Innate Immunity, B Cell Development, and T Cell Antigen Presentation

[L5-6] What is innate immunity?

A broad, nonspecific defense system that includes barriers, pattern recognition, complement, inflammation, phagocytosis, NK-cell activity, and cytolysis.

[L5-6] Does innate immunity have immunological memory?

Generally no. It responds quickly and usually produces a similar magnitude of response each time it encounters the same type of danger.

[L5-6] Why is stomach acid an innate defense?

The low pH creates a hostile environment that prevents many pathogens from replicating.

[L5-6] What is the microbiota or microflora?

The large community of benign bacteria and fungi that live on body surfaces and in places such as the mouth, gut, respiratory tract, and skin.

[L5-6] What is the complement system?

A collection of about 30 serum proteins that help lyse pathogens, promote opsonization, clear immune complexes, and generate inflammatory peptide fragments.

[L5-6] What is the lectin pathway initiated by?

Mannose-binding lectin, or MBL, binding carbohydrate structures on pathogen proteins.

[L5-6] What does MASP do in the lectin pathway?

MBL-associated serine protease cleaves C4 and starts the rest of the complement cascade.

[L5-6] What is the difference between complement fragments ending in a and b?

The a fragment is usually smaller and often contributes to inflammation, while the b fragment usually continues the complement cascade. C2 is an exception.

[L5-6] What is chemotaxis?

Directed movement of leukocytes along a gradient of chemical signals toward the site of infection or injury.

[L5-6] What is phagocytosis?

The receptor-mediated engulfment of a large particle, microbe, or apoptotic cell into a phagosome.

[L7] What domains are in a light chain?

One variable domain and one constant domain, called VL and CL.

[L7] What domains are in a heavy chain?

One variable domain and three or four constant domains, depending on the isotype.

[L7] Are complete immunoglobulin genes already present in the germline genome?

No. The variable portions are assembled from separate gene segments in developing B cells.

[L7] Where are RAG-1 and RAG-2 expressed?

They are expressed in developing B and T lymphocytes, not in mature lymphocytes or non-lymphocytes.

[L7] What is cross-reactivity?

The ability of one antibody or receptor to bind more than one related antigen because their epitopes are similar enough to fit the binding site.

[L8-9] How long do immature B cells remain in the bone marrow after central tolerance?

About 1-3 days before expressing adhesion molecules and homing receptors that let them leave.

[L8-9] What is a transitional type 1 B cell?

A newly emigrated immature B cell that enters the spleen after leaving the bone marrow.

[L8-9] What can T2 B cells become?

They can become follicular B cells in lymphoid follicles or marginal-zone B cells in the spleen.

[L8-9] What immunoglobulins do mature naive B cells express?

They express both membrane IgM and membrane IgD.

[L8-9] How many mature naive B cells does adult bone marrow produce daily?

About 10 million.

[L8-9] How often does a B cell encounter its specific antigen?

Only about 1 in 100,000 B cells encounters its specific antigen.

[L8-9] What are the three major classes of B-cell immunogens?

T-independent type 1, T-independent type 2, and T-dependent immunogens.

[L8-9] What are the three signals required for T-dependent B-cell activation?

Signal 1 is antigen binding to BCRs. Signal 2 is CD40 on the B cell binding CD40L on an activated helper T cell. Signal 3 is cytokines binding receptors on the B cell.

[L8-9] What happens 4-6 days after antigen contact?

Some activated B cells quickly become short-lived plasma cells, while others move into the follicle and begin the germinal-center response.

[L8-9] What happens 6-9 days after antigen contact?

The proliferating B-cell clone displaces naive B cells and forms a follicular mantle around the developing secondary follicle.

[L8-9] What happens 9-12 days after antigen contact?

The secondary follicle develops dark and light zones and becomes a germinal center.

[L8-9] How long can germinal centers last?

Up to about 21 days after antigen contact.

[L8-9] What is somatic hypermutation?

A process in which rapidly dividing B cells accumulate random point mutations in their antibody variable-region exons.

[L8-9] What is affinity maturation?

The selection of B cells with higher-affinity BCRs after somatic hypermutation, producing antibodies that bind antigen more strongly.

[L10] What is the major histocompatibility complex?

A large genetic region encoding proteins that present peptides to T cells and influence transplant rejection and antigen recognition.

[L10] What is the human MHC called?

The HLA complex, or human leukocyte antigen complex.

[L10] Which T-cell coreceptor recognizes MHC class I?

CD8.

[L10] Which T-cell coreceptor recognizes MHC class II?

CD4.

[L10] What kind of peptides does MHC class I present?

Mostly endogenous peptides made inside the cell, including peptides from normal self proteins or intracellular pathogens.

[L10] Does MHC class I decide whether a peptide is self or nonself?

No. MHC presents peptides, but the T-cell receptor determines whether the peptide should trigger a response.

[L10] What does beta-2-microglobulin do?

It stabilizes the MHC class I molecule and is required for transport to the cell surface.

[L10] What kind of peptides does MHC class II present?

Mostly exogenous peptides that entered the cell through phagocytosis or another endocytic process.

[L10] What is antigen processing?

The production of antigenic peptides from larger macromolecules, usually proteins.

[L10] What is antigen presentation?

The binding of processed peptides to MHC molecules and display of peptide-MHC complexes on the cell surface for T-cell inspection.

[L10] What is the cytosolic antigen-presentation pathway?

Intracellular proteins are degraded into peptides, transported into the ER, loaded onto MHC class I, and displayed to CD8 T cells.

[L10] What is the endocytic antigen-presentation pathway?

Extracellular material is taken into vesicles, degraded, loaded onto MHC class II, and displayed to CD4 T cells.

[L10] What is cross-presentation?

A dendritic cell presents an exogenous antigen on MHC class I so it can activate a CD8 T-cell response.

[L10] What is autophagy's role in antigen presentation?

Autophagy delivers intracellular material to vesicles where it can be processed and presented, especially through MHC class II pathways.

[NK] What are NK cells?

Natural killer cells are innate lymphoid cells that recognize and eliminate stressed, virus-infected, or tumor cells.

[NK] Do NK cells have the diversified antigen receptors found on B and T cells?

No. NK cells use a balance of activating and inhibitory receptors rather than a rearranged BCR or TCR.

[NK] What is the main difference between NK cells and CTLs?

NK cells are innate and do not require recognition of a specific peptide-MHC complex by a rearranged TCR. CTLs are adaptive CD8 T cells that recognize specific peptide-MHC I complexes.

[L8-9 EXAM] On the germinal-center diagram, what does step 9 represent?

A selected B cell can reenter the dark zone for another round of somatic hypermutation and selection. This allows multiple rounds of affinity maturation and further refinement of antigen-binding specificity.

[L8-9 EXAM] What is the main germinal-center emphasis for the exam?

Focus especially on isotype switching and B-cell differentiation, followed by eventual exit from the germinal center. Step 9 is the repeat cycle, not the main emphasis.

[L8-9] What occurs during germinal-center step 6?

Isotype switching changes the antibody heavy-chain constant region, changing the antibody class and effector function without changing the antigen-binding specificity.

[L8-9] What occurs during germinal-center step 7?

B cells differentiate into specialized effector or memory fates, mainly long-lived plasma cells or memory B cells.

[L8-9] What occurs during germinal-center step 8?

The differentiated cells exit the germinal center as plasma cells or memory B cells and move to appropriate tissues.

[L8-9] What is the sequence of the germinal-center process shown in the diagram?

B-cell proliferation in the dark zone, somatic hypermutation, centrocyte formation, selection, repeated cycling or progression to isotype switching and differentiation, then exit from the germinal center.

[L8-9] What is the difference between affinity maturation and isotype switching?

Affinity maturation improves antigen binding through somatic hypermutation and selection. Isotype switching changes the antibody constant region and effector function while preserving antigen specificity.

[EXAM REVIEW] What is the format of Exam 2 according to the review slide?

There are 53 questions worth 200 total points, including 2 long-response questions, short-answer questions, multiple-choice questions, true/false questions, and matching. The tested material is Lectures 5-10, from innate immunity through MHC molecules and antigen processing/presentation.

[L5-6] What does TLR4 recognize?

TLR4 recognizes bacterial lipopolysaccharide, or LPS, a major Gram-negative bacterial PAMP.

[L5-6] What are NLRs and what can they detect?

NOD-like receptors are cytoplasmic pattern-recognition receptors. NOD1 and NOD2 detect bacterial peptidoglycan fragments, while other NLRs can respond to intracellular danger signals and help form inflammasomes.

[L5-6] What are RLRs and what do they detect?

Retinoic-acid-inducible gene-I-like receptors are cytoplasmic receptors that detect viral RNA outside membrane-bound compartments and activate antiviral signaling.

[L5-6] What are three examples of antimicrobial peptides or proteins?

Lysozyme, lactoferrin, and defensins are three examples. Other examples include cathelicidin LL-37 and surfactant proteins SP-A and SP-D.

[L5-6] What are three examples of DAMPs?

Examples include extracellular ATP, HMGB1, and uric-acid crystals. Other examples include mitochondrial DNA, extracellular DNA, heat-shock proteins, and S100 proteins.

[L7] What are the five major antibody isotypes?

IgM, IgD, IgG, IgA, and IgE.

[L7] What is the main role of IgM?

IgM is the first major antibody produced in a primary response. It is usually a pentamer, has high avidity, and is especially effective at activating classical complement.

[L7] What is the main role of IgD?

IgD is mainly a membrane-bound receptor on naive B cells. It is coexpressed with IgM and has the same antigen specificity as the IgM on that cell.

[L7] What are the main functions of IgG?

IgG is the major serum antibody. It supports neutralization, opsonization, complement activation, and ADCC, and most IgG subclasses can cross the placenta except IgG2.

[L7] What are the main functions of IgA?

IgA protects mucosal surfaces and is abundant in secretions such as saliva, tears, intestinal fluid, respiratory secretions, and breast milk. Secretory IgA is commonly a dimer joined by a J chain.

[L7] What are the main functions of IgE?

IgE helps defend against large parasites and contributes to allergic reactions. It binds strongly to Fc receptors on mast cells and basophils.

[L7] What is the difference between an antibody isotype and an immunoglobulin isoform?

An isotype is a class determined mainly by the heavy-chain constant region, such as IgM or IgG. An isoform is a structural form of immunoglobulin, such as membrane-bound, secreted, or secretory antibody.

[L7] What is V(D)J recombination?

V(D)J recombination rearranges variable, diversity, and joining gene segments to create unique BCR and TCR antigen-binding regions. B-cell heavy chains use V, D, and J segments; light chains use V and J segments.

[L7] What creates diversity during V(D)J recombination?

Diversity comes from combinatorial joining of gene segments, pairing of different heavy and light chains, junctional changes including P and N nucleotide addition, and nucleotide deletion.

[L7] What happens if RAG1 or RAG2 is missing?

V(D)J recombination cannot occur, so developing B and T cells cannot make functional antigen receptors. This causes a severe lymphocyte-development defect.

[L8-9] What is BAFF?

BAFF, or B-cell activating factor, is a TNF-family cytokine required for the transition and survival of transitional B cells, especially the T1-to-T2 transition.

[L8-9] What happens if BAFF is absent?

T1 B cells have difficulty becoming T2 B cells, and fewer mature peripheral B cells survive, causing impaired humoral immunity.

[L8-9 WORKSHEET 1] What are the two distinct phases of B-cell development?

The two phases are the maturation phase and the differentiation phase. Maturation produces mature naive B cells; differentiation begins after a mature B cell encounters its specific antigen.

[L8-9 WORKSHEET 2] What does naive mean for a B cell?

A naive B cell has matured and has a functional BCR but has not yet encountered the specific antigen recognized by that BCR.

[L8-9 WORKSHEET 3] Is B-cell development in the maturation phase highly dependent on foreign antigen?

False. During the maturation phase, immature B cells are developing in the bone marrow and are screened for self-reactivity; the antigen-dependent differentiation phase begins after a mature naive B cell encounters foreign antigen.

[L8-9 WORKSHEET 4] Where does B-cell development begin, and where does maturation end?

B-cell development begins in the bone marrow. After central tolerance, immature B cells leave the marrow, pass through transitional stages mainly in the spleen, and mature into peripheral follicular or marginal-zone B cells.

[L8-9 WORKSHEET 5] Where does central tolerance occur for immature B cells, and how could a bone-marrow transplant affect it?

Central tolerance occurs in the bone marrow. A transplant changes the source of developing hematopoietic cells, so the developing B cells must be exposed to the relevant self-antigens and stromal environment to establish appropriate tolerance.

[L8-9 WORKSHEET 6] Which mechanism gives an autoreactive immature B cell a second chance?

Receptor editing, in which the immature B cell rearranges immunoglobulin genes, especially the light-chain locus, to create a new BCR specificity.

[L8-9 WORKSHEET 7] What happens if an immature B cell is negatively selected, and why is central tolerance important?

The cell is eliminated by apoptosis if receptor editing does not correct its self-reactivity. Central tolerance prevents self-reactive B cells from entering the periphery and causing autoimmune disease.

[L8-9 WORKSHEET 8] How long do immature B cells remain in the bone marrow after central tolerance?

They remain for about 1-3 days before expressing adhesion molecules and homing receptors that allow them to leave the bone marrow.

[L8-9 WORKSHEET 9] What happens if immature B cells cannot express the proper homing receptors?

They may fail to leave the bone marrow or fail to reach the spleen and other peripheral lymphoid tissues. This could reduce the mature B-cell population and weaken antibody-mediated immunity.

[L8-9 WORKSHEET 10] How could developing B-cell stages be distinguished in the laboratory?

Use flow cytometry with antibodies against developmental markers such as IgM, IgD, CD19, and other B-cell markers, then compare marker expression between stages. BCR gene-rearrangement analysis or single-cell sequencing could provide additional confirmation.

[L8-9 WORKSHEET 11] After leaving the bone marrow, which organ do transitional T1 B cells typically enter, and what happens if it is removed?

They typically enter the spleen and progress through transitional stages there. If the spleen is removed, B-cell development may continue in lymph nodes, GALT, or other sites, but maturation is less efficient and responses to blood-borne antigens, especially marginal-zone responses, are impaired.

[L8-9 WORKSHEET 12] Which cytokine is essential for transition from T1 to T2 B cells?

BAFF is essential. Without BAFF, transitional B-cell survival and maturation are impaired, leading to fewer mature B cells and weaker antibody responses.

[L8-9 WORKSHEET 13] What can T2 B cells become, and where do those cells reside?

T2 B cells can become follicular B cells, which reside in lymphoid follicles, or marginal-zone B cells, which reside mainly in the splenic marginal zone.

[L8-9 WORKSHEET 14] What does the second developmental phase depend on, and what happens when BCR binds antigen?

The second phase depends on antigen. BCR binding initiates B-cell activation, followed by clonal expansion and differentiation into plasma cells and memory B cells; with T-cell help, the response can include isotype switching and somatic hypermutation.

[L8-9 WORKSHEET 15] What is the impact of losing RAG1 and RAG2 expression in a B cell?

The B cell cannot perform additional V(D)J recombination. If loss occurs during development, it prevents formation of a functional BCR; if it occurs after a mature B cell has a functional BCR, the existing specificity is retained but new receptor rearrangement stops.

[L8-9 WORKSHEET 16] What could happen if negative selection were disrupted, and how might it be treated?

Many autoreactive B cells could escape central tolerance and cause autoimmune disease. The worksheet's proposed treatment is irradiation of the recipient bone marrow followed by a bone-marrow transplant from a donor; B-cell depletion with Rituxan is another possible therapeutic strategy.

[L10 LONG ANSWER] Explain the MHC-related odor-preference study and its main result.

Wedekind et al. studied 110 women, ages 18-35, from Newcastle University in the UK; some were taking the birth-control pill and some were not. The women and men were genotyped at HLA-A, HLA-B, and DRB1. Men wore special T-shirts for two nights, and the women smelled and rated the shirts for pleasantness, intensity, and desirability. The study describes MHC-related odor preference as a possible evolutionary mechanism that may discourage mating between relatives. A major result was that women taking the pill were more likely to find men with similar MHC loci attractive, which may discourage the usual disassortative preference for MHC-dissimilar partners.

[L8-9 LONG ANSWER] What is Rituxan, and how does it work?

Rituxan, or rituximab, is a monoclonal antibody that binds a surface protein on mature B cells and promotes B-cell depletion through complement activation, antibody-dependent cellular cytotoxicity, and other killing mechanisms. It can reduce pathogenic B-cell or autoantibody responses in B-cell malignancies and autoimmune disease. Plasma cells and hematopoietic stem cells generally do not carry this target, so they are not all eliminated and B cells can eventually repopulate.

[L5-6 LONG ANSWER] Describe FMT and explain why it can be the most effective treatment for recurrent C. difficile infection.

FMT, or fecal microbiota transplantation, transfers screened stool microbiota from a healthy donor to a recipient. It can be especially effective for recurrent C. difficile because it restores a diverse, healthy microbial community rather than only killing bacteria with another antibiotic. The restored commensals compete with C. difficile for space and nutrients, produce inhibitory metabolites, support the epithelial barrier and immune regulation, and re-establish colonization resistance. Antibiotics can control C. difficile but may also keep disrupting the normal microbiota, allowing recurrence.

[L7-8] What are the four major antibody effector functions?

Neutralization blocks pathogen attachment or toxin activity; opsonization coats targets for phagocytosis; classical complement activation promotes inflammation, opsonization, and MAC-mediated lysis; and ADCC allows Fc-receptor-bearing cells such as NK cells to kill antibody-coated targets.

[L5-6] What is the difference between non-inducible and inducible innate immunity?

Non-inducible mechanisms are pre-existing anatomical and physiological barriers. Inducible innate immunity begins after a recognition event involving PAMPs or DAMPs and PRMs, leading to complement activation, inflammation, phagocytosis, cytokine secretion, or cytolysis.

[L5-6] What are examples of anatomical barriers?

Skin, mucosal epithelium, and the epithelial surfaces of the gastrointestinal, respiratory, and urogenital tracts physically limit pathogen access.

[L5-6] What are examples of physiological barriers?

Sneezing, mucus, saliva, tears, stomach acidity, body temperature, antimicrobial proteins, and the flushing action of secretions reinforce anatomical barriers.

[L5-6] What are the three layers of skin named in the lecture?

The epidermis, dermis, and hypodermis.

[L5-6] How does keratin help the skin barrier?

Dead epidermal cells are filled with keratin, which creates a tough, water-repelling surface that is difficult for microbes to penetrate.

[L5-6] How do sebaceous glands protect the skin?

Sebaceous glands produce sebum, an oily secretion with an acidic pH of about 3-5 that inhibits microbial replication.

[L5-6] Why does rapid epidermal turnover help prevent infection?

Shedding and replacement of epidermal cells can remove microbes attached to the skin surface.

[L5-6] How does the hypodermis contribute to defense?

The fatty hypodermis provides a physical barrier that makes it more difficult for pathogens to penetrate.

[L5-6] What happens when the skin barrier is breached?

Wounds or insect bites can allow pathogens to pass through the skin and trigger inducible innate responses.