PHAR 542 Final Exam Study Objectives - Immunology (McAleer) PDF

**PHAR 542 FINAL EXAM study objectives for Immunology (McAleer)** **Questions 1-12: Exam 1 material** **Questions 13-25: Exam 2 material** 1. Compare and contrast "innate" and "adaptive" immune responses a. Distinguish the different cell types and their functions in host defense S...

**PHAR 542 FINAL EXAM study objectives for Immunology (McAleer)** **Questions 1-12: Exam 1 material** **Questions 13-25: Exam 2 material** 1. Compare and contrast "innate" and "adaptive" immune responses a. Distinguish the different cell types and their functions in host defense Summary Table Feature Innate Immunity Adaptive Immunity ------------------------ --------------------------------------------------- ------------------------------------------------------------- Specificity Non-specific Highly specific to particular antigens Response time Rapid (minutes to hours) Slower (days to weeks) Memory No immunological memory Develops memory for faster and stronger secondary responses Key components Physical barriers, PRRs, phagocytes, complement Lymphocytes (T cells, B cells), antibodies, MHC molecules Examples of mechanisms Phagocytosis, inflammation, complement activation Antibody production, cytotoxic T cell killing, T cell help **[Innate Immunity:]** - **Genetically encoded and similar for all individuals of a species.** This means that the basic mechanisms of innate immunity are pre-programmed and do not change significantly based on individual experiences. - **First line of defense against infections.** It provides immediate protection through various mechanisms, including: - **Structural barriers:** The skin, the epithelial lining of the gastrointestinal (GI) tract and lungs, tight junctions, mucus, and antimicrobial peptides act as physical barriers to prevent pathogen entry. - **Soluble/Humoral barriers:** Natural antibodies (produced without prior immunization) and complement proteins (part of the complement system) act as soluble mediators to neutralize or opsonize pathogens. - **Cellular barriers:** Cells such as macrophages, neutrophils, and natural killer (NK) cells engage in inflammation and phagocytosis to eliminate pathogens. - **Utilizes pattern recognition receptors (PRRs).** PRRs on cells like macrophages recognize conserved microbial structures, like lipopolysaccharide (LPS) on bacteria, and trigger signaling cascades that lead to the production of cytokines, chemokines, and interferons. These molecules help recruit other immune cells and activate various immune responses. - **Rapid response time:** The innate immune response is activated within minutes to hours of infection. **[Adaptive Immunity:]** - **Individual-specific and develops through exposure to antigens.** This means that the adaptive immune response is tailored to the specific antigens encountered by an individual. - **Second line of defense that provides long-lasting immunity.** It takes longer to develop than the innate immune response, but it is more specific and provides long-term protection through: - **Somatic gene rearrangements in lymphocytes:** This process generates a vast repertoire of B cell receptors (BCRs) and T cell receptors (TCRs) on B cells and T cells, respectively, each capable of recognizing a specific antigen. - **Antigen-specific recognition:** B cells and T cells recognize and target specific antigens, leading to a focused immune response. - **Develops memory:** Exposure to an antigen leads to the generation of memory B cells and memory T cells, which allow for a faster and stronger response upon subsequent encounters with the same antigen. - **Mediated by T cells and B cells:** - **T cells:** Helper T cells (CD4+) assist in various immune functions, including B cell antibody production (Th2), macrophage activation (Th1), and neutrophil recruitment (Th17). - Cytotoxic T cells (CD8+) directly kill infected cells. - Regulatory T cells (Tregs) maintain self-tolerance by suppressing immune responses to self-antigens. - **B cells:** Differentiate into antibody-secreting plasma cells that produce antibodies against specific antigens. - **Slower response time:** The adaptive immune response takes several days to weeks to fully develop. 2. Describe the role of lymphoid organs in host defense b. **Lymph nodes** - Lymph nodes are secondary lymphoid organs that **filter interstitial fluid and facilitate adaptive immune responses**. - They **monitor the peripheral environment by draining interstitial fluid and immune cells**, including phagocytes (macrophages and dendritic cells) and lymphocytes (T cells and B cells). - Lymph nodes provide a **site for immune cell interactions**. For example, dendritic cells present antigens to T cells, and T cells interact with B cells to promote antibody isotype switching. - They are also **essential for lymphocyte activation, proliferation, and differentiation**. This includes plasma cells secreting antibodies, helper T cells activating B cells and innate immune cells, and cytotoxic T cells migrating to infected tissues. - The lymph node structure is organized to support these functions: - **Outer cortex:** Contains B cell follicles and germinal centers where activated B cells proliferate and undergo affinity maturation. - **Paracortical areas:** House T cells and dendritic cells, facilitating antigen presentation and T cell activation. - **Inner medulla:** Contains plasma cells that secrete antibodies, and macrophages that help to clear pathogens and cellular debris. c. **Spleen** - The spleen is another secondary lymphoid organ that **filters blood, participates in red blood cell disposal, and contributes to adaptive immunity**. - It **collects antigens and cells from the blood** as blood circulates through trabecular arteries and veins. - The spleen has two main compartments: - **Red pulp:** Responsible for erythrocyte disposal. - **White pulp:** Contains lymphocytes surrounding central arterioles and is involved in adaptive immune responses. - **Periarteriolar Lymphoid Sheath (PALS):** Primarily composed of T cells. - **Corona:** Contains B cells. d. **Bone marrow** - Bone marrow is a **primary lymphoid organ where hematopoiesis occurs, generating all the cells of the immune system, including lymphocytes**. - It is also the **site of B cell development**, where B cells undergo VDJ recombination to generate a diverse repertoire of B cell receptors. - **B cell development in the bone marrow is guided by growth factors and cell-to-cell interactions**, leading to the generation of mature B cells that are self-tolerant and express functional B cell receptors. e. **Thymus** - The thymus is a primary lymphoid organ **responsible for T cell development**. - Within the thymus, lymphoid progenitor cells undergo **T cell receptor (TCR) gene rearrangement**, leading to the expression of unique TCRs on each T cell. - The thymus is also the site of **thymic selection**, where developing T cells undergo positive and negative selection: - **Positive selection:** Selects for T cells that can recognize self-MHC molecules, ensuring that mature T cells can interact with antigen-presenting cells. - **Negative selection:** Eliminates T cells that are strongly self-reactive, preventing autoimmunity. - The thymus **shrinks after puberty, leading to a decrease in T cell production**. - However, the T cells produced before puberty can provide lifelong immunity. - The thymus is organized into two main compartments: - **Cortex:** Contains immature thymocytes undergoing proliferation and thymic selection, as well as macrophages that clear apoptotic thymocytes. - **Medulla:** Contains mature thymocytes, medullary epithelial cells, macrophages, and dendritic cells, contributing to the final stages of T cell development and maturation. 3. Describe the role of RAG, TdT, MHC class I and MHC class II in lymphocyte development - **RAG:** RAG (Recombinase Activating Gene): RAG1 and RAG2 are essential for VDJ recombination, the process responsible for the diversity of B cell receptors (BCRs) and T cell receptors (TCRs)12. This random rearrangement of gene segments in the variable regions of BCRs and TCRs enables recognition of millions of antigens - **TdT:** TdT (Terminal Deoxynucleotidyl Transferase): This enzyme further enhances antigen receptor diversity by adding random nucleotides between V, D, and J segments during VDJ recombination3. This process, known as junctional diversity, generates novel sequences that increase the range of recognizable antigens - **RAG and TdT** create a diverse pool of antigen receptors on B and T cells, allowing the adaptive immune system to recognize a vast range of antigens - **MHC Class I:** These molecules are found on almost every cell type and present intracellular antigens, like those from viruses to cytotoxic T cells (CD8+)45. This interaction allows CD8+ T cells to identify and destroy infected cells6. MHC class I molecules also play a key role in T cell development in the thymus, ensuring T cells can recognize self-MHC molecules (MHC restriction) - **MHC Class II:** Primarily found on antigen-presenting cells (APCs) such as dendritic cells, macrophages, and B cells45, MHC class II molecules present antigens from extracellular pathogens to helper T cells (CD4+)5. This activation of helper T cells leads to diverse immune responses, including activating other immune cells like B cells and macrophages - **MHC class I and II** are crucial for antigen presentation, activating different T cell subsets (cytotoxic and helper T cells) and directing the immune response toward intracellular or extracellular pathogens, respectively 4. Explain how leukocytes are recruited to sites of infection f. Understand the roles for chemokines and adhesion molecules in leukocyte rolling, attachment and extravasation across vascular endothelium - **Inflammation:** The body\'s response to harmful stimuli (pathogens, damaged cells, etc.) is inflammation. This process leads to changes in blood vessels, making them more permeable and expressing adhesion molecules that facilitate leukocyte movement. - **Chemokines:** These signaling proteins act like guides, leading leukocytes toward the infection site by forming a concentration gradient. Higher chemokine levels at the infection site attract leukocytes. - **Adhesion Molecules:** These molecules mediate the interactions between leukocytes and endothelial cells lining the blood vessels. Extravasation, the process of leukocytes exiting the bloodstream into infected tissue, involves - **Rolling:** Selectins on endothelial cells weakly interact with leukocytes, slowing them down and causing them to roll along the blood vessel wall. - **Attachment:** Chemokines activate integrins on leukocytes, strengthening their binding to adhesion molecules on endothelial cells. This results in firm attachment and stops the rolling. - **Transmigration (Diapedesis):** The attached leukocytes squeeze between endothelial cells, leaving the blood vessel and entering the surrounding tissue, aided by integrins and molecules like ICAM-1 on endothelial cells. - **The key takeaway is that leukocyte recruitment is a highly coordinated process, driven by inflammation and orchestrated by chemokines and adhesion molecules.** This process ensures that leukocytes arrive at the infection site to effectively combat pathogens and repair tissue damage. 5. Define pattern recognition receptors (PRRs) - **Pattern recognition receptors (PRRs)** as proteins expressed by cells of the innate immune system. They are crucial for the early detection of pathogens by recognizing **pathogen-associated molecular patterns (PAMPs)**, which are conserved molecular patterns unique to microbes. g. Roles in host defense - **Host Defense:** PRRs act as the first line of defense against infection, playing a key role in initiating the innate immune response. Recognition of infection by PRRs triggers: - Activation of immune cells like macrophages, neutrophils, and dendritic cells. - Production of inflammatory mediators such as cytokines, chemokines, and antimicrobial peptides. - These responses control pathogen growth and alert the adaptive immune system to mount a targeted, long-lasting response. h. Signals that activate PRRs - **Activating Signals:** PRRs are activated by binding to PAMPs, which are essential for microbial survival or pathogenicity. Because PAMPs are highly conserved, they are less likely to mutate, making them reliable targets for PRRs i. Major PRR families - **Toll-like receptors (TLRs):** Found on the cell surface or in endosomes, TLRs recognize a broad spectrum of PAMPs. Their activation triggers the release of pro-inflammatory cytokines, vital for immune response coordination. - **C-type lectin receptors (CLRs):** These transmembrane proteins recognize carbohydrate structures on pathogens, such as fungal β-glucans. Activation of CLRs can initiate phagocytosis, cytokine production, and complement system activation. - **NOD-like receptors (NLRs):** Located in the cytosol, NLRs recognize PAMPs and danger-associated molecular patterns (DAMPs) released by damaged host cells. Upon activation, NLRs can form inflammasomes, multi-protein complexes that activate caspase-1. This, in turn, leads to the processing and release of pro-inflammatory cytokines like IL-1β and IL-18. - **RIG-I-like receptors (RLRs):** These cytosolic proteins detect viral RNA, triggering the production of type I interferons (IFN-α and IFN-β) known for their antiviral activity. 6. NK cells - **NK cells** are lymphocytes that detect and destroy unhealthy cells, like virus-infected cells or tumor cells, by releasing cytotoxic granules1. NK cells are part of the innate immune system j. Roles for NK cells in host defense - Their significance stems from their ability to swiftly **detect and eliminate unhealthy cells without prior sensitization**1. Unlike the adaptive immune response, which relies on T cells and B cells and requires prior exposure to antigens, NK cells can act immediately upon encountering an aberrant cell. - NK cells play a key role in **antiviral immunity**23. They can directly kill virus-infected cells and release **interferon-γ (IFN-γ),** which further activates macrophages to enhance their bactericidal activity4. This dual action makes NK cells potent contributors to controlling viral infections. k. Target cell recognition by NK cells: Step by Step - **Continuous Surveillance**: NK cells are constantly circulating throughout the body, interacting with various cells. - **Checking for \"Danger\" Signals**: NK cells use their **activating receptors** to check for the presence of stress-induced ligands on the surface of cells they encounter. These ligands are often overexpressed on cells under stress, such as those infected with viruses or those that have transformed into tumor cells. - **Looking for \"Safety\" Signals**: At the same time, NK cells use their **inhibitory receptors** to assess the expression of MHC class I molecules on the cell surface. MHC class I molecules are present on most healthy cells and serve as \"self\" markers. - **Signal Integration**: The NK cell integrates the signals it receives from its activating and inhibitory receptors. - **Activation**: If the activating signals outweigh the inhibitory signals, the NK cell is activated. This occurs when a cell is expressing high levels of stress ligands and/or has downregulated its MHC class I expression. - **Inhibition**: If the inhibitory signals from MHC class I binding dominate, the NK cell remains inactive. This prevents the NK cell from attacking healthy cells. - **Targeted Elimination**: Once activated, the NK cell releases its cytotoxic granules, containing perforin and granzymes, to kill the target cell. Perforin forms pores in the target cell membrane, allowing granzymes to enter and induce apoptosis. - **Antibody-Dependent Cellular Cytotoxicity (ADCC)**: This is an additional mechanism by which NK cells can recognize and kill target cells. In this process, antibodies produced by the adaptive immune system bind to specific antigens on target cells. NK cells have Fc receptors that can bind to the constant region of these antibodies, leading to NK cell activation and target cell death. l. Roles for perforin and granzymes in NK cell-mediated cytotoxicity - NK cell-mediated cytotoxicity relies on the release of cytotoxic granules containing **perforin** and **granzymes**, which induce apoptosis in target cells - **Perforin:** Perforin is a pore-forming protein that creates holes in the target cell membrane, disrupting its integrity and allowing granzymes to enter the cell. - **Granzymes:** Granzymes are serine proteases that activate caspases, a family of enzymes that execute the apoptotic program, leading to the controlled dismantling of the target cell. **Granzyme B** is particularly important in this process - The combined action of perforin and granzymes ensures the efficient and targeted elimination of unhealthy cells by NK cells. 7. Antibodies m. Functions for IgA, IgE, IgG and IgM - **IgA**: The primary antibody isotype found in mucosal secretions like tears, saliva, and breast milk. IgA **neutralizes** toxins and bacteria, preventing their attachment to mucosal surfaces. - **IgE**: Primarily involved in **hypersensitivity reactions**, including allergic responses. IgE binds to **Fcε receptors** on mast cells, sensitizing them to allergens. Upon re-exposure to the allergen, IgE cross-linking triggers mast cell **degranulation**, releasing histamine and other inflammatory mediators. - **IgG**: The most abundant antibody isotype in serum. IgG can **neutralize** pathogens, **opsonize** them for phagocytosis, and activate the **complement** system. - **IgM**: The first antibody isotype produced during an immune response. IgM exists as a pentamer, making it efficient at **complement activation**. IgM has lower affinity for antigens compared to IgG. i. Which isotypes are best for neutralization, opsonization, complement activation, or hypersensitivity reactions? Function Best Isotype(s) ----------------------- ----------------- Neutralization IgG, IgA Opsonization IgG Complement Activation IgM, IgG Hypersensitivity IgE ii. Difference between antibody constant and variable regions - Antibodies have a characteristic Y-shaped structure. Each antibody molecule is composed of two identical **heavy chains** and two identical **light chains**. - **Variable Regions**: The tips of the \"Y\" arms form the **antigen-binding sites**, providing specificity. The variable regions of both the heavy and light chains contribute to the antigen-binding site. These regions are highly variable in their amino acid sequence, allowing for a vast repertoire of antibodies, each recognizing a unique antigen. - **Constant Regions**: The stem of the \"Y\" determines the antibody\'s **isotype (IgA, IgE, IgG, IgM)**. The constant regions interact with effector molecules and cells of the immune system, dictating the antibody\'s function. For instance, the constant region of IgG allows it to bind to Fc receptors on phagocytes, facilitating opsonization. iii. How does isotype switching, somatic hypermutation and affinity maturation affect antibody production and function? - **Isotype Switching**: B cells initially produce IgM antibodies. Through a process called **class switch recombination**, they can switch to producing other isotypes (IgG, IgA, or IgE). This process is influenced by signals from T helper cells (specifically Th2 cells) and cytokines. Isotype switching allows for a more tailored response, as different isotypes have specialized functions. - **Somatic Hypermutation**: This process introduces point mutations into the variable regions of antibody genes. These mutations alter the amino acid sequence of the antigen-binding site, creating a diverse pool of antibodies with varying affinities for the antigen. Somatic hypermutation is driven by the enzyme **activation-induced cytidine deaminase (AID)**. - **Affinity Maturation**: As B cells proliferate and undergo somatic hypermutation, those producing antibodies with higher affinity for the antigen are preferentially selected. This process, called affinity maturation, results in the production of antibodies with increasingly stronger binding to the antigen, leading to a more effective immune response. 8. Lymphocyte activation and differentiation n. Compare and contrast how CD4 and CD8 T cells recognize antigens - **CD4 T cells**, also known as helper T cells, recognize antigens presented on **MHC class II molecules**. MHC class II molecules are primarily found on the surface of specialized **antigen-presenting cells (APCs)** such as dendritic cells, macrophages, and B cells. The antigens displayed on MHC class II molecules are typically derived from **extracellular sources** -- for example, pathogens that have been engulfed and processed by APCs. - **CD8 T cells**, also known as cytotoxic T cells, recognize antigens presented on **MHC class I molecules**. Unlike MHC class II, **MHC class I molecules are expressed on nearly all nucleated cells** in the body. These molecules typically display antigens derived from **intracellular sources**, such as viral proteins synthesized within an infected cell or abnormal proteins produced by tumor cells. o. CD4 T cell differentiation iv. Roles for costimulation and cytokines - **Costimulation**: In addition to recognizing the antigen-MHC complex, CD4 T cells require a second signal called costimulation to become fully activated. This signal is provided by **costimulatory molecules** expressed on APCs, such as **CD80 and CD86**, which interact with their corresponding receptors (e.g., **CD28**) on T cells. Costimulation ensures that T cells only respond to genuine threats and not to harmless self-antigens. - **Cytokines**: The specific subset into which a CD4 T cell differentiates is largely determined by the **cytokine environment** present during activation. Different cytokines, produced by APCs and other immune cells, direct T cell differentiation towards specific lineages. v. Roles for Th1, Th2, Th17 and Treg subsets in host defense and inflammation - **Th1 Cells**: - Induced by cytokines like **IL-12** and **IFN-γ**. - Produce **IFN-γ**, which activates macrophages, enhancing their ability to kill intracellular pathogens like bacteria and some parasites. - Promote cell-mediated immunity, crucial for defense against intracellular infections. - **Th2 Cells**: - Induced by cytokines like **IL-4**. - Secrete **IL-4, IL-5, and IL-13**. - Promote humoral immunity by activating B cells and inducing antibody isotype switching, particularly to IgE. - Play a role in defense against extracellular parasites, such as helminths. - Involved in allergic reactions. - **Th17 Cells**: - Induced by cytokines like **IL-6 and TGF-β**. - Produce **IL-17**, which recruits neutrophils to sites of infection. - Contribute to defense against extracellular bacteria and fungi. - Implicated in autoimmune diseases when their responses are dysregulated. - **Treg Cells (Regulatory T cells)**: - Characterized by the expression of **CD25 and the transcription factor FoxP3**. - Suppress immune responses, helping to maintain self-tolerance and prevent autoimmunity. - Secrete immunosuppressive cytokines like **IL-10 and TGF-β**. - Defects in Treg function can contribute to the development of autoimmune diseases p. Cytotoxic CD8 T cells vi. Roles in host defense - Roles in Host Defense: Direct Killing to Eliminate Threats - **Virus-Infected Cells**: CD8 T cells recognize viral peptides presented on MHC class I molecules of infected cells. Upon activation, they release cytotoxic molecules, **perforin and granzymes**, which induce apoptosis in the target cell, thus eliminating the virus\'s replication factory. - **Tumor Cells**: CD8 T cells can also recognize tumor-associated antigens presented on MHC class I molecules of cancer cells. They contribute to tumor immunosurveillance by eliminating nascent tumor cells. However, established tumors often develop mechanisms to evade CD8 T cell recognition and killing 9. Primary immunodeficiencies q. Identify the most common genes associated with primary immunodeficiencies vii. X-linked SCID, X-linked Hyper IgM Syndrome, Chronic Granulomatous Disease, X-linked Agammaglobulinemia - **X-linked SCID (Severe Combined Immunodeficiency)**: The most common genetic mutation associated with X-linked SCID is in the gene ***IL2RG***. *IL2RG* encodes the **common gamma chain (γc)**, a component of several cytokine receptors, including those for IL-2, IL-7, and IL-15. These cytokines play vital roles in the development and function of T cells and NK cells. Mutations in *IL2RG* result in impaired signaling through these cytokine receptors, leading to a severe deficiency of T cells and NK cells and impaired B cell function. - **X-linked Hyper IgM Syndrome**: The most common gene associated with this disorder is ***CD40L***, located on the X chromosome. *CD40L* encodes the CD40 ligand, a protein expressed on activated T helper cells. CD40L interacts with the CD40 receptor on B cells, providing essential signals for B cell activation, proliferation, and **isotype switching**. Mutations in *CD40L* disrupt this interaction, preventing B cells from undergoing isotype switching from IgM to other antibody isotypes like IgG, IgA, and IgE. As a result, individuals with X-linked Hyper IgM Syndrome have low levels of IgG and IgA, but elevated levels of IgM. - **Chronic Granulomatous Disease (CGD)**: This disorder is most commonly caused by mutations in the gene ***gp91PHOX***, also located on the X chromosome. *gp91PHOX* encodes a component of the **NADPH oxidase** complex, an enzyme crucial for the production of **reactive oxygen species (ROS)** in phagocytes. ROS are essential for killing phagocytosed bacteria and fungi. Mutations in *gp91PHOX* lead to defective NADPH oxidase activity, impairing the ability of neutrophils and macrophages to generate ROS and effectively kill microbes. This leads to recurrent and persistent infections, often characterized by the formation of **granulomas**, which are inflammatory nodules that attempt to contain the infection. - **X-linked Agammaglobulinemia (XLA)**: The most common gene associated with XLA is ***BTK*** (Bruton\'s tyrosine kinase), which is located on the X chromosome. *BTK* encodes a tyrosine kinase essential for B cell development. Mutations in *BTK* disrupt B cell signaling, leading to a block in B cell maturation and a deficiency of all antibody isotypes. This results in a severe humoral immune deficiency, making individuals with XLA highly susceptible to infections. r. Compare and contrast common inheritance patterns viii. autosomal vs. X-linked - **Autosomal inheritance**: Refers to genes located on the **autosomes**, which are the non-sex chromosomes. Humans have 22 pairs of autosomes. Autosomal disorders can affect both males and females equally. - **X-linked inheritance**: Refers to genes located on the **X chromosome**. Females have two X chromosomes (XX), while males have one X and one Y chromosome (XY). X-linked disorders tend to affect males more frequently because they only have one copy of the X chromosome. If that copy carries a mutated gene, they will express the disorder. Females can be carriers of X-linked disorders without showing symptoms if they have a normal copy of the gene on their other X chromosome. ix. dominant vs. recessive - **Dominant inheritance**: Occurs when only **one copy of the mutated gene** is needed to express the disorder. Individuals with a dominant disorder have a 50% chance of passing the disorder on to each of their children. - **Recessive inheritance**: Occurs when **two copies of the mutated gene** are needed to express the disorder. Individuals with one copy of the mutated gene are called **carriers** -- they do not have the disorder but can pass the mutated gene on to their offspring. If both parents are carriers of a recessive disorder, there is a 25% chance that their child will inherit two copies of the mutated gene and have the disorder. **Table Summarizing Common Primary Immunodeficiencies, Associated Genes, and Inheritance Patterns:** Immunodeficiency Most Common Gene Inheritance Pattern ------------------------------- ------------------ --------------------- X-linked SCID *IL2RG* X-linked recessive X-linked Hyper IgM Syndrome *CD40L* X-linked recessive Chronic Granulomatous Disease *gp91PHOX* X-linked recessive X-linked Agammaglobulinemia *BTK* X-linked recessive ADA Deficiency *ADA* Autosomal recessive Autosomal Recessive SCID *JAK3*, *RAG* Autosomal recessive DiGeorge Syndrome *TBF1* Autosomal dominant 10. Compare and contrast different types of vaccines s. Attenuated t. Inactivated u. Conjugate v. RNA w. Subunit x. Toxoid - **Live Attenuated Vaccines:** - **Mechanism:** Live attenuated vaccines use a weakened form of the pathogen that can still replicate within the host. This replication stimulates a robust and long-lasting immune response, similar to natural infection. - **Advantages:** Provide strong, long-lasting immunity, often with a single dose. - **Disadvantages:** Not suitable for immunocompromised individuals or pregnant women. - **Examples:** MMR, chickenpox, rotavirus, some influenza vaccines (LAIV4). - **Inactivated Vaccines:** - **Mechanism:** These vaccines use pathogens that have been completely killed and are incapable of replication. - **Advantages:** Generally safe, as they cannot cause disease. - **Disadvantages:** Often require multiple doses (boosters) and adjuvants to enhance the immune response. - **Examples:** Inactivated influenza vaccines (Fluzone, IIV), some polio vaccines (Salk polio), pertussis, plague. - **Subunit Vaccines:** - **Mechanism:** Subunit vaccines deliver specific components of the pathogen, typically proteins, that are known to elicit a protective immune response. - **Advantages:** Very safe, as they contain only a portion of the pathogen and are non-infectious. - **Disadvantages:** May require adjuvants to enhance their effectiveness. - **Examples:** Hepatitis B vaccine, some influenza vaccines (Flublok), DPT vaccines. - **Toxoid Vaccines:** - **Mechanism:** Toxoid vaccines target pathogens that cause disease primarily through toxins. These vaccines use inactivated toxins (toxoids) that retain their ability to stimulate an immune response. - **Advantages:** Safe, as the toxins are inactivated. - **Advantages:** Often given in combination with other vaccine components to boost their potency. - **Examples:** Diphtheria and tetanus vaccines in DTP. - **Conjugate Vaccines:** - **Mechanism:** Conjugate vaccines are a type of subunit vaccine designed to enhance the immune response against poorly immunogenic antigens, such as bacterial capsular polysaccharides. These antigens are linked to a carrier protein that helps activate T cells, leading to increased antibody production. - **Advantages:** Effective in eliciting a strong immune response against polysaccharides, particularly in young children. - **Examples:** *Haemophilus influenzae* type B (Hib) and *Streptococcus pneumoniae* (pneumococcal) vaccines. - **RNA Vaccines:** - **Mechanism:** Relatively new technology, RNA vaccines deliver messenger RNA (mRNA) that encodes for a specific pathogen protein. Cells in the body take up this mRNA and produce the pathogen protein, triggering an immune response. - **Advantages:** Can be rapidly developed and manufactured. \[This information is not from the sources provided. You may wish to verify this independently.\] - **Examples:** Pfizer-BioNTech and Moderna COVID-19 vaccines. y. How do vaccine adjuvants improve their efficacy/immunogenicity? - Adjuvants are substances added to some vaccines to enhance their immunogenicity by activating dendritic cells (DCs), key players in initiating adaptive immune responses. - **Mechanisms:Depot effect:** Create a depot at the injection site, slowing the release of antigens for prolonged exposure. - **DC activation:** Directly activate DCs through pattern recognition receptors (TLRs). - **Cytokine secretion:** Promote the release of inflammatory cytokines that amplify the immune response. 11. Describe the pathophysiology of Autoimmune Polyendocrine Syndrome Type 1 and Rheumatoid Arthritis **Autoimmune Polyendocrine Syndrome Type 1 (APS-1)** - APS-1, also called APECED, is caused by mutations in the AIRE gene. AIRE plays a critical role in the thymus by ensuring that developing T cells are exposed to tissue-specific antigens. This process, called **negative selection**, eliminates T cells that might attack the body\'s own tissues. Without functional AIRE, these self-reactive T cells escape destruction and can go on to target various organs, particularly endocrine glands. - **The result is a collection of symptoms, the most common being:** - **Chronic mucocutaneous candidiasis:** Fungal infections of the skin and mucous membranes due to autoantibodies against IL-17. - **Hypoparathyroidism:** Underactive parathyroid glands leading to low calcium levels in the blood. - **Adrenal insufficiency (Addison's disease):** The adrenal glands don\'t produce enough cortisol. - **Diagnosis often involves blood tests to detect the presence of autoantibodies targeting specific endocrine gland proteins, such as those found in Hashimoto's thyroiditis**. **Rheumatoid Arthritis (RA)** - RA is a chronic disease where the immune system attacks the joints. While the exact cause is unknown, it\'s thought to be a combination of genetic predisposition and environmental factors. - **Here\'s a simplified breakdown:** - **Genetic Risk:** Genes involved in immune regulation, specifically certain HLA (human leukocyte antigen) types, make some individuals more susceptible. - **Environmental Triggers:** These can include smoking and infections, which might activate the immune system in a way that leads to RA. - **Protein Citrullination:** This is a key process in RA where a protein modification called citrullination occurs, particularly in the joints. - **Immune System Activation:** The immune system sees these citrullinated proteins as foreign and mounts an attack. - **Autoantibodies:** B cells produce autoantibodies like rheumatoid factor (RF) and anti-citrullinated peptide antibodies (ACPAs), which bind to citrullinated proteins. - **Immune Complex Formation and Inflammation:** These autoantibodies form immune complexes that deposit in the joints, triggering inflammation and joint damage. - **Cytokine Release:** Inflammatory cells release cytokines, like TNF, IL-1, and IL-6, which further amplify inflammation and contribute to the destruction of cartilage and bone. - **Diagnosis typically involves assessing joint symptoms, medical history, and the presence of autoantibodies like RF and ACPAs**. Treatment often aims to reduce inflammation and slow disease progression using various medications 12. Hypersensitivity z. Compare and contrast allergen sensitization and reactivation phases a. Compare and contrast immediate (type I) and delayed (type IV) hypersensitivity reactions **Breaking Down Hypersensitivity Reactions** -------------------------------------------- ### **a. Allergen Sensitization vs. Reactivation Phases** - Hypersensitivity reactions involve an exaggerated immune response to harmless antigens (allergens) or self-antigens (autoimmunity). These reactions are categorized into different types based on the immune mechanisms involved. - Let\'s focus on **Type I hypersensitivity**, a common type involving allergens. It unfolds in two distinct phases: **1. Sensitization Phase:** - Initial Encounter: The body first encounters the allergen, which could be anything from pollen and pet dander to certain foods or insect venom. - Antigen Presentation: Dendritic cells (DCs) capture the allergen and present it to naive CD4 T cells in lymph nodes. - Th2 Cell Differentiation: The interaction with the allergen, along with specific signals, drives the naive CD4 T cells to differentiate into Th2 cells. - B Cell Activation and IgE Production: Th2 cells then activate B cells that recognize the same allergen through CD40/CD40L interaction. These activated B cells undergo class switching to produce IgE antibodies specific to the allergen. - Mast Cell Priming: The IgE antibodies bind to high-affinity FcεRI receptors on mast cells, which reside in tissues like the skin, respiratory tract, and GI tract. This \"primes\" the mast cells for the next encounter with the allergen. **2. Reactivation Phase:** - Re-exposure: Upon subsequent exposure to the same allergen, it binds to the IgE already attached to mast cells. This cross-linking of IgE triggers mast cell degranulation. - Immediate Response: Mast cells release preformed mediators like histamine, prostaglandins, and leukotrienes. These cause immediate symptoms like vasodilation, increased vascular permeability, smooth muscle contraction (e.g., bronchospasm in the airways), and itching. - Late-Phase Response: After several hours, the released mediators also attract inflammatory cells like eosinophils, basophils, and neutrophils, contributing to a late-phase reaction. This amplifies and sustains the allergic response, leading to more prolonged symptoms. **Anaphylaxis:** - In severe cases, widespread mast cell degranulation can lead to a life-threatening systemic reaction called anaphylaxis. - Symptoms of anaphylaxis: A rapid drop in blood pressure, airway constriction (difficulty breathing), skin reactions (hives, itching), and gastrointestinal distress. - Emergency Treatment: Epinephrine is the first-line treatment for anaphylaxis, along with antihistamines and corticosteroids to control the allergic response. ### b. **Type I vs. Type IV Hypersensitivity: Timing and Key Players** - Feature: Type I (Immediate)Type IV (Delayed)Timing Immediate, within minutes of allergen exposure. Delayed, typically 48-72 hours after allergen exposure. - Key Cells: Th2 cells, B cells, mast cells, basophils, eosinophils Th1 cells, macrophages. - Mediators: IgE, histamine, prostaglandins, leukotrienes, cytokines (IL-4, IL-5, IL-13)IFN-γ, TNF, macrophage-derived enzymes, cytokines (IL-12, IFN-γ) - Mechanism: Allergen cross-links IgE on mast cells, triggering degranulation and immediate release of mediators. Antigen presented to memory Th1 cells, leading to macrophage activation and cytokine release. - Examples: Allergic rhinitis (hay fever), asthma, food allergies, insect sting allergies, anaphylaxis, Tuberculin skin test (TB test), contact dermatitis (e.g., poison ivy), some drug reactions **In summary:** - Type I hypersensitivity is characterized by a rapid onset of symptoms driven by mast cell degranulation and the release of preformed mediators. - Type IV hypersensitivity involves a delayed response mediated by Th1 cells and macrophages, leading to localized inflammation. 1. **Protein Citrullination:** This is a key process in RA where a protein modification called citrullination occurs, particularly in the joints. 2. **Immune System Activation:** The immune system sees these citrullinated proteins as foreign and mounts an attack. 3. **Autoantibodies:** B cells produce autoantibodies like rheumatoid factor (RF) and anti-citrullinated peptide antibodies (ACPAs), which bind to citrullinated proteins. 4. **Immune Complex Formation and Inflammation:** These autoantibodies form immune complexes that deposit in the joints, triggering inflammation and joint damage. 5. **Cytokine Release:** Inflammatory cells release cytokines, like TNF, IL-1, and IL-6, which further amplify inflammation and contribute to the destruction of cartilage and bone. - **Diagnosis typically involves assessing joint symptoms, medical history, and the presence of autoantibodies like RF and ACPAs**. Treatment often aims to reduce inflammation and slow disease progression using various medications. 13. Tumor immunity b. Understand how established tumors are capable of evading recognition by the immune system c. Understand in general terms how genes that regulate cell division contribute to tumorigenesis Understanding Tumor Immunity: Evasion and Tumorigenesis ------------------------------------------------------- ### a. Evasion of Immune Recognition by Established Tumors - The immune system has mechanisms in place to recognize and eliminate abnormal cells, including tumor cells. However, **tumors, especially established ones, develop strategies to evade these immune responses.** - These strategies include: - **Downregulation or Loss of MHC Class I Expression:** MHC class I molecules present tumor-associated antigens to cytotoxic CD8+ T cells, initiating an immune response. Tumors can reduce or eliminate MHC class I expression, making them invisible to CD8+ T cells. - **Lack of Costimulation:** T cell activation requires two signals: the first from antigen recognition through the TCR, and the second from costimulatory molecules like CD80/CD86 on antigen-presenting cells (APCs). Tumors often lack these costimulatory molecules, preventing full T cell activation. - **Production of Immunosuppressive Factors:** Tumor cells can secrete immunosuppressive factors like TGF-β and IL-10, which inhibit T cell activation and promote the development of regulatory T cells (Tregs) that suppress anti-tumor immune responses. - **Induction of T Cell Exhaustion:** Chronic antigen stimulation in the tumor microenvironment can lead to T cell exhaustion. Exhausted T cells lose their effector functions, making them ineffective in eliminating tumor cells. - **Exploitation of Immune Checkpoints:** Tumors can upregulate immune checkpoint molecules like PD-L1, which bind to PD-1 receptors on T cells and suppress their activity. This interaction acts as a \"brake\" on the immune system, preventing it from attacking the tumor. - **Tumor Immunoediting:** Over time, tumors undergo a process of immunoediting, where the immune system exerts selective pressure, eliminating highly immunogenic tumor cells. This process favors the survival and growth of less immunogenic tumor variants that can evade immune detection. ### b. Role of Genes in Tumorigenesis - Tumorigenesis, the development of a tumor, is driven by **mutations in genes that regulate cell division, growth, and survival**. - These mutations can result in: - **Increased Expression of Cell Division Genes:** Genes like STAT3, AP1, and NF-kB, when overexpressed, promote uncontrolled cell proliferation. - **Loss of Function of Tumor Suppressor Genes:** Tumor suppressors like p53 and PTEN normally act as brakes on cell division and promote cell death (apoptosis) when necessary. Mutations in these genes allow uncontrolled cell growth and survival. - **Enhanced Growth Factor Signaling:** Mutations can lead to the overexpression of growth factors or their receptors, causing sustained growth signals that promote cell division. - **Increased Cell Mobilization:** Genes involved in cell adhesion, extracellular matrix degradation (MMPs), and angiogenesis (blood vessel formation) can be dysregulated, allowing tumor cells to invade surrounding tissues and spread to distant sites (metastasis). **In summary**: - Tumors employ multiple strategies to evade immune recognition and destruction, including manipulating MHC expression, suppressing T cell responses, and exploiting immune checkpoints. - Tumorigenesis is a multistep process driven by mutations in genes that control cell division, growth, and survival. These mutations lead to uncontrolled cell proliferation, resistance to cell death, and enhanced cell mobility, ultimately contributing to tumor development and progression. 14. Identify immunological principles of tissue transplantation d. What determines donor/recipient compatibility? x. Whole organ transplantation 1. HLA matching xi. Blood transfusions 2. ABO blood group typing ### Whole Organ Transplantation - **HLA (Human Leukocyte Antigen) matching is the most critical factor in determining compatibility for whole-organ transplantation**. - HLA molecules, also known as MHC (Major Histocompatibility Complex), are proteins found on the surface of cells that are responsible for presenting antigens to the immune system. These molecules play a vital role in the immune system\'s ability to distinguish between self and non-self. - The recipient\'s immune system is less likely to recognize the donor organ as foreign if the HLA molecules are similar, leading to a lower risk of rejection. - When donor and recipient HLA molecules are mismatched, the recipient\'s T cells can attack the transplanted organ, resulting in rejection. - **To increase the chances of successful transplantation, several tests are used:** - **Mixed Lymphocyte Reaction (MLR)**: Lymphocytes from the potential donor and recipient are cultured together to check for reactivity. A positive reaction (proliferation or cytotoxicity) indicates incompatibility. - **Flow cytometry**: This technique identifies the specific HLA variants/alleles present on the surface of cells. - **DNA sequencing**: This method provides detailed information about an individual\'s HLA genes, helping to identify compatible matches. - **Lymphocytotoxicity assay**: This test uses antibodies against specific HLA alleles and complement proteins to determine HLA compatibility. If the donor cells are lysed in the presence of the recipient\'s serum and complement, it indicates incompatibility. - **Cross-matching**: This test detects pre-existing antibodies in the recipient\'s serum that might target donor antigens. If such antibodies are present, they can trigger hyperacute rejection within 24 hours of transplantation. ### Blood Transfusions - **The ABO blood group system is the primary factor determining compatibility in blood transfusions**. - Humans have natural antibodies against the blood group antigens they lack. - Transfusing incompatible blood types leads to the recipient\'s antibodies attacking and destroying donor red blood cells, causing a potentially life-threatening transfusion reaction. - **Blood type AB individuals are considered \"universal recipients\"** because they lack both anti-A and anti-B antibodies, allowing them to receive any blood type. - **Blood type O individuals are \"universal donors\"** since their red blood cells lack A and B antigens, making their blood compatible with all recipient blood types. - **In addition to the ABO system, the Rh factor is also critical**. - **Rh incompatibility between a pregnant woman and her fetus can lead to hemolytic disease of the newborn**. In such cases, an Rh-negative mother can develop antibodies against the Rh-positive blood cells of her fetus, leading to fetal anemia and other complications. - **RhoGAM, an anti-Rh IgG antibody injection**, is given to Rh-negative mothers to prevent sensitization to the Rh factor and protect future pregnancies. - **In both whole-organ transplantation and blood transfusions, compatibility testing and matching are essential to minimize the risk of rejection and ensure the best possible outcome for the recipient**. 15. HIV infection e. Viral life cycle xii. Roles for Gp120, Gp41, reverse transcriptase, integrase protease f. Describe the pathophysiology of Immune Reconstitution and Inflammatory Syndrome (IRIS) ### a. HIV Viral Life Cycle and Key Protein Roles - The HIV life cycle represents the series of steps the virus takes to infect cells and replicate. - Here is a simplified explanation of the cycle, highlighting the roles of key proteins: - **Attachment and Entry**: The HIV virus attaches to a CD4+ T cell (a type of immune cell) using its **Gp120** protein. Gp120 binds to the CD4 receptor and a co-receptor (CCR5 or CXCR4) on the T cell surface. This binding triggers a conformational change in the viral **Gp41** protein, which mediates the fusion of the viral membrane with the T cell membrane, allowing the virus to enter the cell. - **Reverse Transcription**: Once inside the cell, the virus releases its RNA genome. The HIV enzyme **reverse transcriptase** then converts this single-stranded RNA into double-stranded DNA. This step is unique to retroviruses like HIV and is a prime target for antiretroviral drugs. - **Integration**: The newly synthesized viral DNA, with the help of the viral **integrase** enzyme, gets incorporated into the host cell\'s DNA. This integrated viral DNA is called a provirus, and it can remain dormant for years. - **Transcription and Translation**: When the infected T cell is activated, the provirus is transcribed into viral RNA. This RNA serves as a template for the production of viral proteins using the host cell\'s machinery. - **Assembly and Maturation**: The viral proteins and RNA assemble into new viral particles. The **protease** enzyme plays a crucial role in this step by cleaving viral precursor proteins (Gag and Env) into their functional forms, enabling the assembly of mature, infectious virions. - **Budding and Release**: New viral particles bud off from the infected cell\'s membrane, acquiring their lipid envelope in the process. These newly released viruses can then infect other CD4+ T cells, continuing the cycle. ### b. Pathophysiology of Immune Reconstitution Inflammatory Syndrome (IRIS) - **IRIS is a paradoxical condition that can occur in HIV-infected individuals who start antiretroviral therapy (ART)**. It is characterized by the **worsening of pre-existing opportunistic infections or the development of new inflammatory symptoms despite a decrease in HIV viral load and an increase in CD4+ T cell count**. - Here is a breakdown of the pathophysiology: - **Immune Suppression and Opportunistic Infections**: Before ART, the HIV virus suppresses the immune system, particularly by depleting CD4+ T cells, leading to opportunistic infections. These infections may be present but not fully manifested due to the weakened immune response. - **ART Initiation and Immune Restoration**: ART effectively suppresses HIV replication, allowing the immune system, including CD4+ T cells, to recover. - **Exaggerated Immune Response**: As the immune system strengthens, it can mount a robust response to the previously suppressed opportunistic pathogens. This response can sometimes be excessive, leading to an **inflammatory \"cytokine storm\"**. - **Clinical Manifestations**: The excessive inflammatory response damages tissues and organs, causing the symptoms of IRIS. These symptoms can vary depending on the underlying opportunistic infection, ranging from mild to life-threatening. - **The key point is that IRIS represents an imbalance between immune recovery and inflammatory control**. It highlights the complexity of immune reconstitution in HIV-infected individuals and the need for careful monitoring and management during ART initiation.