells are stained using an antibody against insulin which marks beta cells and these are almost entirely eliminated in the diabetic mouse it's hard to see in this figure but the diabetic pancreas on the right also has more t-cell infiltration into the eyelid and these are presumably effector cd8s that are responsible for wiping out all of the beta cells type 1 diabetes is distinct from type 2 diabetes which is instead acquired in response to dietary changes and is not an autoimmune disorder so try not to get these two mixed up type 1 diabetes is a good example of an autoimmune disorder where autoreactive cd8s are directly responsible for killing off healthy cells t cells can also act indirectly by activating other immune cells to mediate autoimmune symptoms and this is the case in rheumatoid arthritis or ra ra pathogenesis begins in the synovium which is a type of connective tissue that lines the joint capsule around bone joints it's unknown what events trigger inflammation at the synovial membranes but once inflammation is established it allows for circulating leukocytes including t cells to enter into the synovium once they're there autoreactive th1 and th17 cd4t cells can activate macrophages and this in turn leads to macrophage production of pro-inflammatory cytokines like il1 tnf alpha and il-6 these cytokines work by activating synovial fibroblasts which then produces an important signal called rank ligand or rankl now rank ligand is significant in ra because it stimulates the differentiation and activation of mature osteoclasts and these are a type of bone resident macrophage that functions by eating away at cartilage and bone in the affected joint this leads to destruction of the joint accompanied by lots of inflammation and this is really painful and decreases joint mobility ra therefore leads to chronic pain a loss of joint function and eventual disability if bone decay progresses severely ra is a little bit complicated because numerous cell types and signaling molecules have been implicated in its pathogenesis this simplified model shows a connection between cd4 t cells macrophages fibroblasts and osteoclasts where the t cells function in an indirect manner by activating other effector cell types b cells have also been implicated in the development of ra and although the specific auto antigen involved hasn't been identified yet autoreactive antibodies and immune complex formation may be important for triggering the synovial membrane inflammation that's responsible for initiating ra pathogenesis in the first place the last autoimmune disorder that we will discuss today is multiple sclerosis or ms and this is a progressive neurodegenerative disorder that affects the brain and spinal cord of the central nervous system which we abbreviate as the cns ms is also a t-cell-mediated disease that is largely driven by th1 and th17 cd4 t cells and these are specific for various antigens expressed in myelin and if you remember to some other physiology or maybe even neuro courses myelin is the fatty protein sheath that covers over neuron axons and is important for action potentials like rheumatoid arthritis multiple sclerosis is initiated by an unknown inflammatory trigger although in ms this inflammation targets the blood-brain barrier which is the sort of endothelial lining between circulation and the blood tissue that usually is responsible for excluding circulating leukocytes from the cns this is why we refer to the brain as being an immune privileged site upon opening of the blood-brain barrier by inflammation myelin-specific cd4s can enter the cns and once they're here they re-encounter myelin epitopes that are presented by brain-resident macrophages called microglia that express mhc class ii this leads to the production of inflammatory cytokines like interferon gamma from the t cells and other cytokines from microglia and this generates more inflammation that recruits even more leukocytes soluble factors such as complement proteins and circulating antibodies can also infiltrate the brain and although this includes myelin-specific antibodies their role in disease pathogenesis is still unclear ms involves the activation and recruitment of many different cell types into the brain but it's unknown exactly which of these effectors are directly responsible for targeting neuronal myelin it's thought that the combined inflammatory functions of all of these effector cells and molecules somehow leads to the removal of myelin from neuronal axons and this is a process called demyelination this leaves the axon vulnerable to destruction and the resulting neuronal loss is characterized by the formation of hard or sclerotic lesions that develop in the central nervous system of ms patients because this is a neurodegenerative condition as neurons are a non-proliferating cell type patients exhibit a variety of neurological symptoms like muscle weakness blindness and even paralysis like with many autoimmune pathologies ms patients typically start off with years and even decades of relapsing remitting disease course although most will eventually enter a second state of steady neurologic decline later in life in this second phase is called secondary progressive ms to summarize today's lecture we've learned that autoimmunity encompasses a variety of diseases that all result from the pathological activation of inflammatory immune responses against self-antigens which are expressed by healthy tissues and this can lead to some pretty devastating clinical symptoms we started off by recapping mechanisms of central and peripheral tolerance and immunity which work in the majority of patients to prevent activation of autoreactive t and b cells however in autoimmune disorders these mechanisms of tolerance are either prevented or broken through a likely combination of genetic and environmental factors we also established some broad categories of different types of autoimmune disorders based on the predominant effector cell types which are either autoreactive b cells or autoreactive t cells we also subdivided autoimmune disorders based on those that affect specific organs due to limited antigen expression in comparison to those that act systemically throughout the body by targeting more ubiquitously expressed self-antigens we then ended today by going over several examples of the most common types of autoimmune diseases and discuss their underlying immune mechanisms and how they lead to the specific symptoms associated with each autoimmune disorder in many cases these types of pathologies lead to pretty severe clinical symptoms highlighting the need to understand mechanisms of autoimmunity in order to design more effective therapies to help cure disease if you're interested in learning more about the types of medications that are used to treat specific autoimmune diseases i recommend that you respond to this week's discussion board prompt as one of your graded discussions for this course that's it for today's lecture here's a gentle reminder that you do have one remaining lecture in week nine which will cover the topic of transplantation immunology