Antigen-receptors, MHC and antigen-presentation

Question 1

Features that discriminate between the PRRs of the innate immune response and the antigen receptors of the adaptive response.
1. Diversity

Answer 1

There are potentially billions of T-and B-cell receptors, whereas even adding up all of the receptors in all the innate immune receptor types, we still only have about 100 or so innate immune receptors.

Question 2

Features that discriminate between the PRRs of the innate immune response and the antigen receptors of the adaptive response.
2. Location

Answer 2

All T- and B-cell receptors are at the cell plasma membrane, whereas innate receptors can also be found in the cytosol and on the endosomal membrane.

Question 3

Features that discriminate between the PRRs of the innate immune response and the antigen receptors of the adaptive response.
3. Germline DNA

Answer 3

All innate immune receptors are encoded in the germline DNA, whereas B- and T-cell receptors are the products of somatic cell gene rearrangements.

Question 4

Features that discriminate between the PRRs of the innate immune response and the antigen receptors of the adaptive response.
4. Evolution

Answer 4

Innate immune receptors have been selected over evolutionary time, while B-cell receptors in fact undergo mutation and selection during the elapsed time of an immune response.

Question 5

Give three examples of receptors that induce phagocytosis of bacteria and indicate whether they induce phagocytosis by binding directly to bacteria or require an additional soluble component.

Answer 5

CLRs (such as mannose receptor, dectin-1, and DC-SIGN) directly activate signaling pathways that induce phagocytosis. Opsonin receptors bind opsonins that have bound to the bacteria. Examples are CD91/calreticulin that binds collectins, MBL, and so on; complement receptors that bind complement components attached to antigens; and Fc receptors that bind immunoglobulins that have bound their cognate antigens.

Question 6

What experimental observations first linked TLRs to innate immunity in vertebrates?

Answer 6

Hoffman and Lemaitre showed that mutations in toll made flies highly susceptible to lethal infection with the fungus Aspergillus fumigatus. B. Beutler showed that lps mice were resistant to endotoxin (LPS) and that the genetic difference in these mice was lack of a functional TLR4 because of a single mutation in the TLR4 gene. R. Medzhitov and C. Janeway demonstrated that a protein with homology to Drosophila Toll (which turned out to be TLR4) activated the expression of innate immunity genes when expressed in a human cell line.

Question 7

What are the five hallmark characteristics of a localized inflammatory response?

Answer 7

Inflammation is characterized by redness, heat, swelling, pain, and sometimes loss of local function.

Question 8

Describe how the process of extravasation and the induction of vascular permeability contribute to inflammatory characteristics.

Answer 8

Cytokines made by PRR-activated resident innate cells act on the vascular endothelium, causing localized dilation of blood vessels (producing redness and heat) and increasing permeability, resulting in the influx of fluid and swelling (producing edema). Prostaglandins generated following the induced expression of COX2, together with mediators such as histamine, lead to the activation of local pain receptors. The swelling and local tissue damage can result in loss of function. The increased vascular permeability allows an influx of fluid containing protective substances, including opsonins and complement (as well as antibodies, if present). Local production of chemokines, together with induced expression of adhesion molecules on vascular endothelial cells, recruits to the site additional innate cells, such as neutrophils and macrophages, which contribute further to innate responses and pathogen clearance through phagocytosis and release of antimicrobial mediators. Proinflammatory cytokines made during this innate response may also act systemically, triggering the acute phase response

Question 9

NETosis

Answer 9

is an inflammatory process that occurs in neutrophils. Granules are translocated from the cytoplasm to the nucleus, where the chromatin rapidly swells, then is vigorously expelled from the cell. These NETs trap bacterial, fungal, and parasite cells, preventing their spread.

Question 10

Fas-mediated apoptosis

Answer 10

is a form of regulated cell death in which the contents of the dying cell are neatly wrapped up in membrane packages and labeled with cell membrane proteins or lipids such as phosphatidyl serine, for efficient recognition by macrophage receptors and subsequent phagocytosis. Apoptosis therefore does not result in inflammation. Any cell expressing Fas can be induced to die by binding of FasL.

Question 11

Immune response type 1

Answer 11

Type 1 cells include ILC1 and NK cells of the innate immune system and TH1 cells of the adaptive immune system. The transcription factor T-Bet must be expressed in Type 1 cells, which secrete TNF-α and IFN-γ.

Question 12

Immune response type 2

Answer 12

Type 2 cells include ILC2 cells and TH2 cells. They express the transcription factor GATA3 and secrete IL-4, IL-5, IL-9, IL-13, and amphiregulin.

Question 13

Immune response type 3

Answer 13

Type 3 cells include ILC3 cells and TH7 cells; they express the transcription factor RORγt. Different subpopulations of ILC3 cells express IL-17 or IL-22 and TH17 cells typically express IL-17.

Question 14

How does the innate immune response prime the adaptive response so that the correct type of adaptive immunity (antibody production, cell-mediated immunity) follows?

Answer 14

after activation /maturation induced by PRR signaling, dendritic cells present peptides from processed antigen to activate naïve CD4+ and CD8+ T cells. Depending on the pathogen and the PRRs to which it binds, dendritic cells are activated to produce certain cytokines that differentially induce naïve CD4+ cells to differentiate into TH subsets with different functions, usually appropriate for the particular pathogen.

Question 15

Describe at least one example in which the adaptive immune response contributes to enhanced innate immunity.

Answer 15

antibodies secreted by B cells can opsonize pathogens that are then recognized by Fc receptors on macrophages, which engulf them and destroy them. Second, cytokines secreted by TH cells can further activate innate immune cells. For instance, the cytokine IFN-γ, produced by activated TH1 cells, is a potent macrophage activator, including activating them to kill intracellular bacteria such as Mycobacterium tuberculosi

Question 16

A single molecule of bound IgM can activate the C1q component of the classical complement pathway

Answer 16

TRUE

Question 17

The enzymes that cleave C3 and C4 are referred to as convertases

Answer 17

TRUE

Question 18

C3a and C3b are fragments of C3 that are generated by proteolytic cleavage mediated by two different enzyme complexes.

Answer 18

TRUE

Question 19

Nucleated cells tend to be more resistant to complement-mediated lysis than red blood cells.

Answer 19

TRUE

Question 20

Enveloped viruses cannot be lysed by complement because their outer envelopes are resistant to pore formation by the membrane attack complex (MAC).

Answer 20

FALSE

Question 21

MBL has a function in the lectin pathway analogous to that of IgM in the classical pathway, and MA´´´SP-1 and MASP-2 take on functions analogous to C1 components.

Answer 21

TRUE

Question 22

Explain why serum IgM cannot activate complement prior to antigen binding.

Answer 22

IgM undergoes a conformational change on binding to antigen, which enables it to be bound by the first component of complement C1q. In the absence of antigen binding, the C1q-binding site in the Fc region of IgM is inaccessible.

Question 23

An absence of C3 in initiation of classical pathways

Answer 23

The initiation of the classical pathway is mediated by the first component of complement, and C3 does not participate until after the formation of the active C3 convertase C4aC2b

Question 24

An absence of C3 in initiation of alternative pathway

Answer 24

The initiation of the alternate pathway begins with spontaneous cleavage of the C3 component, and therefore no part of the alternate pathway can operate in the absence of C3.

Question 25

An absence of C3 in clearance of immune complexes

Answer 25

Clearance of immune complexes occurs only following opsonization of complexes by C3b binding, followed by phagocytosis or binding to the surface of erythrocytes via CR1 binding. Therefore, immune complex clearance is inhibited in the absence of C3.

Question 26

An absence of C3 in phagocytosis of infectious bacteria

Answer 26

Phagocytosis would be diminished in the absence of C3b-mediated opsonization. However, if antibodies specific for the bacteria are present, some phagocytosis would still occur

Question 27

Complement activation can occur via the classical, alternative, or lectin pathway.
a) How do the three pathways differ in the substances that can initiate activation?

Answer 27

The classical pathway is initiated by immune complexes involving IgM or IgG; the alternate pathway is generally initiated by binding of C3b to bacterial cell wall components, and the lectin pathway is initiated by binding of lectins (e.g., MBL to microbial cell wall carbohydrates).

Question 28

Complement activation can occur via the classical, alternative, or lectin pathway.
b) Which parts of the overall activation sequence differ among the three pathways, and which parts are similar?

Answer 28

The terminal reaction sequence after C5 convertase generation is the same for all three pathways. For the classical and lectin pathways, the second step involves binding of the serine protease complexes C4b2a (classical) and MASP-1, MASP-2 (lectin). These each act as a C3 convertase in each respective pathway, and the two pathways are identical from that point on. The alternative pathway uses a different C3 convertase, C3bBb. The formation of Bb requires factor D, and the C3 convertase is stabilized on the cell surface by properdin. The alternative pathway C5 convertase is C3bBbC3b.

Question 29

Complement activation can occur via the classical, alternative, or lectin pathway.
c) How does the host ensure that inadvertent activation of the alternative pathway on its own healthy cells does not lead to autoimmune destruction?

Answer 29

Healthy cells contain a variety of complement inhibitor proteins that prevent inadvertent activation of the alternative pathway. Some of these proteins are expressed only on the surface of host (not on microbial) cells; others are in solution but are specifically bound by receptors on host cells.

Question 30

C1 inhibitor (C1INH):

Answer 30

Induces dissociation and inhibition of the C1 proteases C1r and C1s from C1q. Serine protease inhibitor.

Question 31

C4b-binding protein (C4bBP):

Answer 31

Accelerates dissociation of the C4b2aC3, C3 convertase. Acts as a cofactor for factor I in C4b degradation

Question 32

Decay-accelerating factor (DAF):

Answer 32

Accelerates dissociation of C4b2a and C3bBb C3 convertases.

Question 33

Membrane cofactor of proteolysis (MCP; CD46):

Answer 33

Acts as cofactor for factor I in degradation of C3b and C4b.

Question 34

CD59 (protectin):

Answer 34

Binds C5b678 on host cells, blocking binding of C9 and formation of the MAC

Question 35

Carboxypeptidase N:

Answer 35

Cleaves and inactivates anaphylatoxins.

Question 36

Please describe three mechanisms used by microbes to evade complement actions, giving examples of bacterial, viral, or fungal species that use that mechanism.

Answer 36

The bacterium Staphylococcus aureus has evolved many ways to evade complement action. A small protein called Staphylococcus complement inhibitor (SCIN) binds and blocks the activity of the two C3 convertases, C4b2a and C3bBb. Variola and Vaccinia viruses express complement-inhibitory proteins that bind C3b and C4b and act as cofactors for factor I, thus preventing complement activation. Fungi have evolved mechanisms to destroy complement proteins. The opportunistic human pathogen Aspergillus fumigatus, a fungus that tends to attack patients who are already immunocompromised, secretes an alkaline protease, Alp1, that is capable of cleaving C3, C4, C5, C1q, and IgG.

Question 37

Explain why complement deficiencies in the early components of complement give rise to immune complex–mediated disorders such as systemic lupus erythematosus

Answer 37

Immune complexes are cleared from the body following opsonization by C3b. In the absence of the early components of complement, C3b convertases are not formed, and hence no C3b will be available.

Question 38

Vκ gene segments and Cλ are located

Answer 38

on separate chromosomes and cannot be brought together during gene rearrangement.

Question 39

In generating a T-cell receptor gene, Vα segments

Answer 39

sometimes join to Cδ.

Question 40

Although each B cell carries two alleles encoding the immunoglobulin

Answer 40

heavy and light chains, only one allele is expressed.

Question 41

The variable regions of the β and δ TCR genes are encoded in

Answer 41

three segments, analogous to the V, D, and J segments of the Ig heavy-chain variable region. The Vα and Vγ regions are each encoded in two segments.

Question 42

Recombination of Ig gene segments serves to:

Answer 42

1. Promote Ig diversification.
2. Assemble a complete Ig coding sequence.
3. Allow changes in coding information during B-cell maturation

Question 43

Generation of combinatorial diversity within the variable regions of Ig involves:

Answer 43

2. DNA rearrangement
3. Recombination signal sequences
4. 12/23 joining rule.

Question 44

The mechanism that permits Ig to be synthesized in either a membrane-bound or secreted form is:

Answer 44

Differential RNA processing

Question 45

During Ig VH recombination, the processes that contribute to additional diversity at the third complementarity-determining region of Ig variable regions include:

Answer 45

Introduction of the D gene segments into the heavy-chain V gene.
Exonuclease cleavage of the ends of the gene segments
P-nucleotide addition
N-nucleotide addition

Question 46

RAG1/2 in V(D)J recombination:

Answer 46

Responsible for breaking the DNA at the junction of the V, D, or J region sequences and the relevant recombination signal sequences. It also expresses some endonuclease activity.

Question 47

Tdt (terminal deoxyribonucleotidyltransferase) in V(D)J recombination:

Answer 47

Randomly adds nontemplated nucleotides (N nucleotides) at V(D)J junctions in the heavy chain of Ig genes and TCR genes. Note that TdT activity is low during Ig light-chain rearrangement and absent in the fetal thymus, when waves of γδ T cells leave the thymus for the periphery. However, γδ T cells generated in the adult thymus do display pronounced N-region diversity.

Question 48

Artemis in V(D)J recombination:

Answer 48

Cleaves the hairpin loop formed when a single-strand DNA break generated by RAG1/2 is converted into a double-strand break with subsequent generation of a hairpin loop between the top and bottom DNA

Question 49

DNA PKcs in V(D)J recombination

Answer 49

Forms a complex with Ku70/80. This protein kinase phosphorylates and actives Artemis. It recruits the ligation machinery.

Question 50

DNA ligase IV

Answer 50

Catalyzes the formation of phosphodiester bonds between the recombined V(D)J gene segments of BCRs and TCRs.

Question 51

You have identified a B-cell lymphoma that has made non-productive rearrangements for both heavy-chain alleles. What is the arrangement of its light-chain DNA? Why?

Answer 51

The κ-chain DNA must have the germ-line configuration because a productive heavy-chain rearrangement must occur before the light-chain (κ) DNA can begin to rearrange.

Question 52

Are there any differences in the genetic strategies used to generate complete V genes in TCRs compared with BCRs? If so, what are they?

Answer 52

Whereas N-region addition occurs at the joints of Ig heavy- but not light-chain variable regions, all TCR variable region joints may include N-region nucleotides. Somatic mutation adds diversity to the BCR, following antigen stimulation, but does not contribute to TCR diversity.