Final Exam (New Content) Flashcards
What is the point of the germinal center
It is a site for improving B cell receptors
What do FDCs do inside the germinal center *
- Secrete BAFF for survival of nearby B cells
- FDCs hold some antigen that the B cell receptors bind
- (only one or two) Cognate pair proliferates (b cells that enter the GC are referred to as centrocytes)
What follicle is the GC known as?
The secondary follicle
- Clonal Expansion
- FDCs secrete IL-6, Il-15, and BAFF for B cells to help them proliferate
- Cognate B cells (the ones connected to the few cognate pairs that went into the Germinal Center) become centroblasts and divide into hundreds of daughter cells (more centroblast) and stop expressing B cell receptors on their surface
- They ‘open’ the rearranged V regions of the heavy AND light chain DNA
- Cognate Tfh divide, too
- this is occuring in the dark zone of the GC
Centroblasts
Germinal center B cells that are dividing and mutating heavy and light chain genes that encode the B cell receptor. Centroblasts arise due to cytokines secreted by FDCs
*dark zone
*You are a centroblasts from the moment you recieve signals from FDC to expand all the way until you actually have a mutated BCR (after AID)
Centrocytes
Germinal center B cells that are competing with mutated BCRs for limited antigen from FDCs and co-stimulation from cognate Tfh. They switch the class of BCR that they express under the guidance of cognate Tfh cytokines
- Somatic hypermutation during expansion
*All FDCs do is they stop the B cell from expressing their BCR and opens up their variable regions. To actually create mutations, they need Tfh cell help
– Tfh use CD40L to stimulate centroblasts to express AID enzyme
- AID mutates variable regions of rearranged Ig DNA
- AID mutates both the light and heavy chain and each centroblast mutates differently
AID
Activation-induced cytidine deaminase
Changes cytidines to uracils in ssDNA
AID makes point mutations at a rate of 1 per 1000 base pairs (hypermutation)
Common DNA repair enzymes randomly replace U with A,C,T or G which makes those mutations
(this is because the body knows DNA shouldn’t have uracil, the DNA repair enzymes just see this as damage so they will randomly add a nucleotide that is supposed to be in DNA. this is what creates the hypermutation)
Affinity maturation
Must select the B cells with beneficial mutations. The ones with mutated BCR that have the highest affinity for original antigen
- Somatic hypermutation (2)
After a few days, centroblast become centrocytes that express a mutated BCR, mutations appear as changes to antigen-binding sites
So when the B cell is expressing a mutated BCR after a few days, what kind of cell is it?
- Centrocyte
- Affinity Maturation
- There are 100s of centrocytes expressing differently mutated BCRs. Not all are useful
- Must select the ones that bind antigen with the highest affinity.
- The mutated centrocytes rush to the FDC to bind the limited antigen on FDCs. They need an antigen signal and T cell co-stimulation to survive
- Centrocytes will die if they don’t receive signals within days.
- Dead cells are phagocytosed and cleared by macrophages
What do successful centrocytes express?
- Bcl-Xl thta prevents programmed cell death and induces clonal proliferation
*Affinity maturation is a form of positive selection for useful B cells AFTER they encounter antigen… the adaptive immune system evolves to keep up with rapidly evolving pathogens
*even after hypermutation, a centrocyte can go back into the dark zone and becomes a centroblast again, adn mutates some more
Is proliferations and somatic hypermutation in the dark zone or light zone?
Dark
(competing is in the light)
Centrocytes switch ___ using AID too
Centrocytes switch C regions using AID too
Tfh cytokines instruct centrocytes to switch to various isotypes
- Class (isotype) switching *also occurs in the GC
Cognate Tfh provide signals to guide the isotype of BCR that a centrocyte expresses
- CD40L to induce AID first
- Class-specifying cytokines for different isotypes
What is Class (isotype switching) switching
AID enzyme driven recombination of constant gene segments of the HEAVY CHAIN DNA that leads to switching from IgM or IgD to another isotype (IgG, IgA, or IgE) without changing the specificity for antigen
How does a Pre-Tfh know which cytokines to secrete for isotype switching?
- Pre-Tfh were programmed to secrete class switch cytokines during their earlier activation. (Like after it got the signal to become a Tfh, it got a lot of other cytokines too, especially at the band between T and B cell areas)
- The Tfh secretes those switch cytokines as a cognate pair in the germinal center
When are these cytokines secreted by Pre-Tfh?
When the T cell is in cognate pairs in the germinal center
How does the switching of regions actually work?
- The combination of CD40L and whatever fate-specified cytokines are released will induce NFkB and a specific STAT TF (depending on the cytokine). This will cause the TFs to land upstream of particular constant regions (like the 3 g, e, or a region)
- In front of each region except for D is a switch region
- The RNA polymerase will open up the DNA to transcribe, giving AID the opportunity to come in (because of the repeated nucleotide sequences) and remove all the C’s to replace them with Uracil
- Certain enzymes will see this and try to fix it by cuttign out any regiosn that have the U, creatign nicks in the DNA.
- This process will occur for the Cmu region as well.
- A DNA repair enzyme will come in and put the regions that got nicked together, the Cmu and whichever region was specified.
- This will cut out everything in the middle
- Now you VDJ segment should be in front of the constant region you want to encode and the RNA polymerase will make the mRNA so you can make teh heavy chain protein.
Is hyper-IgM syndrome casued by defective B or T cells?
T cells because they are not giving the fate-specifying cytokines to create certain STAT TFs that will bind to certain parts of the DNA
*Could technically be both since it would constitute a combination of a lot of things
When B cells emerge from the germinal center, what types of cells are they?
- Plasma cells or Memory B cells
Where plasma cells migrate dictates how long they live
Shortest life - tissues like the infected site
Short life - secondary lymphoid tissues
Long life - bone marrow
How long do memB cells live?
They forego this infection and patrol for the next encounter, they live for years !
What cytokines are secreted to make a centrocyte into a memB cell or plasma cell?
IL-21 and IL-10
* this occurs near the end of the response, when the antigen wanes)
Plasma cells
Antibody secreting B cells that secretes one antigen receptor with one affinity
no longer respond to Tfh help
no longer improved antibody
Memory B cells
Long-lived B cell with isotype-switched, high affinity B cell receptor. It partrols secondary lymphoid tissue (spleen, LB, Peyer’s patch) looking for return of the specific antigen due to re-infection. It will activate if it encounters specific antigen for a quick memory response (secondary immune response)
Homeostatic proliferation
Memory B cells GRADUALLY proliferate to replace ones that die naturally
Some SLOWLY DIFFERENTIATE in bone marrow
Become plasma cells and secrete continual low levels of high affinity IgG IgE or IgA (if they differentiate)
Homeostatic proliferation is driven by cytokine survival factors like IL-6, APRIL, BAFF and adhesion molecules in the bone marrow
*can become either short lived plasma cells in tissues or long lived ones in the bone marrow
What happens when memory B cells activate?
They get cognate T help and re-enter germinal centers
They repeat steps (1-5)
This wave of antibody due to activated memory B cells is a memory response (aka secondary immune response)
* the amount of Ab rises sharply at re-exposure because activated memory B cells make 100s of plasma cells
The affinity of the secreted IgG antibodies increases because the activated memory cells underwent improvements in the germinal centers before they differentiated into plasma cells
Humoral response
ANY antibody mediated response. Can neutralize a pathogen, activate complement, inflame or target antigen-expressing host cells for lysis. Humoral responses can be a primary (1st encounter) or a memory response (repeated encounter which your body is on high alert for which is why vaccines are so effective)
What signals does a centrocyte need to progress?
- Antigenic signal from FDC
- Signal from Tfh (CD40L)
Events of the Germinal Center Steps:
Clonal Proliferation
Somatic hypermutation
Affinity maturation
Class switching
Final differentiation
How many events do B cells require T cell costimulation for?
- B cell activation
- Somatic hypermutation
- Centrocyte survival
- Isotype switching
Which type of B cell can isotype switch?
Centrocytes in the light zone
Which chain of the B cell (heavy or light) undergoes class switching?
Heavy
Two arms of adaptive immunity
- T-cell mediated arm
- Humoral arm
- The humoral arm is led by antibodies
What can bind antibodies?
- Antibodies can be bound by Fc receptors
Fc receptoirs are expressed on immune cells. - Most transmit signals in response to antibodies
- Some transport antibodies across cells
What can the Fc portion of an antibody bind to?
- Fc receptors
- C1qrs
- Transport receptors
How does IgM activate the classical pathway of complement?
Pentamer binding multivalent antigen takes a “staple” formation like a landing pad for C1qrs
* essentially it acts as a landing pad for C1qrs
IgG can also activate complement
- IgG have Fc portions that also provide landing pad for C1qrs. Simply need multivalent antigen that brings many IgG together
Which antibodies can fix complement pathway well?
Only IgM and IgG3
How does the opsonization of pathogens occur with antibodies?
- Ab on targets are bound by Fc receptors that induce phagocytosis
- Essentially, Fc portions can be bound by Fc receptors on cells
- Microbes that are opsonized with C3b and IgG are QUICKLY phagocytosed and destroyed BETTER. The reason why is because the clustering of Ab sendings activating signals of kinases and ITAMS on intracellular chains of the FcR
Fc Receptor Structure
alpha chain finds Fc portion of Ab
gamma chain send signal via kinases and ITAMS
ex. FCyRI binds empty IgG1 and IgG3. It is expressed on macrophages, neutrophils, and eosinophils that capture ‘empty’ Ab. Then, antigen that binds the Ab will be phagocytosed
When Fc receptors aggregate they transmit a signal
FcR bind Ab AND the Ab bind multivalent antigen. This brings FcR close to one another (aggregate, cross-link/cluster) SIGNAL SENT and the immune cell responds in some way
Many Fc receptors — Different immune cells use them
- look at the graph on week 11 slide 15 to get comfortable looking at this table
- Some receptors may activate a cell to perform some function once the antibodies aggregate. (uptake stimulation for example)
- Some receptors may inhibit a cell from performing a function once the antibodies aggregate. (uptake inhibition of stimulation)
*On this graph, anything that is green are activating ITAMS and the yellow (ITIMS SPECIFICALLY, NOT EVERYTHING THAT IS YELLOW IS AN ITIM) are inhibitory
Can immune cells use the same Fc receptors (which means they bind the same antibody) but react differently?
Yes
A macrophage and an eosinophil can detect IgG with FcyRI, but they will respond differently. The phagocyte will phagocytose while the eosinophil will degranulate.
This is because macrophages and eosinophils have different gene expression and effector molecules linked to the signal pathway of the FcR
Do individual immune cells express different Fc receptors or just one?
One immune cell can express many different types of Fc receptors on its surface. For instance, macrophages express FcyRI, FcyRII, FceRII, FCaRI to bind IgG, IgA, and IgE
Which receptors and antibodies do NK cells have?
Receptor: FcyRIII
Antibodies: IgG1 and IgG3
Which receptors and antibodies do macrophages cells have?
Receptor: FcyRIII, FcyRIIA, FcyRI, FcaRI
Antibodies: IgG, IgG3, IgA
Which receptors and antibodies do eosinophils cells have?
Receptor: FcyRIII, FceRII, FcyRI, FcaRI,
Antibodies: IgG, IgG3, IgA, IgE
Which receptors and antibodies do basophils and mast cells have?
Receptor: FceRI
Antibodies: IgE
Which receptors and antibodies do neutrophils have?
Receptor: FcyRI, FcyRIIA, FcaRI
Antibodies: IgG1, IgG3, IgA
Some Fc receptors transmit inhibitory signals
If antibody is already binding to a target, then more naive B cells joining the response is wasteful (because there has already been an immune response to the pathogen. They will not join a response that is already underway
The way a B cell knows if an antibody is already binding to a target is to detect IgG with an Fc receptor. They don’t activate if IgG is already binding to the target
e
Naive B cell inhibitory signal
*slide 18
1. At the start (EARLY) of a primary immune response, no specific IgG recognizes the pathogen (the pathogen doesn’t already have any antibodies on it), so the FcyRIIb1 is not engaged. BCR (IgM) transmits activation signals. This naive B cell will activate and eventually make Ab
2. At the climax and resolution (LATE) of a primary immune response, IgG is bound to the pathogen. So FcyRIIB1 on a new naive B cell binds IgG, crosslinks with the BCR, and prevents an activation signal. This naive B cell is too late to help, it will not activate. IT WILL DIE BY APOPTOSIS IN FACT
If the FcyRIIB1 recieves a signal, what does that mean?
It means that it detected IgG antibody already on a pathogen, so it will inhibit the naive B cell from becoming activated
How does FcyRIIB1 transmit inhibitory signals?
- It undoes phosphorylation and disrupts a signaling scaffold.
- FcgRIIB brings the inhibitory phosphatase SHIP
- SHIP interferes with signaling from any linked receptor. It removes phosphate groups, deconstructs signaling scaffold, no PLC-y; very little DAG and IP3 made
*phosphatase destroys PIP3 so the small scaffold can’t be made and signal 1 can no longer be sent out
6 General functions of antibodies
- Neutralize - this is dependent on the variable Fab portion
- Opsonize - this and the rest depend on the constant Fc portion
- Activate complement
- Restrain microbes on other mucosal barriers (epithelia)
- Confer (give) passive immunity
- Instruct immune cells: NK cells ADCC; degranulation of mast cells, basophils and eosinophils; inhibit naive B cell
What are the human IgG sub-isotypes?
IgG1, IgG2, IgG3, IgG4
Which function of antibodies is the only one that’s Fab dependent?
Neutralization
Do different isotypes specialize in localization in the body?
Yea.
*slide 23 week 11. don’t memorize this chart but please familiarize yourself with it
IgM, IgG, and monomeric IgA protect internal tissues
How does circulating antibody get into tissues?
- It can leak out of leaky blood vessels during inflammation (due to TNFa or anaphylatoxins)
- It can be transported by FcRn receptor
*slide is super helpful
- Fluid-phase endocytosis of IgG from the blood by endothelial cells of the blood vessels
- The acidic pH of the endocytic vesicle causes FcRN to associate with IgG, protection it from proteloysis
- On reaching the basolateral face of the endothelial cell, the basic pH of the extracellular fluid dissociates IgG from FcRn
Pinocytosis in relation to transporting antibodies
Blood vessels endothelial cell constantly use pinocytosis (endocytosis or small amount of fluid) to take up blood and clean it by degrading protein. This process also takes up FcRn from the cell surface. In pinosomes, FcRn protects IgG from degradation. Endocytic vessels are transported to the other side of the cell (TRANSCYTOSIS) and the contents are relased into tissues. IgG is delivered to tissues. This transcytosis can go in either direction.
Dimeric IgA and pentameric IgM protect mucosal barriers (how does dimeric IgA and IgM get in the mucosal barriers?)
- Poly-IgR binds to the J chain. So it ONLY binds IgA and pentameric IgM
- Starts in the tissue (lamina propria) because IgA is secreted by a nearby plasma cell in the basolateral region
- Then, the IgA that was just released binds to the poly-IgR receptor on the basolateral face of the epithelial barrier
- The antibody and receptor will be endocytosed
- Transcytosis to apical face of the epithelial cell (so its going towards the gut lumen in this example)
- Release of IgA dimer at the apical face of the epithelial cell and released into the outer mucus layer
Transcytosis
Receptor-mediated transport from one side of a cell to the other. Poly-IgR guides Ab with J chains across epithelial cells (basolaterl to apical direction mainly)
How does dimeric IgA and IgM protect mucosal barriers
- Poly-IgR ensures that there is always a supply of high-affinity IgA and quick, low-affinity IgM on outer mucosal surfaces
- Ab float in the mucus layer. As the mucus flows away, so does whatever is bound to the dimeric secreted Ab.
- Ab will bind bacterial toxins and bacteria to neutralize the threat until they are removed by the flow of the mucus layer.
So how do antibodies get into tissues? How do they get into the mucosal barriers?
They are two different processes.
1. For tissues, it occurs using the FcRn receptor and pinocytosis from the bloodstream to the tissue. This includes IgG, IgM, and MONOMERIC IgA. ENDOTHELIAL
2. For mucosal barriers, it occurs using the poly-IgR receptor. It can only take up dimeric IgA and pentameric IgM due to their J chains. Endocytosis on the basolateral side and spits it out into the mucosal layer on teh apical side of the cell. EPITHELIAL
What are the mucosal surfaces that are protected by secretory IgA and IgM?
- Gastrointestinal (GI) Tract
- Respiratory tract
- Urogenital tract
in the nose the lacrimal gland
in the mouth the salivary gland
Mammary gland
Secretory IgA
Name for the dimeric IgA which is actively transported (secreted) onto external (apical) sides of mucosal epithelial barriers
Distribution of Ab isotypes in a person?
- Blood: IgM, IgG, and monomeric IgA
- Tissues: IgG and monomeric IgA
- All connective tissue and epithelial barriers (skin): IgE
- All epithelial barriers: dimeric IgA, IgM*
Where can IgE also be found?
In connective tissue and under the skin (epithelial barriers)
FcRn transport ___ across the placenta
FcRn transport IgG across the placenta
- A fetus does not make IgG. It receives IgG that is transported across the placenta by FcRn (think of the placenta as a large blood vessel)
FcRn is always associated with blood vessels and endothelial cells
Placenta
Where blood supply of mother and fetus meet
Passive transfer of immunity by IgG (what is the makeup of a babies antibodies?)
All IgG in a fetus is derived from mother’s blood supply– and whatever Ab responses she makes
Their first year is a time when IgG is deficient and mucossal Ab (IgA) are deficient unless they drink breastmilk
Passive transfer of immunity
Transfer of adaptive immunity to a non-immune individual. Can be maternal transfer fo Ab via placenta or breast milk. Can be medical by injection of specific monoclonal antibodies or immune serum, or histocompatible T cells
Poly-IgR transports ____ ____ across mucosal mammary glands
Poly-IgR transports dimeric IgA across mucosal mammary glands
Nursing infants can drink secretory IgA in breastmilk. The Ab withstands conditions in the stomach and protects the infant’s gut and airways
Mammary gland
A type of mucosal tissue that transports dimeric IgA to the apical surface using Poly IgR. Secretory IgA ends up in milk
Role of high-affinity Ab
High-affinity Ab anywhere will neutralize, they do not release antigen
Vaccine-induced high-affinity Ab will _____
Neutralize
ex. High-affinity antiviral IgA was induced by a flu vaccine, an example of active immunization
- The twin with the Ab is protected from extensive flu infection later
- The twin without Ab suffers the flu because it will take her weeks to make the Ab
They have the same innate responses, but that doesn’t include memory T cells, memory B cells or long-lasting antibodies
Toxins and venoms require immunizations
In the case of animal venoms, horses can be immunized to provide anti-venom serum holding antibodies for immediate delivery of neutralizing antibodies (passive immunization)
Childhood vaccine (DPT)
Contains modified harmless toxoids that elicit high-affinity antibodies (ACTIVE IMMUNIZATION) and memory B and T cells
All example of passive immunization that we’ve learned
- Breastmilk IgA
- IgG from the placenta
- Horse antibodies for toxins
- Histocompatability with T cells
- Monoclonal antibodies
Tagging host cells for killing by NK cells (ADCC)
Nk cells express FcyRIII. Clustering this Fc receptor triggers degranulation of cytotoxic granules
Essentially, there is a target cell coated in antibodies that FcyRIII (or CD16) senses. Since there are so many, it clusters, sending a signal for the NK cell to degranulate and release its contents to kill the cell
Do you remember how NK cells typically kill cells?
When the cells are expressing stressors
New Key Concept: Adaptive responses focus general innate defenses on specific targets
ADAPTIVE Specific antigen
IgG1 or IgG3 for instance
- opsonize
- activate complement
- trigger adcc
Innate defenses
phagocytose
MAC attack complex
NK cell cytotoxicity
ADCC can be used by therapeutic mAB therapy
- B cell tumors that express CD20 can be tagged for destruction by anti-CD20 therapeutic mAB so NK cells can cluster and degranulation
Lymphoma
Cancer involving lymphocytes that grow attached to tissues
Leukemia
Cancer involving leukocytes that are in the bloodstream
What makes IgE antibodies unique as opposed to the other ones we’ve discussed?
IgE is “unique”. It doesn’t float freely to protect blood, bodily fluids, or mucosal surfaces… but it protects everywhere - at all connective tissues and under all barriers
It mainly function as a cell-bound Ab, mainly held by FceRI
Mast cells are granulocytes that are _______ sentinels that lie under _______
They gather empty ____ using ______
Mast cells are granulocytes that are long-lived sentinels that lie under ALL surfaces
They gather empty IgE using FceRI
*They degranulate powerful mediators when the IgE binds. multivalent antigen
What are some mast cell mediators?
Histamine and leukotrienes - contract muscles, open blood vessels, more mucus (weep and weep)
Carry “bomb” like inflammatory signals like TNFa, IL-5, CCL3, and PAF
Eosinophils are ____ that are called to ____ sites
They gather empty _____ using ____
Eosinophils are granulocytes that are called to inflamed sites
They gather empty IgE using FceRI
What are some eosinophil mediators?
Major basic protein and prostaglandin - kill parasites and induce histamine from mast cells, contract muscles, make mucus (weep and sweep)
CXCL8, IL-5, PAF - inflammation
Allergies are due to
Type I allergies are due to IgE effects
Allergen
Foreign antigen from the environment that is bound by IgE and triggers inappropriate allergic reaction
Allergic reaction
Inappropriate and damaging adaptive immune response to a seemingly innocuous antigen (non-threat)
Mast cells could be activated causing issues in the heart and vascular system, respiratory tract, and gastrointestinal tract
- WHEN YOU STUDY TOMORROW GO AND MEMORIZE THIS SLIDE
Systemic anaphylaxis
Rapid, onset potentially fatal allergic reaction in which antigen in the bloodstream reaches many tissues at once and triggers widespread activation of mast cells causing circulatory collapse and suffocation
Hay fever
Mistaking pollen as a threat. Then normal way of making IgE
- DC picks up pollen and senses a threat (no one knows why)
- DC activate naive T cell in LN. TFH2 arises that makes IL-4
- In LN TFH2 helps activating B switch and become plasma cells that secrete IgE
Memory T and memory B cells differentiate and live forever in the allergic person - IgE is picked up by mast cells that are sentinels in airways
Priming for allergy
First exposure to allergen induces long-lasting IgE and memory T and B cells that will respond when the allergen is re-encountered. 1st exposure goes unnoticed. But subsequent exposures are swifty and strong memory responses seen as allergy “attacks”A
Allergic memory
IgE armed mast cells live for years. Each pollen season, memory T and memory B cells will reactivate with pollen to create more IgE to arm mast cells so they may replace older ones
IgE sensitization
It is impossible to “cure” IgE allergy, but it can be blocked
Therapeutic anti-IgE literally binds the Fc portion of IgE so it will not be able to bind mast cells
Immune memory
The capacity to mount a quicker, more vigorous and very specific immune response to subsequent encounters with a pathogen. It is antigen-specific
Draw the Parham diagram
What are the four different phases of adaptive immune responses
- Primary adaptive immune response (first infection to about one month)
- Protective Immunity (repeated exposure to pathogen: aborted infections from 1-4 months)
- Immunological memory (low steady-state level of antibodies. you have long lives plasma cells and long lived memory B and T cells)
- Secondary adaptive immune response (second infection spikes more vigorously than primary response)
Primary response
First encounter with microbe that activates effectors and sets memory cells and circulating antibodies
Protective immunity
Effectors (typically Ab) quickly terminate infections
Immunology memory (stage)
Capacity to mount quick vigorous response to re-infection with specific pathogen
Secondary response (recall response)
Recall response activates memory cells and improves B cell/Ab specific for a pathogen. Leaves improved memory cells
What are the three components of immune memory?
- Antibodies from Long-lived plasma cells
- Memory T cells
- Memory B cells
What is the point of immune memory
To be on the constant vigilance for the return of an antigen. It requires constant presence of cells and antibodies that recognize specific antigen.
How do the memory components arise?
- memB arise at the end of germinal center events
- LLPC arise when plasma cells settle in the bone marrow
- memT arise during and after activation of naive T cells
What are the two ways memory T cells arise?
LINEAR DIFFERENTIATION
ASYMMETRIC DIVISION
Linear Differentiation
Memory T cells differentiate from effector T cells as antigen wanes
1. Naive T cell recognizes antigen and activates
2. Effector T cell differentiates to eliminate pathogen
3. Memory T cells derive directly from the T cell precursor
4. Effector memory cells lack CD62L and CCR7 nand migrate to nonlymphoid tissues *resident tissue
Asymmetric Division
Memory T cells differentiate from naive T cells during their clonal proliferation (activation)
- Naive T cell recognizes antigen
- Memory T-cell precursors derived directly from activated naive T cell precursors
- Central memory cells express CD62L and CCR7 and circulate through lymphoid tissues
A closer look at asymmetric division
Asymmetric division delivers signaling kinases unevenly between daughter cells
- Naive CD8 T cell is activated by specific antigen.
- Antigen activated CD8 T cell is reprogrammed and enters mitosis
- CD8 T cell undergoes asymmetric division. The daughter cell that holds mTORC1 can divide rapidly and become effectors (active metabolism)
- Daughter T cells that lost mTORC1 are use a quiet metabolism. They don’t use energy to defend (not effectors) and they don’t need constant survival signals. They persist without joining the fight and are memory cells
mTORC1 complex
signaling kinase complex that drives active metabolism for cell division and mounting effector function. Whichever daughter cell inherits mTORC1 complxes will be more immunoreactive effector cells
Memory T cells require ___, not ___, for survival
Memory T cells require cytokines, not antigen for survival
They use cytokines for SURVIVAL AND HOMEOSTATIC PROLIFERATION
Homeostatic proliferation for memory T cells
Gradual (slow) proliferation of B and T cells in absence of specific antigen that is driven by IL-7 an IL-15 and helped by intracellular anti-apoptotic factors like Bcl-2
Plasma cells (and memB) survive using ____ too
Cytokines
- The bone marrow has many survival factors to support long lived plasma cells (LLPC)
Survival factors:
Stromal cells provide a foothold so there is adhesion molecule interaction
Survival signals like IL-6, BAFF, and APRIL
Do B or T cells use IL-7 to maintain their memory cell lineage?
T cells
Also IL-15 and Bcl-2
Do B or T cells use IL-6 to maintain their memory cell lineage?
IL-6 and BAFF and APRIL
also adhesion molecules provides by stromal cells
Memory B cells persist for decades
- Memory B cells survive using cytokines and adhesion molecules like BAFF and APRIL which induce low levels of proliferation (homeostatic proliferation) by patrolling B cell follicles in secondary lymphoid tissues
- Plasma cells survive long term by using cytokines and adhesion molecules like IL-6, BAFF, and APRIL to induce low levels of proliferation in the bone marrow
Are memory cells always isotype switched?
Yes, because they are the result of the germinal center events
Do plasma cells and memory B cells use the same survival factors?
Almost. Plasma cells use adhesion molecules, BAFF, APRIL, and IL-6. MemB cells only use BAFF and APRIL
What happens when memory cells bind their antigen?
They activate. They do it ‘better’ than naive T cells and B cells
What do central memory T cells use to patrol
-L selectin (CD62L)
- CCR7
* this is the same thing naive T cells use to patrol so they patrol the same area, lymph nodes
Do the subsets of memory T cells response to antigen differently? If there are cytokines, which ones
Yes.
- When CD8 T cells bind antigen, they don’t release any cytokines but they proliferate highly (+++)
- When naive CD4 T cells bind antigen, they release IFN-y, IL-4 or IL-17 highly (+++). They proliferate a little (+)
- Tcm cell binds antigen, it doesn’t really make many cytokines (+) but it proliferates a lot (+++)
- When Tem bind antigen, it releases IFN-y, IL-4, Il-17 moderately and proliferates moderately (++)
- When Trm binds antigen, it releases a high amount of IFN-y, IL-4, or IL-17 (+++) but it doesn’t proliferate a lot (+)
List the three T subsets of memory T cells
Central memory
Effector memory
Resident memory
Central memory cells
Same patrol route as naive T cells to activate in secondary lymphoid tissue. They act more QUICKLY than naive T cells (so essentially they patrol the blood to the lymph nodes and secondary lymphoid tissue)
They (1) Proliferate vigorously when they recognize antigen
(2) differentiate into whichever T helper subset is dictates by fate-specifying cytokines (kind of a clean slate)
(3) help memory B cells with improvements in germinal center
Effector memory cells
Use integrins to patrol inflamed sites and activate when they recognize specific antigen ( blood, tissue, lymph)
Resident tissue cells
- LARGEST population of memT. They wait at barrieres where they have previously been infected
- QUICKEST in activating when a pathogen re-infects
- Can activate when they recognize specific antigen OR strong inflammatory cytokines
- They are already committed to an effector type (TH1, TH2, and TH17)
How does a secondary B cell response start?
A secondary B cell response starts in a secondary lymphoid tissue with T cell help
- Antigen flows into the B cell area of the lymph node and it is held by follicular DCs
- Patrolling memB and naive B will bind the antigen with their BCRs. They compete for the antigen
MemB have high-affinity BCR for their antigen, naive B do not.
MemB get more activation signal 1 (BCR crosslinking)
MemB endocytose more Ag and get more help from Tfh
There are more memB that can bind the antigen than naive B - Some activated memB becomes Ab-secreting plasma cell – some go to germinal centers
Why might memory T cells react quicker than naive?
- Because of their location (already at the tissue)
- Because they don’t require second and third activation signals like B7 or IL-2.
What are the reasons why memB cells will outcompete naive B cells for repeated antigens?
- MemB have high-affinity BCR for the antigen (because they’ve actually seen it). Naive B do not
means memB get more activations signal 1
means memB endocytose more Ag and get more help from Tfh - There are more memB that can bind the antigen than naive B
means greater number of memB are activated - Naive B cells express FcyRIIB1 while memB cells don’t so there is nothing stopping them even with IgG bound
Activated memB cells can enter the germinal center with the help of activated memTfh (4 things associated with every secondary response)
MEMTfh
- Activated memB undergo the unial rounds in GCs with steps 1-5
- You can have several immunizations. If so, each secondary response that involves germinal centers produces:
- high levels of secreted Ab
- Affinity maturation for higher affinity of Ab
ALSO
- Further isotype switching to other IgG sub-isotupes of IgA or IgE
- Mutated BCRs that recognize new epitopes (this broadens the specificity)
What is immunological imprinting (original antigenic sin)
- A consequence of preferentially activating memory cells over naive cells.
- The tendency to mount a more vigorous antibody response to previously recognized epitopes on antigens. It is mediated by preferential activation of memory B cells rather than naive B cells to “new’ epitopes
Does having IgG bound to the pathogen stop the memory B cell from activating?
No. The memory B cel does not have a FcgRIIB1 receptor, meaning nothing can tell it to sense IgG. This is another reason why memory B cells will be able to respond to the antigen first
Phenomenon of immunological imprinting, what is the drawback?
There is a drawback to suppressing naive B cells in subsequent encounters when a pathogen READILY mutates
1. First encounter with a pathogen. No Ab exist that bind to the viral antigens yet
2. Second encounter with a mutated variant of the same pathogen.
- IgG that binds viral antigens at the “old” epitopes
- memory B cells activate (because they are just recognizing pathogen and IgG doesn’t stop them even though its old)
- naive B cells don’t activate IgG-bound antigens bc of FcyRIIB1
So ultimately, you aren’t giving your naive B cells the chance to create antibodies against the “newer” antigens of the mutated virus.
So what is the big problem with immunological imprinting?
Basically, IgG will bind old epitopes on a virus that mutated. This will prevent naive B cells from activating and creating defenses against some of the newer pathogens. However, it doesn’t stop memory cells from seeing the pathogen with the IgG and taking it in to refine its BCR for that same old antigen that IgG detected. Essentially, the problem is that the immune system will get better and better at refining their BCR to detect the old epitope,but since the virus is mutating, that isn’t giving naive B cells the opportunity to take in other epitopes that might appear in the next mutation
Primary vs Secondary response on pathogen specific cells
Primary: Small number of pathogen-specific cells
Secondary: A large number of pathogen specific cells
Primary vs Secondary response on antibody delay
Primary: Delay before specific antibodies are made
Secondary: Specific antibodies are already present
Primary vs Secondary response on isotype switching
Primary: Starts with IgM of low to medium affinity and can eventually undergo germinal center events
Secondary: NEVER have IgM. Antibodies are isotype-switched and of high affinity
Primary vs Secondary response on activation threshold
Primary: high threshold of activation
Secondary: low activation of threshold
Primary vs Secondary response on effector cell delay
Primary: delay before effector T cells are activated and enter infected tissues
Secondary: Effector T cells are present and activated in infected tissue
Primary vs Secondary response on the relationship between the innate and adaptive immune responses/
Primary: Innate immunity works alone until an adaptive response is activated and ongoing
Secondary: There is close cooperation between innate and adaptive immunity from the start of infection
Cowpox disease is caused by
Cowpox virus
Smallpox disease is caused by
Variola virus
What was Jenner’s conclusions?
Infection with a related “weaker” virus protects from the disease that is caused by a pathogenic virus
Vaccination with related “weaker” virus protects from serious disease
What are the 3 ways to be actively immunized against smallpox?
- Actual infection with variola virus (dots)
- Infection with less virulent cowpox virus
- “Articial”/Vaccination with related weaker cowpox virus or vaccinia virus
What are the two forms of immunization
Active Immunization
Passive immunization
Active Immunization
The host’s immune system must generate immunity and long-lasting
- infection with virulent pathogen (the disease-causing agent)
- Infection with less virulent (Attenuated) agent that shares ‘protective’ antigens
- Vaccination with live, avirulent agent or killed pathogen or antigens of pathogen
Passive Immunization
Immunity is delivered to the person and is temporary
- Maternal transfer of antibodies (planetal, breastmilk)
- Medical transfer (IVIG (donating antibodies from plasma) convalescent sera (used for ebola with serum of ppl who’ve had it, therapeutic monoclonal Ab)
- Medical transfer of personalized CAR-T cells (sometimes long lasting)
Do immune boosting vitamins or antivirals count as immunization?
NO because there is no antigen-specific response that is elicity (B and T cell response)
How does cowpox virus infection protect against smallpox?
- Cowpox virus shared some antigens with variola virus. Ag-specific B cells, T cells and Ab recognized the shared antigens and prevented both viruses from causing severe disease
This is an example of CROSS-PROTECTIVE immunity to shared antigens
Whole, live attenuated vaccine
Vaccine platform that uses an intact microbe that is less virulent (due to natural attenuation or targeted mutations and attenuations). Typically, elicits the most protective immunity of all platforms but the riskiest due to chances of reversion, transmission to others, or overwhelming immunocompromised hosts
Vaccinia virus
Modern smallpox vaccines use the mysterious, animal adapted vaccinia virus
Vaccinia virus-based vaccines are currently used for monkeypox because the monkeypox virus aslo shares genes
BUT VACCINIA DOES NOT PROVIDE PROTECTION AGAINST CHICKEN POX
Vaccine doses are named by when they are given
- Prime (first dose): The first dose induces a primary adaptive immune response, protective immunity, and memory (primes protective immunity) and sets memory cells
- Essentially your first dose creates the first 3 phases of the adaptive immune response
- Boost (subsequent doses): doses that follow shorty after IMPROVE and EXPAND centrocytes and T effectors that are still in the lymph nodes! (mainly boost protective immunity bc TCR can’t be improved). The more B cells and T cells activated, the more likely that memory cells are generated
Doses that follow after a longer period activate memory B and T cells. Some B re-enter germinal centers to improve affinity and expand range (breadth) of antigen specificity. New memory cells arise as the secondary response finished and replenishes the memory pool. Includes memory B cells that are improved
Does having booster doses make more memory cells?
Yes, new memory cells arise at the end of the secondary response to replenish the pool and to include memory B cells that are improved.
Do memT cells improve their TCR?
No, never.
Childhood vaccines have boosters and are given ASAP
- Infants and children are susceptible to these diseases so they all need boosters so their immunity can last for a lifetime.
- Influenza is given every year because it mutates so often
What are the 4 vaccine platforms (4 types of vaccine)
- Live attenuated
- Killed pathogen
- Subunit
- Genetic (nucleic acids)
What is live attenuated and what are its pros and cons
Live attenuated is when you put an attenuated virus (whether natural attenuation or it was mutated) into your body to trigger an immune response
PROS:
+ Most effective
CONS:
- Least safe (reactogenic, risk of reversion and disease, risk of transmitting to others, not controlled by the immunocompromised
Four reasons why live attenuated viruses are dangerous
- Reactogenicity (side effects)
- There is a chance that if you mutated the virus to be attenuated, it can revert and cause disease
- This is transmissible
- Not good for immunocompromised people because it might not be seen as “attenuated” to them
*polio, vaccinia
What is killed pathogen vaccine and what are its pros and cons
It is where you take the killed version of a pathogen and put it in someone
PROS:
+ Safer than live
CONS:
- Requires larger dose than live
- May not induce complete response (i.e., poor CD8 T cell response)
- Not fully mimic natural infection (poor persistence of Ag)
*POOR CD8 T Cell and Poor Ag response)
* Polio, hepatitis, rabies
What is subunit vaccine and what are its pros and cons
This is when the only thing in this vaccine is a subunit of the virus that your body can recognize and build defense against this antigen.
PROS:
+ Concentrate immune response on the protective antigen (target the immune response on one antigen)
+ No risk of introducing the disease
+ Typically, less side effects depending on the adjuvant
CONS:
- May not be immunogenic (need adjuvant)
- May not induce a fully effective response
*DTaP
What is genetic (nucleic acids) vaccine and what are its pros and cons
In this vaccine, you just insert the genetic material that will encode for a specific antigen of the virus so your body makes the harmless antigen of the virus and releases it
PROS:
+ Easy to change the ‘nucleic acid instructions’ for mutated antigen
- many not be immunogenic (engineer adjuvant/MAMP into nucleic acid strand)
- may be difficult to store
- public distrust
How can live vaccines be attenuated
- Naturally attenuated to a different host, like vaccinia virus or cowpox means natural attenuation
- Recombinant DNA technology deletes or mutates virulence genes
- Long-term cell culture mutates virulence genes: pathogenic virus is isolated from a patient and grown in cultured human cells. Then the cultured virus is used to infect monkey cells. Virus acquires several mutations to allow it to grow well in monkey cells. Virus no longer grows well in human cells (attentuated) and can be used as a vaccine
COVID-19 Vaccine *Subunit
Subunit is a PROTEIN BASED vaccine
- Vaccines that contain spike antigen (protein)
Need adjuvants to stimulate innate dendritic cells for antigen presentation (immunogenicity)
- Some contain whole proteins
- Some contain protein fragments
Spike glycoprotein is the most protective antigen for neutralizing Ab that prevent entry via the ACE2 receptor on human cells
COVID-19 Vaccine *Whole, live attenuated
Created from attenuated coronaviruses that were grown in non-human cell culture and then inactivated or mutagenized with chemicals
COVID-19 Vaccine *Genetic vaccine
Deliver coronavirus genes (encoding Spike) to be expressed as antigens by host cells
- mRNA are the “genes” of coronaviruses
How COVID mRNA vaccines work
- Stabilized form of mRNA in a lipid carrier is injected. This mRNA is immunogenic and recognized by TLRs (elicit the antiviral protocol). Carried lipids also recognized as a MAMP somehow
- Human cells express mRNA to make protein ANTIGEN (if you were injected in the muscle, the antigens would appear there as well)
- Spike ANTIGEN is shed or picked up by DCs and taken to draining lymph node and presented by cDCs and FDCs
- Naive T and Naive B are activated and become effectors and memory cells
*remember the antiviral response will release cytokines to recruit immune cells for help
Viral vectored, another type of genetic vaccine
- Viruses engineered to carry DNA encoding antigen. Host expresses the antigens, typically spike ag
- Also called Genetic vectored DNA vaccine
- Adenoviral vector infects host cell and injection site. Vector delivers DNA into nucleus. Host cells express spike antigen on their surface and a similar response ot mRNA vaccine ensues
REITERATED
1. Any cell takes up the vector DNA vaccine
2. Any cell expresses viral protein
2. DC take up viral protein released by cells and presented it to naive T cells
4. Effector T cells help activate B cells so they can produce antibodies`
What exactly occurs at the site of an mRNA vaccination?
- Many host cells make spike antigen. Some release it. Local antigen presenting cells pick up the antigen or express it. They are activated by the RNA because it is a MAMP (TLRs). The Lipid carrier is also a MAMP
- In draining lymph nodes, naive B and T cells are activated bc T cells see antigen through DC and B cell activates through FDC and Tfh
- Primary adaptive response ensues
What are the 3 goals for vaccines
- Induce short-lived protective immunity in an individual
- Temporarily block reinfection and disease
- Typically, hi-affinity Ab and cytolytic T cells are responsible
- Lasts for a couple of months for COVID-19 and flu vaccines - Induce long lasting immunological memory
- Does not block reinfection, but lessens disease severity
- Due to rapid activation of MemB, MemT and LLPC secreting low levels of Ab
- Last for years or decades - Reduce disease in a population - herd immunity
- immune individuals typically shed less pathogen
- lessens likelihood of non-immune individual contracting disease
The smallpox vaccine program eradicated small pox, why was it so easy to do so?
The vaccine fulfilled the 3 goals
1) It doesn’t mutate antigens rapidly
2) Immunity in a person typically last a lifetime
3) The causative agent does not exist in animals or insect reservoir
- Didn’t have a latency period
Herd immunity
When a population does not have enough susceptible individual to support transmission of an infectious disease
What does herd immunity depend on?
- The agent
- The host
The agent
Mode of transmission (air vs sexual contact, for instance)
How easily the agent infects a host (infectivity)
Duration that an agent can spread from a host (contagious period)
Host
Susceptibility of the host (immune or not)
Behavior in the environment (winter vs. summer)* (or wearing mask, just things that people do that increase or decrease their likelihood of
Likelihood of host encountering susceptible people
First- estimate how well a disease spreads
When a new infectious agent enters a non-immune population you can measure how many people are infected and see how disease spreads
- Contact tracing, mode of transmission, and mathematical modeling of people come into contact
Basic Reproduction Rate (R0)
How many new cases will arise from 1 infected individual
The higher the R0, the more likely the infectious agent spreads
Which factors affect R0
Infectious period and mode of transmission
How do we estimate how much of the population must be vaccinated for herd immunity?
1- (1/R0) = % of the population that needs to be immune
What numerical value do we use when some of the population becomes immune and R0 is no longer useful?
Re
Effective Reproduction Number (Re)
Estimates # of cases that an infected person generates (spreads) in a partially immune population at a given time
This Re continually changes as level of immunity changes, behaviors change and the pathogen changes
Why are the Re and R0 values helpful?
Helps public health officials to set public health measures, like targets for vaccine uptake, mask wearing and limited gatherings
For instance, if measles pops up in an unvaccinated group, health officials are really concerned
Why is it so important to have herd immunity (the perk)?
Some individuals CANNOT become immune. They are always susceptible.
List of individuals who CANNOT become fully immune to vaccination
- Infants less than 3 months
- Extremely elderly
- Taking immunosuppressive drugs
to treat inflammation
to keep an organ transplant
to remove cancerous immune cells
to prepare for stem cell transplant
genetic immunodeficiency (clinical cases and AIDs) - Extremely malnourished
- People who refuse vaccination
*They can be offered passive immunity
Serotype
A strain of a pathogen that is distinguished from another strain by antibodies that bind their different surface antigens
Serogroup
Simply a group of strains that have some common surface antigens (common serotypes)
Vaccines must be _____
Immunogenic
Immunogenicity
The ability of a vaccine to elicit protective Ab and T cells that act shorts after vaccination AND patrol for years as immune memory
(ability to create an adaptive immune response)
What threats do DCs need to sense to fully activate CD4 and CD8 T cells?
- MAMPs or DAMPs
- Or strong inflammatory cytokines
- Antigen should be plentiful for sustained presentation to the T cells (on teh matter of days to weeks)
What are the 3 vaccine ingredients?
- Antigen (or nucleic acid that encodes the atnigen)
- Often ADJUVANT to activate innate immune cells (provide the THREAT)
- Preservatives/stabilizers (sometimes)
Vaccine liposome
The liposome can carry antigen or be mixed into a vaccine. It has different MAMPs (MPLA-4) and saponin (QS-21)
How do adjuvants work?
- Some adjuvants make antigen last longer so more APCs pick up antigen and present Ag better
- Some bind PRRs, NLRs/RLRs, TLRs
- Some induce fate specifying cytokines for activating T cells to differentiate into particular T helper cells
Actions of adjuvants that enhance effectiveness of vaccine
- Binding to cytosolic PRRs in antigen-presenting cells
-Causing formation of DAMPs - Inducing pro-inflammatory cytokines
-Inducing caspase-1 inflammasome activity in macrophages - Inducing fate-specifying cytokines
- Increasing the time that an antigen persists at a vaccination site
Reactogenicity
Refers to the inflammatory response that is induced by a vaccine, causing discomfort such as injection-site pain, swelling, fever, myalgia (pain in muscle group), malaise (general feeling of discomfort or illness) or headache
*side event of vaccination that usually occurs soon after being vaccinated. Typically, mild and rarely have medical consequences. It is also self limiting which means it clears up in a few days
What causes reactogenicity?*
- MAMPs or DAMPs trigger strong inflammation that causes the side effects. Innate immune cells and tissue cells sense with PRRs at the delivery site and response too “strongly”
- Pyrogenic cytokines (IL-1beta, TNFa, IL-6) and prostaglandin E2 are released
- Vasodilators (bradykinin)
- They (the soluble material above) act on pain receptors (nociceptors), the brain, blood vessels, and the liver for instance.
- Can occour quickly when interacts with the nociceptors to the brain to induce pain response or slowly when it goes through the bloodstream to the liver to promote the acute phase response
Vaccines can elicit adverse effects
Adverse effect (a very severe side effect) refers reaction (not inflammation) to the vaccine that causes serious and sometimes long lasting disease
- Allergy reaction is the most common
- Vaccines can worsen pre-existing conditions such as PANDA or autoimmune conditions
- COVID vaccine liked to fatal thrombosis and myocarditis and pericarditis
Subunit vaccines contain an ____ of interest
Subunit vaccine scontain an antigen of interest
For bacteria, the antigen of interest is sugar. high affinity IgG antibodies opsonize these capsules.
Subunit vaccines sugar antigens are often modified
Often, they will attach a protein to a polysaccharide antigen to get T cells involved.
This approach relies on linked recognition (different epitopes on the same antigen) one for B cells and a different epitope for T cells
Conjugate vaccine
A subunit vaccine that has an ANTIGEN conjugated to a carrier PROTEIN (often a harmless inactivated toxoid)
antigen could be a sugar and protein could be a harmless inactivated toxoid
Toxoid
Protein toxin that’s been inactivated by heat or chemicals so that it’s no longer toxic but retains antigen activity. In this case, it is not to make a protective response against a toxin, but to have peptide to present to T cell (carrier protein) and elicit help for sugar-specific B cells
*essentially only activates T cells so it can formed the linked recognition/cognate pair so it can help B celsl that actually have sugar antigen. Also need T cells so the B cells can enter the germinal center and have high responses
Types of polysaccharide conjugate vaccines
- HibC vaccine against pneumonia caused by Haemophilus influenzae
- Polyvalent pneumococcal vaccine for infants for pneumonia caused by Streptococcus Pneumoniae
- Meningococcal vaccine against meningitis caused by Neisseria meningitidis
Pathogens that challenge vaccines
- Pathogens that mutates quickly
- Complex life cycle
- Can jump to non human reservoirs
- Novel pathogens
- Pathogens that attack the immune system
- Pathogens that evade immunity
Vary the antigen
- Many strains of a pathogen (serotypes mean that they have different outer antigens)
- Mutate easily (like RNA virus)
3 ways that pathogens evade immunity
- Vary the antigen
- Hide from the immune system
- Actively modify the immune system
These last 2 strategies often result in chronic infections - the pathogen is not fully cleared by the immune response
Hide from the immune system - as latent infection
- Not replicate means little or no antigen to detect
- Hide in cells that don’t present much antigen (like neurons)
*Can cause chronic infection
Actively modify the immune response - immunoevasins
- Interfere with antigen processing/presentation
- Interfere with cytokine communication or subvert it (dampen it so it’s less serious)
*Can cause chronic infection
Latent infection
Involves little or no expression of antigen and escapes immune recognition
Chronic infection
Resists quick elimination and not fully cleared by the immune response
How do vaccines try to solve the problem of antigenic variation among strains
Streptococcus pneumoniae
To protect against multiple strains… make a polyvalent vaccine that has many antigen sin it
Adults polysaccharide vaccine (PPSV23): polysaccharides from 23 serotypes
Children polysaccharide conjugate vaccine (PCV13) - polysaccharides from 13 common serotypes, each conjugated to diphtheria toxoid for T help like the HibC vaccine approach
Polyvalent vaccines are _____ vaccines that contain many ___ to elicit immunity to all included ____
Polyvalent vaccines are multivalent vaccines that contain many antigens to elicit immunity to all included antigens
Why are RNA viruses that constantly mutate antigen a challenge?
Influenza virus
RNA viruses that mutate constantly due to error-prone replication by RNA polymerases cause antigenic drift by point mutations
When strains are in the same cell, they will exchange genome segments called antigenic shift by new gene segments
What do hemagluttinin and neuramindase bind to?
These are the antigen receptors of influenza
- Hemagglutinin binds to the ACE2 receptor on human cells
- Neuraminidase helps the virus fuse to the cell wall and also leave
Antigenic drift
Common in RNA viruses like influenza and the coronavirus
- Due to error-prone replication of RNA genome.
- Antigenic drift causes seasonal epidemics.
- Point mutations in RNA changes the structure of viral surface antigens. This causes slightly different strains of influenza viruses to appear each year
Antigenic drift plays a role in immunological impringing
Due to antigenic drift, antigenic molecules contain “old” epitopes and “new” epitopes
Antigenic shift (MANY antigens vary)
Due to exchange of RNA genome segments in a co-infected host cell
Antigenic shift trades ENTIRE antigenic molecules (not just creates new epitopes) between strains like a new hemagglutinin
–> now you have no antibodies at all to any of these epitopes because it is essentially like a new virus. At least with drift, the antigen was just changing a bit so some epitopes still worked)
Antigenic shift causes seasonal pandemics because large portions of the population are not immune to the new antigen (has a large R0)
Change the vaccine to keep up with mutating antigens
To make an effective flu vaccine… you must constantly change the antigens
Each year, polyvalent vaccines are based on recommendations by an Advisory Commitee that looks at prevalent strains for Type A and Type B influenza viruses
Immunoevasins is how viruses modify the immune system. Can you name what they interfere with?
- Innate responses
(like IFN responses)
(like inflammatory responses) - Adaptive responses
(like Ag recognition)
(like actions of Ab)
Diagram on page 44 - how do immunoevasins interfere with the interferon response in the anitviral response
Typically, there is supposed to be
- Production of additional interferons that act on other uninfected cells
- Production of restriction factors that block viral replication in the interferon-activated cells
Herpesvirus and why is it such an effective virus
Herpesvirus family
- Extensive family of enveloped dsDNA (VERY IMPORTANT)
- carry immunoevasins
- can hide from immune surveillance
Herpesvirus and latency
Latent infection is a challenge
These viruses avoid detection by effector T cells,, NK cells, and memory T cells
NO REPLICATION - LITTLE or NO ANTIGEN TO DETECT
Herpes simplex viruses:
HSV-1 infects epithelial cells at the nose and mouth, then it travels to the facial ganglia nerve where it goes latent
Latency
The full viral genome is in the host, but its expression is dramatically restricted, such that a few viral antigens and no viral particles are produced. Latency can last for a lifetime, or the virus can reactivate (stress, poor nutrition, stimulation of the cell, hormone changes). Reactivation is followed by an active infection with replication and expression of antigens. Goes latent again in the case of HSV
ICP47 (HERPES) and US6 (for HCMV)
Immunoevasisn that interfere with MHC I peptide loading
They block antigen presentation by preventing peptide movement through the TAP peptide transporter
ICP47 stops peptides from passing through on the inside
US6 stops peptides from passing through on th outside
*inside outside refers to the location in the cytosol or ER
E19 (Adenovirus)
E19 takes the place of tapasin, but it fails to hold empty MHC I correctly. So the MHC I is not loaded, and it is trapped on the ER
*HEAVY ON THE MHC I
Many DNA viruses target cytokines
- Vaccinia virus uses a IL-1Beta receptor to trick actual IL-1B to bind to the decoy instead of the actual receptor
-Epstein Barr induces its own IL-10, ebvIL-10, to down regulate immune activity even if there isn’t supposed to be IL-10 there
The failure with herpes virus vaccines thus far
To make an effective herpesvirus vaccine to reduce disease and shedding you need an antivrial CD8 T cell to control it
Vaccines have failed due to poor immunogenicity
- Glycoprotein subunit vaccines
- Attenuated live virus vaccines
- DNA vaccines
Vaccines against mononucleosis and EBV-induced cancers have failed in neutralizing
- Subunit vaccines based on glycoprotein failed pre-clinical trial
Viruses present unique challenges
- Obligate intracellular microbes hid from antibodies and complement
- Hijack host cellular machinery
- Look much like us to innate immune cells
HIV present more challenges
- A latent provirus phase when no antigen is expressed
- Infects and kills immune cells that are central to adaptive immunity
- Readily mutates antigen which evades protective Ab and T cells
What are the three key features of HIV particle
- Spike for cell entry (key antigen)
- Reverse transcriptase
- Integrase
HIV has an envelope and trimeric spikes that protrude to bind and infect host cells
Retro
Refers to the fact that it has an RNA genome that is reverse-transcribed to a DNA intermediate (backward to retro from the usual direction of nucleic acid instructions)
Lenti
Means slow. It refers to the fact that lentiviruses cause persistent, slowly progressing disease
Make sure you can label the HIV graph on slide 6 of week14/15
HIV-1
Originated in chimpanzees, more virulent (quicker progression; guaranteed death if not treated)
HIV-2
Originated in sooty mangabeys; causes slower progresing disease but still deadly
Do both HIV-1 and HIV-2 cause death?
Yes, the only difference is where they originated and how quickly the virus progresses
Fluids that transmit HIV
- Blood
- Semen and pre-seminal fluid
- Rectal fluid
- Vaginal fluids
- Breast milk
- Fluid must come in contact with a mucous membrane, damaged tissue, or injection with a needle
So its easy to transmit through sex, drug use, breastfeeding, childbirth, in utero (from mother to fetus), contaminated blood products
Actions that do not spread HIV
Hugging
Kissing
Sharing toilet. seats
Through air
Shaking hands
Sweat
Tears
Saliva
Sharing dishes
Mosquitoes, ticks, or other insects
Host is typically infected at a mucosal surface
- DCs and macrophages use innate phagocytic receptors (PRRs) to bind to HIV at barrier
- DC-SIGN and Mannose Receptor easily bind with sugars on the gp120 spike of HIV for phagocytosis
- Then DC’s carry the virus to the nearest secondary lymphoid tissue - An HIV virion MUST infect al; CD4-expressing cell to start an infection
- Plenty of CD4+ T cells, macrophages, and DCs in the lymph node
HIV infects cells that express a combination of 2 receptors
An immune cell must express 2 receptors to be permissive for infection
1. CD4
2. Chemokine Receptor (CCR5 or CXCL4) - referred to as a co-receptor for the virus
What are the two antigens for HIV
gp120 and *gp41
Which cells are the target for HIV
CD4 expressing cells like macrophages, DCs, and CD4 T cells
R5 virus
Also known as M-tropic
1. CD4 receptor
2. Targets cells expressing CCR5 such as
- Macrophages
- Dendritic cells
- Tem cells
- Trm cells
- TH1
- TH17
X4 virus
Also known as T-tropic
1. CD4 receptor
2. Targetes cells expressing CXCR4
- Naive T cells
- Tcm
Successful infection of HIV permanently incorporates a silent ____ into the cell’s DNA
Successful infection of HIV permanently incorporates a silent provirus into the cell’s DNA
What is the co-receptor for HIV referring to?
The chemokine receptors CCR5 and CXCR4
How does HIV infect a CD4 expressing cell
- Virion binds to CD4 and co-receptor on T cell (CCR5 or CXCR4)
- Viral envelope fuses with the cell membrane, and viral genome enters cell
- Reverse transcriptase copies viral RNA genome into double stranded cDNA
- Viral cDNA enters nucleus and integrates into host DNA
This cell is now “latenlty” infected even though its different than the Epstein Barr latency
Provirus
The DNA form of a retrovirus when its INTEGRATED into the host-cell genome. In this state it is (transcriptionally inactive for a long time)
How do CD4 T cells replicate HIV once the virus is no longer latent
- The first thing that occurs is that the T cell has to be activated normally from recognizing antigen or cytokine
- NF-kB (and NFAT which is primarily used by T cells) are also TFs for provirus genes (so the T cell normally uses this. It is unknowingly transcribing the provirus)
- Viral Tat and Rev proteins (that are being transcribed from provirus) start automatic viral replication and bidding from the cell
- Tat amplifies transcription of viral RNA. Rev increases transport of RNA to cytoplasm
- Gag, Pol, and Env are made and assembled with viral RNA into virions which bud from the cell
- The immune cell dies in the process
Are all CD4 expressing cells able to allow for HIV replication
No, this is why its mainly done in CD4 T cells
Productive infection
The active expression of viral enes, assembly, and assembly and release of infections virions
*essentially making more of the virus
How can we detect the presence of HIV (aka how would we know its not latent anymore)
A productive infection is detected as the presence of HIV antigens in the bloodstream
Once you start having some virions floating, they can enter more CD8 T Cells causing catastrophic damage and high multiplying numbers of the virus
Does HIV continually seek out infection in new cells?
Yes, any cell that previously had HIV will die and fairly soon.
Pathogenesis
How a disease develops
4 phases of HIV disease
- Viremia - first phase of HIV infection that is marked by high levels of viral particles in the bloodstream, often present with flu-like symptoms
– Seroconversion: when an infected person first has pathogen-specific antibodies detected in their blood - Asymptomatic phase (aka clinical latency) no symptoms, variable length of time, strong enough CD4 T cell response for threats
- Symptomatic phase - # of CD4 helper T cells insufficient to protect against opportunistic pathogens and cancers and many diseases arise as a result
- AID is diagnosed when CD4 T cell counts in blood fall below 200/uL in the bloodstream
A silent battle rages during the ASYMPTOMATIC phase
- The battle is raging in secondary lymphoid tissues (Lymph nodes and spleen)
- Antigen-presenting cells hold virions on their surface, like FDCs. Or infected macrophages and DCs that activate produce virions
- So, CD4 T cells are continually being infected adn killed as they activate. VAST numbers of CD4 T cells are produced and die here. It is an improtant reservior for the host
What is the reservoir for the HIV virus?
The secondary lymphoid tissues
An adaptive immune response controls, but doesn’t eliminate HIV
There are not enough CD4 T cells to help the immune responses here because the CD4 T cell population has been continuously diminished by the HIV infection
DRAW THE GRAPH
Do you directly die from AIDS?
AIDs patients do not die directly from the HIV virus
They die from other pathogens or cancers that they cannot control when HIV destroys T-cell mediated immunity
David Kirby
AIDs activist
Antiretroviral drugs are required for survival from AIDs
Drugs stop viral replication and decrease infectious virions in the blood. 2 weeks after starting cART, th eload of virus drops to just 5%
Antiretroviral drugs attack multiple targets simultaneously
The virus is always mutating drug targets, so multiple drugs are combined 9cART)
The drugs stop activities durign infection and active replication
UNFORTUNATELY cART drugs have no effect on the provirus stage of the infection
-cART can inhibit viral entry
- cART can inhibit reverse transcriptase
- cART can inhibit viral integrase
- cART can inhibit protease
- cART can inhibit viral assembly
Why does cART have so many attempts to inhibit things?
Because HIV mutates all of the time so it wants to make sure there’s no way it can inhibit all of its important functions, especially those that need to be conserved.
How long do you have to be on cART?
Forever
After a few weeks of cART, only CD4+ memory T, some macrophages and DCs remain infected. As they slowly activate, they express the infectious virion.
By taking cART, CD4+ T cells will not be able to take up this virion, but if you stop taking it, the problem will start again.
Rare infected individuals resists AIDs with broadly neutralizing Ab
A minority of HIV-infected individuals develop Ab that neutralize many strains of HIV (broadly neutralizing AB, bnAB)
Discovery of such bnAB have raised the possibility of using Ab as an anti-HIV treatment
bnAB
Ab that neutralize many strains of HIV since HIV mutates so often. (typically bind to conserved sites of spike that cannot mutate without losing function)However, there are certain parts that need to stay conserved like binding to the CD4 receptor
Rare individuals lack the CCR5 co-receptor for HIV infection
CCR% delta 35 mutations deletes a stretch of the CCR5 gene, and about 1% of people of European descent do not express CCR5. They are resistant to HIV infection
What are 3 possible solutions for handling HIV?
- cART
- bnAB
- lacking CCR5 (mutation CCR5delta35)
- CRISPR to remove pro-virus
Can we develop effective gene therapy approaches for HIV?
Unfortunately, a bone marrow transplant is an unrealistic and risky treatment for the estimated 38 million people living with HIV today
CRISPR-based gene therapy (EBT-101) delivered by adenoviral AAV9 vector to remove the provirus from infected CD4 T cell is directed to HIV-1 LTR U3 upstream promoter regions.
*Would remove the provirus
Immunological tolerance is based on ____
Antigens
It is the failure to respond destructively to an antigen. Meaning there is no Type 1,2, or 3 T cell response
Also, it’s a failure to mount an immune response
Immunological tolerance
Failure to mount an adaptive immune response against an antigen
How does the immune system use its rules to become tolerant and not respond against certain antigens?
- Self vs. non-self theory
- 2-sginal theory
- Infectious non-self theory
- Danger model
Self vs. non-self theory
Remove self-reactive B and T cells; hide self antigens
2-signal theory
Require different cells to sense the threat (APCs, cognate recognition)
Infectious non-self theory
Limit co-stimulation (B7) to a few cells that sense a threat; inactivate T and B cells that bind antigen without costimulation (B7)
Danger model
Require tissues to agree there is credible danger using DAMPs
Protect some tissues by dampenign their danger signals
Many self-tolerance mechanisms operate at the same time
- Central tolerance
Peripheral tolerance: - Antigen segregation (physical barrier to self antigen across to lymphoid system)
- Peripheral anergy (cellular inactivation by weak signaling without costimulation)
- Regulatory T cells
- Functional Deviation (differentiating to create regulatory T cells)
- Activation induced death
- Immunologically privileged sites
Central tolerance
Is mediated by eliminating immature, self reactive B or T cells in primary lymphoid tissue (bone marrow and thymus)
Peripheral tolerance
Is mediated by many mechanisms that limit activation and actions of. B cells and T cells in the periphery (anywhere outside of the bone marrow)
First: remove most self-reactive B and T cells by negative selection
Central tolerance only occurs in bone marrow or thymus
- Negative selection deletes MOST self-reactive T and B cells (clonal deletion)
- Self reactive B cells may change their receptor specificity
- Some immature T cells are re-programmed to be suppressive nTreg that recognize self-Ag
Is central tolerance sufficient to remove all self reactive T and B cells?
No, some escape into the body
Also, somatic hypermutation that occurs in germinal centers generates some self-reactive B cells
Negative selection continues in the periphery for B cells
Deletion of transitional B cells occurs mainly in the spleen
- Transitional B cells that bind antigen will die
- The reason is because if a B cell binds antigen shortly after entering the body without BAFF, it is more likely that it is binding self-antigen as opposed to foreign antigen. So its safer to eliminate it
All four of the ___ are used in the ___ to ensure immunological tolerance
All four of the rulse are used in the periphery to ensure immunological tolerance
Which rule is used in central tolerance
Self vs. non-self
Peripheral T cell anergy based on lack of 2 signals
In lymph nodes, if B7 isn’t there to also activate the mature naive T cell that binds antigen, the T cell becomes anergic
Anergic
A deactivated T or B cell but not dead, but it can’t respond to the antigen that it binded. Can be due to inactivation of signaling enzymes or loss of high affinity IL-2 receptor chain so that the T cell does not proliferate in response to antigen
Peripheral deletion of centrocytes based on lack of 2 signals
B-2 centrocytes ned CD40L co-stimulation or they die during affinity maturation
What happens if the BCR on the a centrocyte did somatic hypermutation and now it can bind self antigen
The requirement for linked recognition by the cognate Tfh prevents this newly self-reactive cell from survingin because Tfh doesn’t recognize a self-antigen
Peripheral deletion/inhibition of ACTIVATED T cells
CTLA-4 sends out inhibitory signals and dominated B7 to slow costimulation
T cells that have been activated for a long time express Fas. This binds to FasL on APCs and induces programmed cell death of activated T cells
PD-1 too !
Peripheral regulatory tolerance by regulatory T cells
Self-reactive Tregs are made in the thymus and periphery
Both types of Treg effectors activate when they bind self-antigen
Their effector function remains the same, its to suppress the APC they are bound to and the other T cells on the same APC
Tregs make IL-10 and TGF-beta to supress neighboring reactive T cells
Can retinoic acid induce Tregs
Yes it induces iTregs with the help of TGF-beta
Some tissues are immune privileged
- Immune privileged means poorly immunogenic which means its tolerogenic
- They are usually segregated from most T and B cells and lymph nodes
Brain
Eye
Testis
Uterus
What are ways tissues ensure they are immune privileged?
Healthy tolerogenic tissues express
- suppressive cytokines
- FasL
- fate-specifying TGF beta (suppresses inflammation and TH1 and TH2 responses)
- avoiding sending Ag to draining lymph nodes.
The eye is an example of an immune privileged tissue
Multiple factors cause this:
- constant TGF-beta
- Limited release of Ag to draining lymph nodes
- Little MHC presentation on cells in the eye
- Healthy eye tissue express FasL and PD-1 (also tells T cells to die) that kill activated T cells that bind to them (induce AICD)
Autoimmunity is the consequence of broken ____ _______
Autoimmunity is the consequence of broken self tolerance
Regulatory tolerance is crucial. Give an example of the inactivation of an important gene and what its results would be
Rare genetic mutations inactivate FOXP3 gene
Infants with this immunodeficiency lack all FoxP3
They suffer widespread autoimmunity and allergy syndrome, IPEX
This is fatal within a year
Symptoms such as:
Dermatitis
Diarrhea and gut inflammation
Type 1 diabetes
Failure to thrive
Food allergy
The only cure is a hematopoietic stem cell transplant to reconstitute stem cells that can make functional FoxP3 and become regulatory T cells
Central tolerance is crucial. What would happen if you couldn’t get this?
Rare genetic mutations inactivate AIRE gene
People lacking AIRE do not delete tissue-specific cells
Symptom :
glands and ovaries are attacked by T cells and autoantibodies (Addison’s disease , infertility, hypoparathyroidism)
Widespread inflammation of mucosal membranes, skin, organs leads to damage (liver disease, renal disease malnutrition)
Autoantibodies to IL-17 and IL-22 interfere with Type 3 immunity to fungi (susceptible to opportunistic fungi)
Prognosis:
incurable. a bone marrow or thymus transplant wont work sometimes
APECED
Lack of AIRE function leads to release of many tissue reactive B cell (which in turn allows for tissue reactive B cells)
Injury can break tolerance and cause autoimmune attack
Injury can release antigen (like from eye) and DAMPs that cause inflammation and activate DC
Dendritic cell would take the eye antigen and activate self-reactive T cells
Then, self-reactive effector T cells find the inflamed injury and patrol ALL nearby tissue and attack
In rarre instances, both eyes are attacked, although one is injured, due to recognition of ocular antigen (sympathetic opthalmia)
