Immunology 201 Transcript PDF

PROPRIETARY. DO NOT SHARE. Transcript: Immunology 201 Section 1: Non-Specific Immunity Welcome This course will discuss the immune system, how it prevents disease, and how these functions are used in biotechnology. This course is broken into three sections. The first and second sections will discus...

PROPRIETARY. DO NOT SHARE. Transcript: Immunology 201 Section 1: Non-Specific Immunity Welcome This course will discuss the immune system, how it prevents disease, and how these functions are used in biotechnology. This course is broken into three sections. The first and second sections will discuss the two different types of immunity, non-specific immunity, and specific immunity; respectively. Lastly, section 3 will put the entire story together by illustrating how the immune system is activated and responds to eradicate diseases in our bodies. Section 1: Non-Specific Immunity Objectives In this section: • We will first differentiate between the primary and secondary non-specific immune response. • We will then list the non-specific immune response functions. • Lastly, we will explain how the non-specific immune system recognizes, responds, and eliminates a pathogen. Non-Specific Immune Response Overview Let’s begin this section with a reminder from the last section that the immune system is broken down into two categories: the non-specific or innate immune system and the specific or adaptive immune system. This section will discuss the non-specific system, while the next section will cover the specific immune system. If we look closer at the non-specific immune response, we see that it is further broken down into two types of response: primary and secondary. The primary responses are physical and chemical barriers. The primary non-specific response is always present and always provides the same response every time, regardless of the pathogen. The secondary responses are mediated by certain immune cells and chemicals. The secondary non-specific response includes these first two characteristics enjoyed by the primary response but also has added features of being able to recognize pathogens in general, meaning there are molecules on a pathogen that say I’m a dangerous microbe. I need to be killed. 1 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. That’s all the secondary response cares about. Simply that it’s a pathogen, it doesn’t care what type of pathogen -- it is just able to recognize the fact that this microbe is a pathogen. The response is pretty much the same every time. The non-specific immune system activates itself in seconds to hours. The intensity of the response can be modulated meaning - the more pathogen is present, the stronger the response. However, there is no memory of the pathogen, so the cells of the secondary response can see the same pathogen over and over again, but it’s just going to respond to it exactly the same way. There won’t be any increase or decrease in response, only the same as it always has been. Immune System Functions The job of the non-specific immune response is to recognize pathogens, respond to pathogens once recognized, and eliminate or neutralize pathogens. Let’s now discuss some examples of the primary and secondary immune defenses in the non-specific immune system. Primary Defense Examples The primary defenses of your body are your preformed defenses and take effect in phase one of the complete immune response- that critical 0-4 hours when your body encounters a pathogen. Physical barriers, such as your skin, keep out pathogens. Your skin also secretes proteases, enzymes that break down proteins on pathogens. This is why you always clean a cut thoroughly because a scrape or a cut is a breach in your skin barrier and an excellent place for pathogens to enter your body. But we know that our body has natural breaches, such as our mouth and our nose, where pathogens can easily enter our body. In these places, we have mechanical protection such as a cough or sneeze. It is our body’s way of expelling pathogens. A cool fact about sneezes is that they happen fast- sneezes travel at 100 miles per hour. If the pathogen does gain entry, say into our mouth, we have special molecules that destroy pathogens. Again, we rely on a class of proteins called proteases. Proteases in your saliva break down pathogenic proteins. 2 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. If a pathogen gets past our saliva, then a low pH in your stomach’s environment hopefully will take care of the problem. Low pH causes the proteins in viruses and some bacteria to denature. Other preformed defense examples during phase one are runny nose and fever. These are all things that either are trying to expel, kill, or slow down the replication of the pathogen. Secondary Defense Examples The secondary defense includes an arsenal of tricks. First, we have small molecules that include things like nitric oxide or hydrogen peroxide. Yes, your immune cells make hydrogen peroxide, the same stuff that you buy in the drugstore. Nitric oxide and hydrogen peroxide are made by your immune cells. These are highly, highly reactive chemicals, so when they interact with cells, the cells are killed. Peptides, which are larger than small molecules and smaller than large molecules, are critical to the secondary defense. Cytokines, a signaling molecule, will be discussed in great detail later, so I’ll just name them here. Host-defense proteins are non-signaling proteins, meaning they don’t bring other molecules to the fight; they do the fighting themselves. Moving up in size, we have large molecules such as complement proteins. Complement proteins circulate through your blood, and when they find a bacteria cell, they pile up on top of the bacteria’s cell membrane in a very complex sequence. Once that pile of complement protein is completed, it causes a hole to form in the bacterial cell membrane, and all the components of the bacteria cell leak out, and the bacteria cell dies. To round out this overview, there are certain secondary non-specific immune cells that protect us from pathogens. These include neutrophils, eosinophils, and macrophages. Both neutrophils and macrophages engulf or ingest pathogens, and specifically, the macrophage signals other immune cells that the pathogen is present. Eosinophils secrete toxic substances to destroy pathogens. Host Defense Proteins (HDP) As mentioned, host defense proteins are non-signaling proteins, meaning they don’t communicate with other molecules. Host defense proteins - abbreviated HDP - are proteins that essentially act like antibiotics. These are like your own self-made antibiotic proteins, which help to destroy 3 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. bacterial cells. These are also known as antimicrobial proteins or AMPs. Some examples of host defense proteins are defensins and lactoferrin. Host Defense Proteins in Action: Direct Killing Let’s look at a specific host defense protein, defensin, in action. Defensins are very small, very stable peptides – remember peptides are short sequences of amino acids. When these defensins interact with a virus or bacteria, they can interfere with its function through direct killing. How, you might ask? Defensins stick on a bacteria cell membrane and puncture a hole in the membrane. It is fast and effective. In fact, several companies are looking at defensins as a therapeutic molecule for hard-to-treat drug-resistant bacterial disease as a replacement for antibiotics. Complement Proteins Complement proteins are large proteins that have a signature stacking ability. When complement proteins recognize bacteria, one will stack upon another until they puncture a hole in the bacterial cell membrane- as you can see here. Neutrophils Neutrophils make up about 70% of your white blood cells. Their job is to engulf and destroy pathogens. As you can see, the bacteria are engulfed and destroyed. You may have heard another term other than engulf or ingest – that term is phagocytize. All these terms- engulf, ingest, and phagocytize are fancy ways of saying neutrophils “eat” bacteria. Phagocytize is the action of phagocytosis. A major mechanism of the human immune system, phagocytosis, is used to remove pathogens and cell debris. And as you have probably already guessed, the term is Greek. Coming from phagein: meaning “to devour”, kytos: meaning “cell”, and –osis: meaning “process, “and it is the process by which a cell engulfs a solid particle. Eosinophils Eosinophils secrete toxic substances, called cytotoxins, which destroy pathogens. Some examples of cytotoxins are nephrotoxins and neurotoxins. Macrophage Like Neutrophils, Macrophages also engulf or phagocytize pathogens. However, they also signal to other immune cells that a pathogen is present. They do this by breaking down the pathogen 4 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. and taking those pathogen pieces to the lymph nodes, where it presents those pathogen pieces to the cells of the specific immune system, especially T-cells and B-cells, to activate them. Because the macrophage is a secondary non-specific immune response and also communicates with T- cells, and B-cells of the specific immune response, we say macrophages are a bridge… meaning they are involved in both the non-specific and the specific immune response. We will discuss their ability to activate T-cells and B-cells in more detail in the next section. Pattern Recognition Receptors (PRRs) If the first step is recognition, then how do you think this is achieved? How does our immune system recognize pathogens? One of the key ways to recognize pathogens is by pattern recognition receptors, or PRRs, that are located on our immune cells. PRRs are specific to our secondary non-specific immune system. PRRs recognize two classes of molecules – Pathogen- associated molecular patterns, also known as PAMPs, and Damaged-Associated Molecular Patterns, abbreviated DAMPs. For example, if you cut open your skin and get infected with Clostridium tetani, your macrophages, and neutrophils have a receptor – a pattern recognition receptor- for Clostridium tetani. Your macrophage’s PRR binds to the Clostridium tetani’s PAMP. Let’s take a look at this in action. PAMPS and DAMPS Just a few quick definitions here. PRRs interact with Pathogen-Associated Molecular Patterns, or PAMPs, which are proteins on the surface of bacteria and viruses. The PAMP identifies them as pathogens. PRRs may also interact with Damage-Associated Molecular Patterns, or DAMPS, which are your cell components that are released during cell damage or death. PAMP Locations PAMPs aren’t only found on bacterial cell membranes. They may also be found inside viral DNA or RNA, and on the long, whip-like extensions, called flagella, that bacteria use to swim. PRR Location on a Macrophage Returning to the idea of pattern recognition receptors. Here, we have a very simple schematic of where you might find a pattern recognition receptor on a macrophage. 5 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. First, notice the PRR is embedded in the cell membrane. This receptor is a transmembrane protein, meaning part of it is on the outside surface of the macrophage, part of it traverses the cell membrane, and part is inside of the macrophage. Recognition and Response: Cytokine Synthesis As with all of our other receptor examples, I will use a lock and key-analogy. The PRR is like a lock in the door and the PAMP is the key that fits into the lock. The PRR can recognize the PAMP and remember that PAMPs are present in all pathogenic viruses, bacteria, and fungi. As the PAMP is floating through your tissue or your bloodstream, it is captured by the PRR. When the PAMP and PRR bind, an event in the cell membrane is triggered. The binding triggers another PRR to migrate towards the occupied PRR and they do what’s known as dimerize. That is di means two, and mer means a unit, so we form two units. Once our PRRs dimerize, they activate each other. Once they’re activated, a protein inside the cell known as MyD88, a signaling transducer, now associates with a protein that is already associated with our PRR called TIRAP. Once MyD88 associates with TIRAP, which has been activated by the PRR dimerization, the MyD88 becomes activated, which triggers the activation of a protein called IRAK4. The IRAK4 then moves over to the PRR and the IRAK4 is phosphorylated as indicated by those little Ps. Two phosphate groups activate IRAK4. Now this protein is activated and it’s ready to go. Up to this point in the process, the goal has been to get the IRAK4 activated. And now IRAK4 leaves the PRR and moves to a protein called TRAF6 where it activates TRAF6. TRAF6 then migrates through the cell to a complex of proteins, that is several proteins associated with one another, known as the IKK Complex. Once TRAF6 associates with the IKK Complex, that complex becomes activated. It begins to disassociate into individual proteins, and you can see after disassociation there’s a protein called IKB and there are two proteins that are identical and known as NFkB. It stands for Nuclear Factor Kappa B, or NFkB. NFkB is the star of the show and it has been the subject of lots of research in terms of how to control inflammation. Now that the IKK complex has been activated, its components are revealed. And the IkB disassociates, it comes apart, and the NFkBs are now released. 6 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. The NFkBs move into the nucleus of the cell where they activate the expression of proteins called cytokines. Cytokines are signaling molecules of the immune response. In this case, we’re using TNF (tumor necrosis factor) as our example so the gene that contains the information to make TNF is now activated by the presence of this NFkB. Then tumor necrosis factor, as you will see in the next slide, goes on to trigger an inflammatory response. All of this happens simply because the pathogen’s PAMP was recognized by the macrophage’s pattern recognition receptor. A cascade, if you will, where a very specific sequence of proteins interacting with each other, ultimately leads to gene activation. In that gene activation, cytokines are made. In this case, we gave the example of tumor necrosis factor as our cytokine. Response: Cytokine Activation of Immune Cells What exactly do cytokines do? Let’s continue with our example using tumor necrosis factor, the cytokine produced by a macrophage in response to PRR activation. TNF is a pro-inflammatory cytokine, that is, it is a cytokine that triggers inflammation. Once made, tumor necrosis factor is secreted from the macrophage into the blood. Tumor necrosis factor can self or auto-stimulate the macrophage because the macrophage has cytokine receptors for TNF, but the TNF can also activate other cells in your body. In this case, it’s a very specific receptor called TNF R2. The R stands for receptor and 2 simply means that there’s a series of tumor necrosis factor receptors. Here, once again, we have our cytokine receptor. Did you notice that it is another transmembrane receptor? The protein receptor spans from the outside of the macrophage to the inside of the macrophage. Let’s imagine our TNF has now been secreted. It’s floating around. The TNF-alpha fits into the receptor. Again, think lock and key analogy. Once the receptor is occupied, it is activated. That triggers the migration of a protein called TRAF2 to interact with the receptor, which is now bound to the cytokine. This only happens if the cytokine – TNF – occupies the receptor. The TRAF2 is activated. Once TRAF2 is activated, it is released from the receptor and it travels to and activates another protein called MAPK or MAP Kinase. The MAPK is activated and MAPK then activates JNK, another protein. Once the JNK is activated, it activates yet another protein called C-jun. Once C-jun is activated, it goes inside the nucleus and binds to a specific sequence of DNA. A different sequence of DNA than the previous slide, 7 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. so it’s going to activate different sets of genes, and these genes then trigger the inflammatory response. They promote things like cell survival, cell proliferation, and differentiation of cells into a more useful type of immune cell. This process that we illustrated on the last two screens, is known as signaling pathways or signal transduction pathways. We’re giving you just a very simple view of this. These signaling pathways consist of tens of proteins. There are sometimes 10 or 20 proteins that all must interact with each other in a very specific stepwise sequence to get the result. Here, we’ve just put in a few of the key proteins to illustrate to you that this is indeed a complex process. Having this level of complexity gives your cells a lot more control over the level of the response, how long the response is going to last, and exactly where it occurs. Cytokines Just to quickly review, Cytokines are the signaling molecules of the immune system. These are small proteins, specifically peptides, which means they’re coded for by a gene. For a cytokine to work, because it is a signaling molecule, there must be a corresponding receptor. There are many different classes of cytokines and they have many different shapes. Examples of cytokines include tumor necrosis factors, interleukins, interferons, and colony-stimulating factors. All of these are different cytokines so all of these regulate or control some aspect of an immune response. Section 1: Non-specific Immunity Summary To summarize this section: • We first defined the primary non-specific immune response as a response that is always present and provides the same response every time regardless of the pathogen and the secondary non-specific response as a response that recognizes pathogens in general and the intensity of the response is modulated. • We then explained that the function of the entire non-specific immune response is to recognize, respond and eliminate the pathogen. • There are a few ways that this occurs, these are: o Macrophages and neutrophils recognize pathogens through interactions of their pattern recognition receptors (PRR) with the pathogen’s pathogenassociated molecular pattern (PAMP). 8 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. o Cells of the non-specific immune system respond to a pathogen by releasing signaling molecules that activate other immune cells o Cells of the non-specific immune system eliminate a pathogen by puncturing holes in its membrane, engulfing it, or killing it with cytotoxins. 9 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. Section 2: Specific Immunity In this section, we will discuss how the specific immune response occurs when the primary and the secondary non-specific immune defenses fail. In essence, your immune system has been overwhelmed because you’ve probably received too high a dose of a pathogen. Section 2: Specific Immunity – Objectives In this section: • We will first name the major cells involved in the specific immune response and their functions. • We will then list the specific immune response characteristics in more detail. To further explain the specific immune system, we will then have to compare and contrast the terms antigen and immunogen. • Lastly, we will describe how B-cells and T-cells are activated, and the role of both cells in the specific immune response. Specific Immune Response B-cells & T-cells circulate through the blood and lymph system patrolling for pathogens. Mostly, they are in your lymph nodes waiting to meet the one pathogen that the T-cells and B-cell have been designed to recognize and eliminate. When B-cells and T-cells encounter and recognize a pathogen, the specific immune system mounts an attack. Specific Immune Response Characteristics The specific immune response is set off when the B & T cells recognize a specific pathogen or diseased cell. Therefore, it takes several days to reach maximum activity because you are starting with only one B-cell or one T-cell and these must be replicated and that takes time. Anywhere from a few days to 10 days. In addition, the B-cells and T-cells form memory cells, so upon secondary exposure, instead of just having one cell respond, there are tens of thousands of immune cells responding. These cells distribute themselves throughout the lymph system so you get a much faster response, a much stronger response. 10 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. Components of The Specific Immune Response There are various components of the specific immune response. This screen is only meant as an introduction. We will discuss each of these in more detail later in this section. Let’s go from smallest to largest. Key molecules involved in the specific immune response include cytokines and antibodies. As we discussed the main immune cells are B and T cells. T-cells produce cytokines, and B-cells produce antibodies. B-cells and T-cells both originate in the bone marrow and become activated in the lymph nodes. Immunogens and Antigens To understand how our specific immune system recognizes pathogens we must first introduce you to some terms. Let’s look at immunogens and antigens. These are scientific terms we use to describe specific parts or, more accurately, specific molecules found on a pathogen or diseased cell. These molecules are depicted on the ends of the surface receptors of the virus shown here. An immunogen is a molecule that can activate an immune response. Immunogens are molecules that are associated with pathogens. An antigen is a molecule that is recognized by the immune system but does not necessarily stimulate an immune response. A paraphrase often used is, all immunogens are antigens. That is, all immunogens are going to be recognized by your immune system. But not all antigens are immunogens. That is, not every antigen is capable of activating the immune system. That being said, people often use the term “immunogen” and “antigen” interchangeably as if they are the same thing. Epitopes Now that you can define the term immunogen, we’d need to take it one step further and introduce you to the term epitope. An epitope is the specific molecular pattern or sequence on an immunogen that is recognized by your specific immune system. 11 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. Immunogens and Epitopes Immunogens are also found on the surface of pathogenic bacteria. Different proteins on the surface of the bacterial cell may be recognized by your immune system, but not every protein will create an immune response. Do you remember what we called the protein on the surface of pathogens that do NOT induce an immune response? You are correct- they are antigens. Do you remember which protein does trigger an immune response? Again, you are correct - an immunogen. What is the name of the molecular sequence on the immunogen that is recognized by the immune system? Again, correct - an epitope. Let’s look more closely at the immunogen. An immunogen is a protein, an immunogenic protein, meaning it can cause an immune response. As you may recall proteins are made out of building blocks called amino acids. Here I am showing you that the entire epitope is made out of a sequence of amino acids. However, there are specific amino acid sequences, within the total, overall amino acid sequence that make up the epitope. These epitope sequences are represented in red. If each red sequence represents an epitope, how many epitopes does this immunogen have? Correct 4. So, now you know that each immunogen may have more than one epitope. In the case of this one, there are 4 epitopes. This means that there are 4 different B cells or T cells that can recognize this immunogen as pathogenic. It also means that we could develop 4 different therapeutics- one targeting each epitope to fight off this disease. Common Classes of Immunogens As we just saw, proteins are immunogenic, meaning they can elicit an immune response. However, there are different classes of immunogens and these can be grouped by how strongly they can trigger an immune response. I’m going to list here the types of molecules in order of increasing immunogenicity. The least immunogenic are small molecules. These are typically synthetic organic compounds and drugs. Things like aspirin and caffeine. These molecules are so small that by themselves, they are not recognized by your immune system. Small molecules will not be immunogenic. They 12 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. will not trigger an immune response. They have to be associated with a larger molecule to be immunogenic. Then comes nucleic acids: DNA, and RNA. Lipids are not very immunogenic, but some lipids can trigger an immune response and can be recognized by your immune system. Complex carbohydrates are immunogenic. Proteins are by far the most immunogenic molecules. These are the molecules that are frequently used for vaccines or to trigger the creation of antibodies. If we add a carbohydrate to the protein, the protein becomes even more immunogenic. Proteins that have carbohydrates in them, you may recall, are known as glycoproteins. Glycoproteins are proteins that are glycosylated or have carbohydrate sequences present as part of the protein structure. Immunogenicity is important because patients can go into shock and potentially die if their immune system responds vigorously to a medication made out of proteins. B-Cells B-cells ultimately secrete antibodies. These are the cells most associated with the specific immune system. There is a different B-cell for each pathogen. B-cells are highly specific and they respond to a specific threat. B-Cell Membrane The specificity of B-cells comes from their receptor, known as a B-cell receptor or BCR, which is embedded in the B-cell membrane. The external portion of this BCR – the portion outside of the B-cell – has a specific shape that recognizes a specific immunogen. BCR and Immunogen B-cells become activated when their B-cell receptors (BCRs) bind to their complementary immunogen. Remember, this is a recognition process, and the B-cell receptor has a specific threedimensional shape, that is going to be complementary to the three-dimensional shape of the immunogen. It’s the age-old lock and key concept where the lock is the B-cell receptor and the key is the immunogen. When the key fits into the lock, the B-cell becomes activated. 13 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. Role of B-Cells To recap, each B-cell is circulating in your body, mainly in the lymph and blood. Each B-cell has a uniquely shaped receptor that recognizes a specific immunogen. Upon binding of that immunogen, the B-cell becomes activated. Activated B-Cells Differentiate and Multiply Activated B-cells multiply and differentiate into two kinds of B-cells. One is a plasma cell. This is just a special name given to B-cells that synthesize and secrete or release tens of thousands of antibodies. Antibodies are simply soluble versions of the B-cell receptor. This means that the plasma cell continues to make the receptor protein, only instead of being inserted into the plasma cell membrane, it is secreted from the cell. The secreted antibody recognizes the same immunogen that the B-cell receptor did. The other type is called a memory B-cell. Which helps to protect the body if there is a re-exposure to the same pathogen. Since the immediate danger is eliminating the current disease, many more plasma cells are made. Plasma B-Cells Plasma B-cells synthesize and release millions of antibodies and in fact, is estimated that active plasma cells secrete about two thousand antibodies per second! Antibodies Neutralize Pathogens Antibodies play a key role in the elimination of pathogens in your body. Here, what we’re illustrating is whether it’s a virus or bacteria. You can make antibodies that recognize and bind to these different viruses and bacteria. For every different virus and every different type of bacteria that you’re exposed to, there will be a specific unique set of antibodies made that can recognize each of those different pathogens, bind to specific proteins or immunogens on that pathogen, and make it easier for the other cells of the immune system to destroy the pathogen. The first way this occurs is simply by a large number of antibodies binding to the pathogen. When a large number of antibodies are bound to a pathogen, the immune system will recognize that as a warning that whatever is bound by the antibodies is bad news. Additionally, the antibodies binding to the pathogen will prevent those pathogens from entering cells or binding to them to spread the pathogen. 14 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. Antibodies Trigger Macrophage Response In addition, the binding of antibodies to the pathogen or even cells that have already been infected will stimulate white blood cells such as neutrophils and macrophages to come and recognize these pathogens, and engulf them or phagocytize them, resulting in their destruction. Antibodies Trigger Complement Response Antibodies also trigger the complement system which as we discussed earlier leads to the destruction of the pathogen. The complement cascade is built on the surface of the pathogen in response to antibodies binding to the pathogen, and then punches a hole in the pathogen, leading to its destruction. Memory B-Cells Memory B-cells migrate into various lymph nodes throughout your body, and they just wait there until the next time that you’re exposed to the same pathogens. Let’s give an example of this process with which you are probably familiar. October 1st you get the flu. You recover from the flu by October 10, but because you did get the flu, your B-cells were activated. You made lots and lots of plasma cells which eliminated the initial flu infection, and you also made memory B-cells which will remember this year’s strain of the flu. Those memory B-cells migrate to lots of different lymph nodes throughout your body. Later on in the year, if you’re exposed to the flu again, those memory B-cells will quickly recognize and activate themselves to attack the flu before you get ill again. Immune System Functions Let’s pause here. As we learned previously, the job of the non-specific immune response is to recognize pathogens, respond to pathogens and once recognized eliminate or neutralize pathogens. The specific immune system does all of these actions as well but in addition, the specific immune response also remembers which pathogens have attacked previously. To remember is to create many cells with a memory of the pathogen that will mount a more robust response on subsequent exposure. It also will modulate the immune response. To modulate is to increase or decrease the level or intensity of the immune response as needed. Therefore, when your body is under attack your body will increase plasma cell production and increase antibody production and on and on until 15 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. the pathogenic threat is eliminated. Once eliminated the body will stop production and only the memory B-cells will remain. T-Cells Let’s move on to T-cells, another critical immune cell in our specific immune system. T-Cell Origins T-cells originate from stem cells in the bone marrow, but they migrate out of the bone marrow and move to the thymus gland where they then mature into either cytotoxic T-cells or helper T-cells. T-cells get their name from Thymus. Either one of these T-cells, cytotoxic T-cells or helper T-cells, have unique receptors aptly named T-cell receptors or TCRs which are able to recognize specific immunogens. In addition, T-cells have coreceptors that are required for a fully functioning T-cell. The cytotoxic T-cell coreceptor is referred to as CD8; the helper T-cell coreceptor is CD4. Cytotoxic T-Cells Cytotoxic T-cells secrete cytotoxins, a poison that kills a virally infected cell or cancerous cell. Cytotoxic T-cells are often called Killer T-cells. Cytotoxic T-cells work by recognizing antigens presented on virally infected body cells or by recognizing antigens found on cancer cells. Remember that immunogens are found on pathogens, and antigens are found on your body cells. Recall I said antigens can trigger an immune response too and in this case, these antigens are triggering an immune response. Again, cytotoxic T-cells kill host cells that are infected by viruses or other pathogens and they kill damaged or dysfunctional cells such as cancerous cells. They are also responsible for the rejection of tissue and organ grafts. Cytotoxic T-cells release chemicals called cytotoxins, which create holes in the target cell membrane, which leads to their death. Cytotoxic T-Cells Bind to Virally Infected Cells Let’s put the last few screens together and witness how CD8 and TCR interact with an MHC molecule. The job of the MHC is to present fragments of an immunogen to the T-cell receptor, the TCR. Those little green circles represent the immunogens that are held in the MHC molecule on this infected cell. 16 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. In either case, whether it’s a virally infected cell or a macrophage that’s destroyed a virus, these pieces of the pathogen, these immunogenic molecules- these immunogens, are trapped in the MHC protein and presented on the surface of the cell. In some cases, cancer cells have mutated to such an extent that they will also present immunogens that are recognized by T-cells. This presenting cell floats through your lymph system until it finds a matching T-cell receptor. Cytotoxic T-Cells Release Cytotoxins When the cytotoxic T-cell recognizes its target via the MHC complex, it releases toxic molecules that directly kill the virally infected cell or cancer cell. Cytotoxic T-cells kill host cells that are infected by viruses or other pathogens. They kill damaged or dysfunctional cells such as cancerous cells. They are also responsible for the rejection of tissue and organ grafts. Cytotoxins create holes in the target cell membrane that causes a reaction inside the targeted cells that leads to their death. Macrophage Bridges the Non-Specific and Specific Immune Systems Let’s go back to our macrophages. Recall that macrophage ingests pathogens. The second part of the story, which I have not told you yet, is that once a pathogen is ingested, the macrophage breaks it down and then packages some of the immunogen pieces into MHC proteins. Then the macrophages circulate through your body where they enter the lymph nodes until they find the matching T-cell receptor. Macrophages are just as the title states: Macrophages bridge the nonspecific and the specific immune systems because they play an important role in both. Let’s move on to helper T-cells now. Helper T-Cell In a helper T-cell, instead of a CD8 protein, we have a CD4 protein, and as you guessed it, helper T- cells are sometimes referred to as CD4 cells, while cytotoxic T-cells are sometimes referred to as CD8 cells. Essentially, the process of activating helper T-cells is the same as what we’ve described for a cytotoxic T-cell. That is, there’s a T-cell receptor. It interacts with an antigenpresenting MHC molecule. Helper T-cells recognize antigens presented on other immune cells, such as macrophages, neutrophils, dendritic cells, or B-cells, that have engulfed the antigen and are now called “AntigenPresenting Cells” (APC). 17 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. Helper T-cells help coordinate the overall immune response by secreting signaling proteins called cytokines, which include the interleukins and interferons, to activate and direct other immune cells (such as cytotoxic T-cells and macrophages). For instance, interleukin 2 stimulates T-cells to proliferate and, is therefore, released by Helper T-cells during a viral infection. Helper T-cells can also activate B-cells, by the cytokines released, which will produce antibodies to help clear the pathogen. Helper T-cells cannot kill infected host cells or pathogens. They recruit other immune cells to do this. Cytokines Cytokines are proteins that act as signaling molecules that regulate the immune system. Cytokines may stimulate or suppress the activity of different white blood cells. Cytokines work by binding a specific receptor on the target cell’s surface. Some of the key classes of cytokines are tumor necrosis factor, interleukins, and interferons. Memory T-Cells Once we generate memory T-cells, we have thousands of memory T-cells able to recognize a particular pathogen. Which are now distributed throughout the lymph nodes within your body so the next time you’re exposed to the same pathogen, you can mount a much faster and much more robust response to that pathogen, and hopefully eliminate it before any illness occurs. Section 2: Specific Immunity Summary In this section: • We first introduced the major cells of the specific immune response, the B-cell and the T-cell. • Next, we described the characteristics of the specific immune response. The specific immune response is induced by a pathogen and is specific and unique to that pathogen. Unlike the non-specific response, it requires days to reach maximum effectiveness. Once it reached this maximum it is extremely effective and, unlike the non-specific response, it has a memory so that it will be even more effective if the same pathogen invades the body again in the future. • With this basic understanding, we then defined the terms immunogen and antigen. An immunogen is a molecule that can activate an immune response, while an antigen is a molecule that is recognized by the immune system. 18 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. • We lastly described how B-cells and T-cells are activated. B-cells are activated when their B-cell receptors (BCR) bind to a complementary immunogen. T-cells are activated when their T-cell receptors (TCR) bind to a complementary immunogen that is presented by other cells such as macrophages. 19 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. Section 3: Immune System Activation: Putting it All Together Section 3, the last section of the course, will put everything that we have learned so far into practice by describing the story of a pathogen activating the immune system and all the steps in the immune response to eradicate the pathogen. Section 3: Immune System Activation: Putting it All Together Objectives In this section: • We will first describe pathogen recognition by macrophages and neutrophils. • Once we know how these cells recognize pathogens, we will then discuss macrophage and neutrophil responses to these pathogens. • Next, we will explain the role of macrophages and T-cell activation. • Lastly, we will take a look at B-cell activation and differentiation as well as define the role that the helper T-cells play in B-cell activation. Immune Challenge: Exposure to Pathogen Here you are walking down the street and you’re all happy and you suddenly get exposed to a virus. Somebody sneezes on you or it’s just floating in the air, but for whatever reason, you now begin to become sick. You get such a high dose of this pathogen that even though your innate immune system, your macrophages, and neutrophils try to neutralize it, there’s so much virus in you that it begins to replicate. Here we have our simple graphic to represent all of our little virus particles with their immunogen protein on their surface. PRR and PAMPs The first thing that happens is your macrophages and neutrophils respond to this foreign invader, to this pathogen. We’re exposed to our pathogen. We’re just going to work with the single one, but you can imagine this is occurring for every pathogen that’s in your body. That immunogen is really a pathogen-associated molecular pattern. Within that pathogen-associated molecular pattern is the epitope, the specific sequence that is recognized by the BCR, the TCR, and antibody, and on your neutrophils and macrophages, the PRR (pattern recognition receptor). The pattern recognition receptor isn’t quite as specific as the TCR, the BCR, and the antibody, but it can recognize a protein that is present on the surface of a pathogen. That’s how it knows pathogenic bacteria, for example, from non-pathogenic bacteria. 20 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. Because remember that in and on your body, there are lots of bacteria. There are lots of bacteria which are in your mouth, which are in your throat, which are in your intestine. They’ve been there your whole life but they don’t cause a disease and, therefore, they’re not recognized by your immune system, because they lack that PAMP (pathogen-associated molecular pattern). If we get infected with bacteria that will make us sick, then the macrophage will recognize the PAMP associated with that type of bacteria, and become activated. Once activated, the macrophage will phagocytize, or eat, the pathogen. The Process of Phagocytosis Once the pathogen, that is the bacteria or virus, has been phagocytized and has been eaten by the macrophage or neutrophil, it is then degraded. It’s killed. It’s broken down into individual fragments. The way that works is the macrophage and neutrophil have a variety of tools, an arsenal of weapons, if you will, to break down this pathogen whether it’s a virus or bacteria. They have a whole series of enzymes and remember enzymes are molecules that carry out chemical reactions. These particular enzymes are degradative. They break down molecules. Now the bacteria are hopefully degraded and destroyed. Cytokines are synthesized and then they are secreted. Lots of cytokines are secreted and these cytokines can in turn go back and activate the macrophage even more so the macrophage becomes even more effective at destroying the pathogen that’s causing the disease. It can also activate our B-cells. Pathogen Fragments Are Presented on MHC Molecules Fragments of that pathogen that was just phagocytized are then presented on MHC molecules on the surface of the macrophage. Helper T-Cell Recognition and Cytokine Release We have a macrophage with a loaded MHC molecule. It’s presenting this immunogen. It’s circulating through your blood and lymph, and it’s trying to find the matching BCR and TCR. It’ll interact here with a T-cell receptor. Once again, we have lots of T-cell receptors, and once this interaction occurs, the T-cell is activated. In this case, if it’s a helper T-cell. Do you remember 21 Copyright 2023 Biotech Primer, Inc. PROPRIETARY. DO NOT SHARE. what helper T-cells do? They synthesize and secrete even more cytokines. There is some redundancy in the response, but it ensures that we get a very robust response. T-Cells Activate Memory B-Cells The activated helper T-cell, which remembers releases cytokines, some of those cytokines interact with cytokine receptors on memory B-cells, helping their conversion into antibodyproducing plasma cells. Once reactivated, memory B-cells produce antibody-producing plasma cells. Once reactivated, memory B-cells produce antibody-producing plasma cells, which release antibodies that attach to pathogens. Memory B-Cells Are Quickly Reactivated When B-cells are activated, they differentiate into Plasma cells or Memory cells. Most B-cells become Plasma cells that produce and secrete antibodies. Some B-cells become long-living Memory cells which will circulate and patrol for a future invasion of that particular antigen. This allows the body to respond quickly if infected again with the same pathogen. Section 3: Immune System Activation: Putting it All Together Summary To summarize this section: • We first described how Macrophages and neutrophils recognize pathogens through interactions of their pattern recognition receptors (PRR) with the pathogen’s pathogen-associated molecular pattern (PAMP). • We then showed how once activated macrophages and neutrophils can destroy pathogens by eating them and breaking them down, a process known as phagocytosis. • Additionally, once the macrophages break down the pathogen, the macrophages activate helper T-cells by “displaying” immunogens that interact with the T-cell receptor. • Lastly, we discussed two ways in which B-cells can be activated. B-cells are activated when their receptors interact with a complementary immunogen; they then differentiate into memory B-cells and plasma cells, and helper T-cells release cytokines that enable B-cells to become fully activated. 22 Copyright 2023 Biotech Primer, Inc.