Midterm I material Flashcards
1
Q
What are the most fundamental barriers to infection?
A
Physical and chemical barriers, such as scales, skin, and mucosal layers
2
Q
Where can we find epithelial linings? And what is the similarity between all these locations?
A
digestive, respiratory, urinary, and reproductive tracts. All have openings to the environment which makes these areas vulnerable to pathogens.
3
Q
How do epithelial linings protect against pathogens?
A
Provide a physical barrier and make secretions (mucus, enzymes, and stomach acid) which often ensnare, destroy or wash away pathogenic material.
4
Q
Name and describe eight physical barriers of infection.
A
- epidermis
- provides a physical barrier
- periodic shedding removes microbes - mucous membranes and mucous
- traps microbes and foreign particles - hair
- within the nose -> filters air - cilia
- lines the upper respiratory tract
- traps and propels inhaled deposits - lacrimal apparatus
- produces tears that cleanse the eye - saliva
- dilutes the number of microbes
- washes the teeth and mouth - urine
- flush microbes out of the urethra - defecation and vomiting
- expel microbes
5
Q
What are AMPs and what kind of barrier of infection do they provide?
A
Anti-microbial peptides which provide a chemical barrier to infection
6
Q
How do AMPs create an immune response (2)?
A
- direct killing
- immune modulation by acting as markers of infection that recruits and activates immune cells
7
Q
How does the different composition of animal cell membranes vs bacteria membranes affect AMP binding?
A
AMPs are highly charged; whereas animal membranes are not, and they also contain cholesterol which creates gaps, which doesn’t allow for stable binding of AMPs; ultimately preventing auto destruction.
Bacteria membranes are charged and do not contain cholesterol which allows the alpha-helices of the AMP to effectively bind the membrane
8
Q
What are the three ways that AMPs disrupt bacterial membranes?
A
- barrel staves that create pores
- torodial (reshape the membrane)
- carpet (encapsulate membrane)
9
Q
What is the general purpose of primary lymphoid organs?
A
Sites where immune cells are made and matured
10
Q
What are the two primary lymphoid organs and what process occur in each?
A
- bone marrow - hematopoiesis
- thymus - lymphopoiesis
11
Q
Describe hematopoiesis
A
blood cell development that occurs in the bone marrow where hematopoietic stem cells (HSC) goes through asymmetric cell division, where one daughter cell remains as an HSC and the other becomes a progenitor cell
12
Q
What are the two types of progenitor cells that arise from hematopoises and what does each type arise into?
A
- common myeloid progenitor (CMP) -> innate
- common lymphoid progenitor (CLP) -> adaptive
13
Q
Describe lymphopoiesis
A
T-cell maturation that occurs in the thymus (of all vertebrates) to give rise to a T-cell progenitor
14
Q
What is the role of the secondary lymphoid organs?
A
adaptive immune responses occur predominately in the secondary lymphoid organs
15
Q
Name four secondary lymphoid organs
A
- spleen
- intestine
- lymph nodes
- tonsils
16
Q
Name and describe the main four tissues/organs that make up the secondary lymphoid system
A
- mucosa associated lymphoid tissues (MALT -> tonsils + Peyer’s patch)
- deal with pathogens entering the mucosa - bronchus associated lymphoid tissues (BALT)
- deals with pathogens that are inhaled - lymphatics and lymph nodes
- deal with any pathogen that has succeeded in entering tissue - spleen
- filters blood
- deals with pathogens that have entered the blood vasculature (i.e systemic infections)
17
Q
What secondary lymphoid tissue are M-cells apart of and what is their role?
A
Part of GALT and they internalize intestinal microflora and transport them to Peyer patches in the lamina propria
18
Q
Where are B and T cells found?
A
Primarily: aggregate into secondary lymphoid organs
Secondarily: blood stream, but they have a shorter life due to no survival signals
19
Q
What are the three main compartments in the spleen?
A
- primary follicles
- marginal zone B cells (MZ B cells)
- periarteriolar lymphoid sheath (PALS)
20
Q
What is the purpose of the primary follicles in the spleen, and what are the main constituents?
A
Purpose: essential for Ab optimization in adaptive immune responses
Constituents: naive B cells and follicular DCs (FDCs; good APCs)
21
Q
What is the purpose of the marginal zone B cells (MZ B cells) in the spleen?
A
Purpose: non-circulating mature B cells (also found in follicles)
22
Q
What is the purpose of the PALS in the spleen, and what are the main constituents?
A
T cell compartment directly surrounding the so-called central arterioles and they are present with blood borne Ags via myeloid DCs
23
Q
What enters the lymph node through the affect lymphatics, and what exists via the efferent lymphatics?
A
Enter: Ag.s, and APCs
Exit: lymphocytes, APCs
24
Q
Which cells are found in the follicle of a lymph node and which cells are found in the paracortex
A
follicle: B cells
paracortex: T cells
25
What does a humoral response broadly refer to\?
not directly associated with cellular acitivites
26
What are the differences between innate and adaptive immune responses?
Innate:
-limited/fixed specificity
- immediate response
- no lag time from exposure
- no immunological memory
- short-term defense
Adaptive:
- diverse specificity
- delayed response (on purpose - adaptive immune system is adaptive)
- lag time from exposure
- immunological memory
- long term defense
27
What makes up an innate cellular response?
1. granulocytes
2. monocytes
3. macrophages
4. NK cells
28
What makes up an innate humoral response?
1. complement
2. AMPs
3. enzymes
4. cytokines
5. mucus
29
What makes up an adaptive cellular response?
1. T cells
2. B cells
30
What makes up an adaptive humoral response?
1. Ab.s
2. cytokines
31
What are the best phagocytosing cells?
1. macrophages
2. neutrophils
32
What are the steps of phagocytosis?
1. pathogen binds to receptor
2. structural changes occur
3. pathogen is brought in as a phagosome
4. phagosome fuses with a lysosome to create a phagolysosome
5. the pathogen is destroyed
6. the pathogen debris is either presented on an MHC II complex or exocytosed which can signal to other cells
33
Which cells perform degranulation?
Granulocytes (mast, basophil and eosinophil) and NK cells
34
What are the steps of degranulation?
1. antigen binds to membrane-bound IgE -> activation
2. preformed vesicles (granules) which are already present in the absence of activation are exocytosed from the cell (degranulation)
35
What are three general triggers of degranulation?
1. receptor-binding agonists
2. physical activators
3. cell-cell contact
36
What are three main constituents that granules release?
1. preformed molecules
2. T and B cell ligands
3. newly synthesized mediators
37
What are the four main functions that innate immune cells can demonstrate (note: not all innate immune cells preform all of them)
1. phagocytosis
2. degranulation
3. ROS production
4. NET release
38
What are the functions of a macrophage and where are they localized?
Function: phagocytosis foreign pathogens and cancer cells; stimulates response of other immune cells
Localization: migrates from blood vessels into tissues
39
What are the functions and localization of DCs?
Functions: professional APC, triggers adaptive immunity, phagocytosis
Localization: present in epithelial tissues (skin, lung, and digestive tract), migrates to lymph nodes upon activation
40
What are the functions of neutrophils and where are they localized?
Function: first responders at the site of infection or trauma, releases toxins that kill or inhibit bacteria and fungi (degranulates), recruits other immune cells to the site of infection
Localization: migrates from blood vessels into tissues
41
How do T cells function in cell-mediated immunity?
1. lysis infected cells
2. activates macrophages which leads to microbial killing
42
How do B cells function in cell-mediated immune responses?
internalize Ab-coated pathogens -> facilitates their maturation into plasma B cells
43
What is the range of AMPs?
broad spectrum -> highly specific
all together, they can kill all types of pathogens
44
Name broad activity AMPS
1. defensins (alpha and beta)
2. dermcidin
45
Name specific activity AMPs
1. cathelicidin (LL-37)
2. histatins
46
What is the role of chemokines?
- facilitate the recruitment and migration of immune cells to sites of infection
- act as beacons for circulating immune cells and change adhesion properties around sites of infections
47
Which cells produce Ab.s?
B cells
48
Why are Ab.s considered to be specific?
They are made against very small portions of a pathogen
49
What are the three important experimental tools that help us identify cell types?
1. hybridoma technology and monoclonal Ab.s (MAbs)
2. fluorescence activated cell sorting (FACS)
3. CD Ag.s (cluster of differentiation or determinants)
50
How are mAbs made?
Ag with multiple epitopes is injected into a mouse -> spleen cells are isolated -> plasma cells are fused to immortal cancer cells to make immortal hybridoma -> cells are selected in media which only hybrids survive -> hybrids clones are sorted and isolated -> monoclonal Abs
51
How can cells be identified (what properties of cells can differentiate them from others) and which detector in FAC determines the differnces?
- shape and size of the cell (scatter)
- absence or presence of specific surface markers (red PMT)
- differences in their internal complexities
52
Is CRISPR adaptive or innate immunity
adaptive
53
What processes require cytokines for proper regulation?
1. release of tissue mediators
2. inflammatory cell recruitment
3. killing of microbes
4. vascular response
5. DC maturation
6. T cell priming in lymph nodes
54
What is a cytokine signal?
any event that instructs a cell to change its metabolism. function, or proliferative state
55
How do cytokines change a cell's state?
cytokine signalling causes change in the transcriptional program of the target cell which changes the gene regulation and influences the protein production
56
What macromolecule are cytokines?
proteins
57
How can cytokines act in the body?
1. endocrine
2. paracrine
3. autocrine
58
How do cytokines demonstrate pleiotropy?
1. one cytokine can elicit different outcomes on different cells
2. different outcomes on the same cell - depends on the signal intensity
59
How can different cytokines interact with the cell and affect the outcome? Give an example for each interaction type
1. redundant: several different one -> same outcome (e.g. IL2, IL4, IL5 -> B cell proliferation)
2. synergistic: different cytokines cooperate to create a response (e.g. IL-4 + IL-5 -> B cell class switch to IgE)
3. antagonistic: different cytokines can block each others actions (e.g. IFNgamma + IL-4 -> block class switch to IgE by IL4)
60
how can cytokines be amplified?
1. enhance the production of the original cytokine
2. produce other cytokines
61
What are some examples of local effects produced by cytokines?
1. vascular endothelial
- increase adhesion molecule
- increase permeability
- decrease flow rate
- increase chemokine expression
2. parenchymal
- increase chemokine expression
- increase cytokine synthesis
3. tissue leukocytes (MCs and DCs)
- increase activation
- increase degranulation
62
What are some examples of systemic effects of cytokines?
1. liver
- increase acute phase proteins
2. hypothalamus
- increase fever
3. bone marrow
- increase neutrophil mobilization
63
What are the six cytokine families?
1. interleukin-1 family
2. class 1 cytokine family
3. class 2 (interferon) cytokine family
4. tumor necrosis factor family
5. interleuckin-17 family
6. chemokines
64
What are some characteristics of the IL-1 family of cytokines?
- promote inflammation
- stimulated by viral, parasitic or bacterial Ags
- secreted very early in the immune repsonse by macrophages and DCs
- act locally on capillary permeability to pull leukocytes to infected tissues
- act systemically on the liver -> production of acute phase proteins
- can help activate adaptive immune responses (e.g. regulates types of immune cell to be differentiated into)
- Pro-IL-1 is cleaved to its active form IL-1
65
What is the receptor family of IL-1 family of cytokines and name a ligand?
receptor: immunoglobulin superfamily receptors
ligands: IL-1B
66
What are some characterisitcs of the hematopoietic class 1 cytokines?
- promote cellular differentiation
- lineage-restricted cytokines play an essential and specific role in hematopoietic differentiation
67
What is the receptor family of hematopoietic class 1 cytokines and name a few ligands?
receptor: class 1 cytokine receptor (hematopoietin)
ligands: IL-4 and IL-6
68
What are the two types of interferon cytokines in the class II (IFN) family, and what are characteristics of each?
1. type I IFN
- IFNa and IFNb are small dimers with antiviral effects
- secreted by activated macrophages and DCs
- induce synthesis of ribonucleases and inhibit protein synthesis
2. type III IFN family (IFNgamma)
- secreted by specialized DCs
- upregulate genes controlling viral replication and HC proliferation
- both pro- and anti-inflammatory effects
69
What is the receptor family of class II (IFN) cytokine family and what are some ligands?
receptor: class II cytokine R (IFN)
ligands: IFNalpha -> gamma, IL-10
70
What are some characteristics of TNF cytokine family?
- regulates: development, effector function and homeostasis of skeletal, neuronal and immune cells
- are soluble or membrane bound
- short intracytoplasmic N-term regions -> used for signalling
- longer extracellular C-term region
- generally type 2 transmembrane proteins form as trimers when binding to TNFR-1
71
What is the receptor for TNF cytokines and what is a ligand for this receptor?
receptor: TNFR
lignads: TNFa
72
What is a major source of IL-17 cytokines?
gammadeltaT cells
note: TH17 cells intial function was characterized on their production of IL17
73
What is the function of IL-17 cytokines?
Promote neutrophil accumulation and activation, proinflammatory
74
What are some characteristics of chemokines?
- promote chemotaxis, cell adhesion, and mediator release
- subdivided into 4 classes based on their structural characteristics
- alter the environment such that immune cells can arrive to the site of infection
75
What is the receptor family of chemokines?
receptor: GPCRs
76
Describe the steps of how chemokines recruit immune cells to the site of infection
1. damage to tissues/cells within a region relaease inflammatory molecules (cytokine/chemokine)
2. chemokines act as beacons for regions where damage has occured
3. immune cells circulating within the blood recognize the presence of chemokines and follow a gradient to site of infection
4. chemokines alter the expression of adhesion proteins near the site of an infection (epithelial cells affected)
5. immune cells transfer from the blood into infected and/or damaged tissue whereby they become activated to cytokines
6. activated immune cells destroy pathogens
77
Name some proinflammatory cytokines and describe their role?
cytokines: TNF, IL-1, IL-6, chemokines
role: induce inflammatory activities of immune cells
78
Name some antiinflammatory cytokines and describe their role?
cytokines: IL-10, IL-1ra, TGFbeta
role: help in resolution of inflammation
79
Name cytokines that inhibit viral replication, and describe their role
cytokines: IFNalpha, IFNbeta
role: viral infection protection
80
Name some macrophage-activating cytokines and describe their role
cytokines: IFN-gamma
role: activate innate immune responses
81
Name some B cell activating cytokines and describe their role
cytokines: IL-4 -> 6, IL-21
role: help in activation and generation of plasma and memory B cells
82
Name some T cell activating cytokines and describe their role
cytokines: IL-2, IL-4, IL-12, IFN-gamma
role: help in producing adaptive immunological responses
83
Name some eosinophil and/or mast cell activating cytokines and their role
cytokines: IL-3 -> 5, IL-13
role: help induce parasitic immunological responses
84
Describe three properties of receptors?
- can be transmembrane proteins
- can be peripheral proteins (need other proteins to create a signal)
- have extracellular binding domains and intracellular signalling domains
85
Describe the general steps of receptor activation
1. upon binding to ligands, receptors become activated
2. signal transduction signaling - recruitment and activation of additional proteins
3. activation of cellular responses
86
How can molecular changes occur in a receptor upon ligand-receptor binding?
- conformational
- dimerization/clustering
- location in the membrane
87
How do receptor alterations lead to a cascade of intracellular events?
- activation of enzymes
- changes in intracellular locations of molecules
88
Give examples of conformational changes that can happen to a receptor upon activation
1. binding of ligand -> transmembrane of receptor change shape -> opens a channel from the outside to the inside of the cell
2. binding of ligand -> changes the organization of the receptor's cytoplasmic tail -> intracellular signalling
- tail goes from disorganized, which blocks proteins from interacting with them -> locked, which allows proteins to interact with them
89
How can dimerization alter ligand specificity of a receptor?
- TLRs can generate homodimers or heterodimers
- differences in the combinations of extracellular domain alters the ligand-specificity of the dimer itself
- different dimers and/or ligand types can activate distinct cellular responses from cells due to differences in their signaling activities
90
How can ligand binding alter a receptor's localization on the membrane?
- after ligand binding, the cytoskeleton of the are becomes broken
- this alteration of cytokeletal framework -> proteins move freely
- resting -> primed -> engaged
- resting state = confined (limited mobility)
- primed state = reduced confinement (increased mobility)
- engagement = tethered (immobile)
91
What is receptor aggregation and how do cell-cell interactions strength aggregation intracellular signaling? Give an example.
aggregation = due to ligand binding it enhances subsequent ligand binding
- cell-cell interactions rely on a binding affinity to maintain contact over long periods of time
- extended contact facilitates signal transduction and exchange of cytokine signals
- cytoskeletal reorganization may occur upon extended binding
e.g. activated B cells have greater cellular activity upon ligand binding than naive b cells because it takes less time for the proteins to aggregate due to high concentration of proteins
92
Describe how aggregation allows for enhances cell-cell interactions
1. proteins can be mobilized to the sites of cell-cell contact
2. the mobilization of these proteins to these regions' strengthens cell-cell adhesion
3. stronger adhesion -> stronger protein-protein interactions between cells
4. stronger protein-protein interactions enhances signaling and can help promote alterations to immune cell functions
93
Describe how aggregation is important for Tc cells to recognize infected cells
- strong cell-cell interactions allow for the health of the cell to be properly identified by the Tc cell
- strong cell-cell interactions are important for targeted cell killing
94
Describe how a cell can move from different receptor states if it receives other signals (e.g. cytokines)
Cytokines can alter the activity of the cell, which can turn on expression of beta and gamma chains to join an alpha chain which will make a high affinity R
95
How are cells able to integrate extracellular information?
intracellular signaling dynamics
96
Describe the characteristics of inhibitory and stimulatory receptors
- some R's are inhibitory, some are stimulatory
- sometimes i/s Rs can share ligands or have distinct ligands from each other
- communication between i and s R-types is what determines the cellular response of the cell
- Ri's contain signaling motifs within their CYT termed ITIMs which will recruit and activate phosphoptases to inhibit signaling
- Rs's contain short CYT which require the recruitment of adaptor proteins that contain ITAM motifs that recruit and activate kinases to induce signaling
97
Why is there an inhibitory threshold and how do cells overcome it?
Immunity exists at an inhibitory state (b/c overactivation is bad for the host)
Mechanisms to overcome the threshold:
1. stimulatory signal is stronger than inhibitory
2. inhibitory R's and/or lignads are removed from the cell surface
- both of these are due to cytokine signalling
98
Give an example of how activation of a single R-type can engage in stimulation of multiple signalling pathways
When an Ab-covered pathogen binds to an Fcgamma R, this will activate a phagocytic pathway and a respiratory burst in the phagosome (digestion) which are both important for pathogen killing
99
What does it mean if receptors have plastic functionality?
The R-type can be both stimulatory and inhibitory
100
What are the two definitions of cross talk?
1. the alteration of a cell's state (active vs resting) due to the absence or presence of at least one cellular product (e.g. cytokines or pathogen related molecules) OR due to interactions with other cells
2. the interaction of at least two signalling pathways within a cell, which facilitates signalling modulation (i.e turning something on or off)
101
How is information provided through a cell? Give an example of each type.
- extracellular molecules such as cytokines, chemokines and other immune-related compounds. e.g. adipocyte releases cytokines to an immune cell which causes the immune cell to release TNFa and cytokines to the adipocyte which causes it to produce more cytokines
- cell-cell interactions that lead to the engagement of protein-protein interactions between two cells (immunological synapse). e.g. R-R binding between an adipocyte and an immune cell that leads to both cells making cytokines
102
Give an example of a receptor-receptor interaction
Icam-1 and LFA-1 is important for adhesion
103
Give an example of a receptor-ligand interaction
PD-1L and PD-1 stops T cells from killing HCs
104
What are the four types of signalling molecules?
1. adaptors
2. scaffolds
3. kinases
4. phosphotases
105
Give examples of adaptors/scaffolds, and describe the function of adaptors and scaffolds
Example: DAP10, FcRgamma, DAP12 (adaptors), Grb2, and LAT (scaffolds)
Functions:
- allow for the aggregation of signalling proteins at specific regions within the cell
- adaptors can bind to receptors and they contain ITAMs
- scaffolds act as an anchor site for the aggregation of multiple signalling moelcules
106
Give examples of kinases and describe the function of kinases
Example: Src, Syk, Akt, p13k
Functions:
- contain enzymatic regions that will alter the activation state of other signaling molecules through phosphorylation
107
Give examples of phosphotases and describe the function of phosphoatases
Example: SHP-1, SHP-2 and SHIP
Functions;
- deactivation of signaling molecules via the removal of phosphorylations (dephosphorylation)
108
How does phosphorylation make a protein active?
Changes the shape of the protein
109
Give an example of stimulatory cross-talk within cells
- IFNg binds to IFNgR
- activates the kinase JAK-1 which phosphorylated STAT1
- STAT1 can then dimerize with another STAT1 molecule which then translocates to the nucleus
- binding of STAT1 complex to DNA leads to the production of a variety of proteins: TLRs, MD2, CD14 and SOCS
- proper activation of the cell requires the aggregation of CD14, MD2 and TLR4 on the cell membrane
110
Give an example of inhibitory cross talk within a cell
- binding of a ligand to TLR/IL1R dimer leads to the activation of IKK (IkB kinase)
- IKK facilitates the activation of NF-kB by inducing the removal of the inhibitory regulatory subunit of the complex IkB
- NF-kB is a TF that will be translocated to the nucleus of the cell
- NF-kB generates the production of the protein A20
- A20 protein stops the signaling of the TRAF2/5 complex
- signaling for further cellular activity is stopped
- blocking of the pathway leads to decreased activity of the cell
111
What is the stranger hypothesis?
Mammals use pattern recognition to initiate immunity; anything foreign is bad
112
What is the danger hypothesis?
the "patterns" recognized were the result of damage to self; recognize the damage caused by pathogens
113
Generally describe how healthy cells show that they are healthy, and how cells that are in harmful states can show that they are stressed and what this results in
Healthy = marker of normal self; ligand for inhibitory receptors
Infected for transformed cell = marker for infected, stress, or transformed cell; ligand for activating receptors -> assisted apoptosis
Senescent or apoptotic cell = marker of apoptotic or senescent cells; ligand for phagocytic receptors -> phaogcytosis
Necrotic cell = marker of tissue damage; ligands for receptors that induce repair response -> tissue repair
114
What is an Ag?
any substance that is recognized as foreign and can trigger an immune response (nonself)
115
What are some antigenic determinants?
1. surface markers present on foreign bodies in the blood and tissue (includes bacterial, fungal, viral, and parasitic markers)
2. the self markers of cells from a different organism
116
How does the immune system distinguish what is nonself or what is dangerous to the host?
HCs have self markers that tell the immune system that they are part of the host
Ag (nonself) markers communicates to immune cells that they are foreign
117
What are self markers, what cells are they found on and how does it work?
Self marker = major histocompatibility complex molecules class 1
Cells = all nucelated cells
Function = presents both self and nonself derived molecules (intracellular) and can be used for self and nonself recognition, if a Tc cell recognizes a pathogen associated with MHC-1 the cell will be killed
118
How are peptides loaded onto MHC-1?
1. proteosome degrades proteins into peptides
2. peptides are transported into the ER by TAP
3. peptides are then loaded onto MHC-1
4. MHC-1-peptide complex is presented on the cell surface
119
Which cells express MHC-2, what is presented on MHC-2, and which cells recognize MHC-2?
APCs express MHC-2
Exogenous (extracellular) peptides are presented
Pathogens internalized via phagocytosis can be degraded and these newly produced Ag.s are presented on the surface of the APC
Th cells will recognize the Ag.s on MHC-2 and release cytokines that activate additional immune cells
120
How are peptides loaded onto MHC-2?
1. pathogen (or Ag) is internalized and degraded in lysosome
2. invariant chain that block the MHC-2 binding site (prevents self peptides from binding) are removed
3. MHC-2 molecules are transported to the cell surface in exocytotic vesicles
4. endosomal vesicle with microbial peptides fuse with exocytic vesicles containing MHC-2
5. invariant chain is degraded and MHC-2 binds peptides
6. transported to the cell surface
121
What are PAMPs? Give examples of viral and bacterial PAMPs.
PAMPs = pathogen associated molecular patterns that are highly conserved and are often components that are fundamental (little selective pressure to get rid of) to the survivability of a pathogen
Bacterial: LPS, PG, glycolipids, lipoproteins
Viral: ssRNA (has modification at 5' end), env proteins
122
Why is LPS a good PAMP?
- fundamental component of G- OM
- provides structural integrity and permeability of the membrane
- because it is fundamental, it is not likely that the bacteria will alter it
- due to the conserved nature of LPS, a single R can recognize at least 29 bacteria
123
Describe how DNA can be a good PAMP
- bacterial and viral DNA (and RNA) have structural differences compared to those of mammals due to methylation
- the structural characteristics of bacteria and viruses are important for the integrity of their DNA, making them highly conserved
124
Describe how flagellin is a good structural PAMP
- flagellin is a characteristic of many types of bacteria and are important for their ability to move
- mammalian cells do not contain flagellin (other than sperm)
- due to their importance in the mobility of bacteria, they are highly conserved
125
Do PAMPs bind to activating or inhibitory receptors and why?
activating, so that cellular responses can be activated
126
If a cell does not present MHC-1 on its surface what will happen?
NK cell's inhibitory receptors will not be activated and thus the NK cell will kill the HC
127
What are DAMPs, and give two examples of DAMPs and explain why they are good DAMPs? What does this tell us about the relationship between DAMPs and PAMPs?
DAMPs = damage associated molecular patterns
Example = mito DNA and mito membrane
- both retain ancestral bacterial features and thus can be seen as PAMPs
- therefore DAMPs and PAMPs are not mutually exclusive
128
What are endogenous DAMPs and what are exogenous DAMPs?
endogenous: DAMPs that are produced or exist within or on a cell, can be constitutive (released by necrotic cells or exposed on the surface of stressed cells) or inducible by PRR signalling (actively secreted out)
exogenous: DAMPs that originated outside of a cell
129
Give an example of a protein and a non-protein DAMP
Protein = histones
non-protein = ATP
130
How do macrophages distinguish necrotic from apoptotic cells?
necrotic cell -> chromatin clumping, swollen organelles -> disintegrate -> release intracellular contents (DAMPs) -> inflammation
apoptotic cell -> mild convolution, chromatin compaction and segregation, condensation of cytoplasm -> apoptotic bodies, nuclear fragmentation -> phagocytosis -> inflammation supression
131
How can ATP act as a DAMP?
- through cellular damage or death, ATP is released into the extracellular environment
- ATP should not be present in extracellular spaces
- free ATP is bound to R's on immune cells
- immune cell generated appropriate immunological responses
132
What are some characteristics of PRRs?
- recognize PAMPs and DAMPs
- proteins encoded in the genome (germline encoded) and expressed on many different cells
- allow for rapid detection/profiling of the most common pathogens due to the conserved nature of PAMPs
- initiates cellular innate immune responses and appropriate anti-microbial mechanisms
133
Where in a cell can PRRs be found?
on the surface or within a cell
134
How can a single pathogen elicit different cellular responses?
- multiple PRRs can bind the same pathogen
- each R can induce its own intracellular signalling event (e.g R1 secretes cytokines and chemokines, R2 enhances ROS generation, R3 induces phagocytosis; all facilitate pathogen killing)
- multiple Rs engaging the same pathogen significantly enhances targeted responses
135
What are the four major types of PRRs?
1. TLRs
2. CLRs (C-type lectin)
3. NLRs (NOD-like)
4. RLRs (Rig-like)
136
What are some characteristics of TLRs?
- recognize DAMPs and PAMPs
- horseshoe-like structure allows for multiple R-L interactions
- different TLRs can induce R-specific responses due to adaptor proteins (i.e. which adaptor(s) bind determine the signaling pathway initiated)
- adaptor binding tailors the R activities toward the appropriate response (viral vs bacterial)
- adaptors bind to the TIR domain
137
What are some common adaptor proteins associated with TLRs?
- TIRAP
- MyD88
- Trif
-TRAM
138
Which TLRs recognize extracellular PAMPs?
1, 2, 4, 5, 6, 11, and 12
139
Which TLRs recognize intracellular PAMPs?
3, 4, 7, 8, and 9
140
For the following TLR dimers give the PAMP that they recognize:
- TLR4/4
-TLR5/5
-TLR3/3
-TLR7/7
TLR 4/4
- plasma memb = G- bacteria
- endosome = viral proteins
TLR5/5 = bacterial flagellin
TLR3/3 = viral dsDNA
TLR7/7 = viral ssRNA
141
Give an example of how a TLR can directly bind to a PAMP
TLR5 recognized a conserved component required for the structure of the flagellum
142
Give an example of a how a TLR indirectly binds a PAMP
TLR4 requires help from CD14, MD-2 and LBP to bind to LPS:
- LBP binds to LPS -> CD14 binds the immobilized LPS associated with LBP -> MD-2 engages with the LPS/CD14 on the surface of the cell -> TLR4 binds with the LPS and MD-2 -> intracellular signalling
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What are some characteristics of NLRs?
- subfamilies are determined based on structural make up of their domains
- recognize stress and infectious stress
- important for the generation of the inflammasome
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Where are NLRs localized?
restricted to the intracellular regions of a cell because they all recognize intracellular PAMPs and DAMPs
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What is the importance of the inflammasome?
inflammasone formation helps produce Caspase 1 which activates cytokines (cleaves pro-IL-1B into IL-1B)
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What kinds of microbes can NLRs recognize?
bacteria, viruses and fungi
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What is the role of NOD-1?
activates NF-kB which transcribes IL-8
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What is the role of NLRP3?
versatile NLR that can recognize PAMPs and DAMPs
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What are some characterisitcs of RLRs?
- include RIG-1 and MDA5 which are cytoplasmic sensors of RNA viruses
- RLRs have distinct adaptors, but the outcome is similar: they may amplifiy an anti-viral or a pro-inflammatory repsonse
- 2 major pathyways associated with RLR activities = NF-kB and IRF3/7
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Describe how cross-talk can occur between TLR and RLR pathways
- TLR 7/8 and TLR9 recognize pathogen DNA and RNA
- RLRs recognize pathogen DNA or RNA
- to better modulate immune repsosnes to an anti-viral activity, these pathways cross talk to one another to produce cytokines and interferons
151
Describe some characteristics of CLRs
- there are three major types (1, 2 and soluble)
- these types are based on their extracellular binding region structure
- CLRs bind to carbohydrates
- unique because they can have soluble forms
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Describe how CLRs are unique in comparison to TLRs and NLRs
- each CLR has a distinct structure
- CLRs can be memb-bound or soluble
- contain both inhibitory and stimulatory types
- signaling domains of CLRs differ
- CLRs are a large receptor family
- different sets of CLRs can recognize different types of pathogen assoc carbohydrates
- all types of pathogens can be recognized
- carbohydrates are good PAMPs because they are highly conserved
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What are some pro-inflammatory activities of CLRs?
1. induce phagocytosis
2. activation of NF-kB which regulates both innate and adaptive immunity
3. generation of IL-B from its inactive form through caspase activity
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Which cells are pAPC's and which ones are the major ones?
DC, macrophage, B cell
DC and macrophages are the major ones
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What are the key features of DCs and macrophages that make them pAPCs?
- phagocytic
- express Rs for apoptotic cells, DAMPs and PAMPs
- localize to tissues
- localize to T cell zone of lymph nodes following activation (DCs)
- express high levels of MHC-II and Ag processing machinery
- express co-stimulatory molecules following activation
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What are the key features of B cells that make them pAPCs?
- internalize Ags via BCRs
- express MHC-II molecules and Ag processing machinery
- express co-stimulatory molecules following activation
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Which cells do DCs present to and what is the response?
cells: Naive Th cells
response: activation leading to clonal expansion and differentiation into effector T cells
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Which cells do macrophages present to and what is the repsonse?
cells: effector Th cells
response: activation of macrophages (cell-mediated immunity)
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When a pAPC encounters a pathogen what three steps take place?
1. start secreting chemokines and cytokines to attract and activate other immune cells
2. phagocytose and digest the pathogen
- turn on a proteosome that breaks down pathogen proteins into peptides
- present peptides on their surface via MHC-II
3. they upregulate co-stimulatory molecules require for optimal activation of Th cells
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What are the differences between an immature and mature DC?
Immature:
- low co-stimulatory molecules
- low MHC-II expression
- low secretion of pro-inflammatory cytokines
- high phagocytic capacity
Mature:
- high co-stimulatory molecules
- high MHC-II expression
- high secretion of pro-inflammatory cytokines
- low phagocytic capacity
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If a pathogen is degraded and released into the surrounding tissue what does this accomplish?
1. activates cells around it
2. can be transferred into secondary lymphoids
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What are some characteristics of a immuno-proteosome?
- immune cells, especially APCs, express a high number of immunoproteosomes even at rest
- immunoproteosomes produce peptides with a hydrophobic C-term that can be properly processed to fit in the binding site of MHC-I molecules
- IFNg enhances the generation of subunits that make up the proteosome (i.e. immune related signals increase the amount of proteosomes present)
- increased number of proteosomes enhances the degradation of pathogen-related material and increases the number of pathogen-related Ags
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What happens if a naive T cell only receives signal 1 or signal 2, but not both?
- clonal anergy
- apoptosis
- ignorance
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What co-stimulatory molecules do pAPCs upregulate when a PRR is activated?
CD40L and CD80
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Describe TCR activation
1. in the resting T cell the ITAMs are not phosphorylated
2. binding of ligand to the receptor leads to phosphorylation of the ITAMs via receptor-assoc kinases
3. ZAP-70 binds to the phosphorylated zeta chain ITAMs and is phosphorylated and activated by Lck when the co-receptor binds to the MHC ligand
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What is a cytokine profile?
the type of cytokines that a differentiated immune cell releases
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How is Th cell fate determined?
cytokine type, signal intensity and signal combinations which tailor the T cell to a specific type
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What are the two ways a T cell can be activated
classical: Ag presenetation, co stimulation and cytokine activity
certain conditions: strong cytokine recognition and the activation of PRRs on their surface
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How can a B cell be provided an Ag?
1. soluble Ag in lymph
2. APC coming into secondary lympoid organ
3. resident APCs within nodes collect soluble Ag and present
4. Ag provided by T cells
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Describe T cell dependent B cell activation, where the BCR binds to soluble Ag
1. B cell BCR binds to Ag
2. Ag is internalized
3. B cell presents Ag on MHC-II
4. MHC-II with Ag is recognized by TCR on Th cells
5. engagement of TCR-MHC + cytokine stimulation fully activates B cells
6. B cells undergo differentiation and expansion
7. IL-4, IL-5 and IL-13 will be released by the Th cell to help initiate and promote Ab production
171
Describe T cell dependent B cell activation, where an APC-Ag engages the BCR
1. APC-Ag engages BCR on B cell
2. B cell internalizes and degrades the Ag and present it via MHC-II
3. Th cell TCR engages MHC-II on B cells
4. MHC-II and TCR interaction along with co-stimulatory activities (CD254-CD40) and cytokines induce B cell differentiation to produce Abs
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Describe T cell independent B cell activation
1. soluble Ag form the lymphatic system can be directly recognized by the BCR of a B cell
2. Ag-BCR binding stimulates naive B cell to become secreting plasma cell
3. due to lack of T cell activities, this cell will become a short-lived plasma cell
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How can PRRs regulate B cells?
- in B cells, TLRs interact with PAMPs to induce Ab responses that are T cell independent
- TLRs in B cells can synergize with BCR signaling to induce a very powerful Ab response by promoting AID expression and class switching responses (CSR)
- e.g. LPS which binds to a TLR4, without additional signals can induce a specific CSR event; however, LPS + IL-4 -> different CSR
174
Which cytokine makes antiviral pro Tc cells and what cytokines do they release?
Makes: IL-12
Release: IFNgamma
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Which cytokines makes proinflammatory Th17 cells and what cytokines do they release?
Makes: IL-6 and IL-23
Release: IL-17
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Which cytokine makes pro-Ab Th2 cells and what cytokines do they release?
Makes: IL-10 + IL-3/IL-4
Release: IL-4, IL-5 and IL-13
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Which cytokine makes regulatory "brakes" Treg cells and what cytokines do they release?
Makes: IL-10 and TGF-beta
Release: IL-10 and TGF-beta
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How can DC cells activate Tc cells?
1. presentation via an MHC-1 molecule
2. co-stimulation (DC CD80, Tc CD28)
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What are the symptoms of inflammation?
1. Heat
2. Redness
3. Tenderness
4. Swelling
5. Pain
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What causes the symptoms of inflammation?
1. capillary widening -> increased blood flow
2. increased capillary permeability -> release of fluid
3. attraction of white blood cells -> migration of white blood cells to injury
4. system response -> fever and proliferation of white blood cells
181
What are the four phases on inflammation?
1. initiation
2. amplification
3. resolution
4. repairing
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What are necrotic cells?
cells that are dying not on purpose
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Describe the steps of phase 1 of inflammation: initiation
1. necrotic cells release DAMPs and/or PAMPs from pathogens as signals
2. DAMPs and/or PAMPs activate tissue macrophage phi (M phi)
3. activated M phi's recruit neutrophils and monocytes by producing inflammatory cytokines and chemokines such as TNF and IL-6
184
Describe immune cell mobility under normal conditions
- selectin-mediated adhesion to leukoycte's mucin is weak, which allows leukocytes to roll along the vascular endothelial surface
- IL-1B/IL-6 secreted by activated macrophages can alter the adhesion properties of the membrane
185
Describe the cytokines and chemokines that PRR activated macrophages secrete
1. TNFalpha
- stimulates production of the chemokines IL-8 and e-selectin on endothelium
-> both facilitate recruitment of macrophages and neutrophils
- induces macrophages to produce IL-1B
2. IL-B
- promotes production of IL-6 and ICAM-1 (adhesion molecule)
-> ICAM-1 is needed for leukocyte extravasation and recruitment (blood vessel exit) through its binding to LFA-1
3. IL-6
- acts on the liver (endocrine activity) to produce acute phase proteins
186
What are the four steps of blood vessel exit?
1. rolling adhesion
2. tight binding
3. diapedesis
4. migration
187
Briefly describe the steps of phase 2 of inflammation: amplification
1, immune cells reach the site of infection
2. proinflammatory cytokines will activate resident and recruited immune cells
2. immune cells activate innate immune responses
188
What receptors on a macrophage can induce phagocytosis?
- mannose R (CLR)
-Dectin-1 (CLR)
- complement R
- lipid R
- scavenger R
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How can phagocytosed microbes be killed?
1. oxygen dependent killing
- ROS and RNS
2. oxygen independent killing
- enzymatic killing
190
Name some examples of ROS and RNS
ROS:
- O2- (superoxide anion)
- H2O2
RNS:
- NO (nitric oxide)
- NO2 (nitrogen dioxide)
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Name some examples of oxygen independent enzymes and their functions
1. bactericidal permeability increasing protein (BPI) -> phosholipase activation -> phospholipid membrane degradation
2. lysozyme -> hydrolysis of murNac
3. lactoferrinn -> binds iron -> prevents bacterial proliferation and invasion
4. major basic protein (MBP) -> cytotoxic action to parasites
5. defensins -> form holes in bacterial membranes
192
Which cells release NETs and what is the function of NETs?
cells: neutrophil
function:
- bind/trap bacteria
- degrade virulence factors and kill bacteria
- prevent bacteria spread by ensuring a high concentration of local antimicrobial agents
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What are NETs comprised of? What is the role of its components
1. chromatin (DNA + histones)
- forms extracellular fibres
2. elastase (neutrophil granular protein)
- destroy virulence factors released by viruses
3. MPO (neutrophil granular protein)
- provide broad antimicrobial activities
4. Lactoferrin (neutrophil granular protein)
- sequesters iron -> starvation of pathogens and blocks pathogens from binding to HCs
194
Name an important acute phase protein made by the liver
complement proteins
195
What are some functions of complement proteins?
1. lysis of target cells
2. opsonization of pathogen
3. degranulation of granulocytes
4. extravasation (migration of WBC from blood to tissue)
196
What are the three complement pathways?
1. classical pathway (anything foreign)
- Ag-Ab complexes lead to complement activation
2. lectin pathway (not self pattern)
- lectin binding to pathogen surfaces lead to complement activation
3. alternative pathway (missing self)
- pathogen surfaces lead to complement activation
197
What are the active complement forms and what are their roles?
C3a: inflammation
C3b: opsonization
C5b: lysis
C5a: inflammation
198
Where does C3b's specificity come from?
only binds surfaces that do not contain sailic molecules
199
What are the three main functions of C3b?
1. opsonization and phagocytosis
- C3b binds to microbe -> phagocyte recognizes bound C3b by phagocyte C3b R -> phagocytosis
2. stimulation of inflammatory reactions
- binding of C3b to microbe -> release of C3a and proteolysis of C5 release C5a -> recruitment and activation of leukocytes by C3a and C5a -> destruction of microbes by leukocytes
3. complement-mediated cytolysis
- binding of C3b to microbe -> activation of late components of complement -> formation of membrane attack complex (MAC) -> osmotic lysis of microbe
200
Describe the steps of phase 3 of inflammation: resolution
1. once an infection has been dealth with, immune responses need to be inhibited
2. neutrophils that have provided antimicrobial responses will be induced into an apoptotic state
3. apoptotic neutrophils release cytokines (e.g TGF-B) and express decoys that removes pro-inflammatory cytokines to stop neutrophil migration
4. apoptotoc neutropils will release and express find me/eat me signals to surrounding macrophages
201
What are the chemokine depletion mechanisms used by apoptotic neutrophils?
1. chemokine truncation
- proteases degrade chemokine
2. chemokine sequestration
- use structural or functional decoy Rs
202
Name an example of a "find me" signal
nucleotides
203
Name an example of an "eat me" signal
PS (phosphotidylserine)
204
How does TGF-B stop cellular functions during resolution?
- inhibits proliferation
- inhibits cytotoxic killing of infected macrophages
- inhibits killing of extracellular bacteria
205
Desribe the steps of phase 4 of inflammation: repair
1. M2 macrophages and fibroblasts will begin secreting growth factors (VEGF, TGF-B)
2. generation of collagen will help bridge damaged regions together
3. keratinocytes will seal up damage sites
4. MMPs will re-organize the tissue to re-epithelialize the damage tissue
206
How do macrophages transition from pro- to anti-inflammatory states?
Proinflammatory M1 phenotype phagocytosis microbes, clears cellular debris and produced pro-inflammatory mediators. Removal of neutrophils causes the macrophage to display a repearative M2 phenotype that releases anti-infammatory mediators and GFs.
207
What cells are ILCs generated from?
common lymphoid progenitor (CLP)
208
What TFs are involved in differentiating a CLP into ILCs?
GATA
T-bet
RORgammaT
209
What is the relationship between ILCs and Th cells?
TFs of ILCs are the same as Th cell subsets
210
What is the primary difference between ILCs and T cells and how does this affect the activity of iLCs?
ILCs lack a TCR and use PRRs and they reside in tissues which makes their response time much faster than Th cells
211
Describe ILC activity during infection
populations of "specialized" lymphocytes reside in tissues that have the capacity to respond to infection during the period of time between activation of macrophages and the activation of T and B cells
212
Where do NK cells reside?
all major immune organs
213
What are some characteristics of NK cells?
- originally describes as large granular lymphocytes
- do not require the thymus for maturation
- do not express a TCR or BCR but possess killer activation and inhibitor Rs
- can innately recognize and kill virally infected and tumour cells
- when activated they release their lytic granules into the target cell causing it to die
- activated NK cells secrete IFNgamma which activates macrophages
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How do NK cells recognize targets?
1. healthy cells express MHC-I which inhibits NK cells
2. unhealthy cells may not express MHC-I which does not inhibit NK cells
3. unhealthy cells can induce self-ligands that bind to activating Rs that override the inactivating activity of MHC-I
4. ADCC: tumour cells have Ags that Abs bind to activating Rs that override the inactivating activity of MHC-I
215
Describe the NK cell killing mechanism
- perforin forms a pore in the target cell membrane
- granzymes pass through the pore and induce apoptosis
216
How do NK cells protect themselves from their own lytic granules?
Create a lipid shield (densely packed and highly ordered presynaptic lipid membranes) that prevent puncture by perforin
217
Describe ADCC
1. Abs bind Ag on the surface of target cells
2. NK cells Fc Rs (CD16) recognize cell-bound ABs
3. cross-linking of CD16 (aggregation) triggers degranulation into lytic synapse
4. cells die by apoptosis
218
Describe ILC2 cells
- Th2 like
- facilitate parasite/allergen related responses
- activate B cells to produce IgE, recruit eosinophils, activate basophils and mast cells via IL-4
- facilitate Th2 and DC activities
219
Describe ILc3 cells
- Th17/22 like
- facilitate mucosal related responses
- release IL-22 and IL-17 which helps maintain mucosal barriers
- regulate Treg cells for immune tolerance of commensal bacteria
- dampen immune responses of T cells that will recognize commensal bacteria
