final Flashcards
how do we manage to stay healthy
manybarriers need to be crossed (physical and immunological)
Most infections are prevented by physical barriers
If viruses bypass these physical barriers, a series of immune responses are engaged
coordinated host response (4 steps)
1) continuous (most immediate)
* Physical barriers: These may seem primitive but these barriers block majority of infections
2) immediate
* Intrinsic barriers: These are cell-autonomous responses and can be achieved by a single cell in isolation
3) innate
* minutes/hours
* Induced by infection
* Non specific response
* Natural killer cells
4) hours/days (last thing to happen)
* Adaptive response: Tailored to pathogen so a Specific response
* T cells
* B cells
how do individual cells detect a virus
Receptor-mediated recognition of MAMPs (microbe-associated molecular patterns)
most cells will interact with MAMP on the pathogen and cause a change in the cellular behaviour triggering the innate immune response
intrinsic responses: PRR action and examples
Pattern recognition receptors recognize MAMPs
These receptors may be located on the host cell surface, endosomal membranes, cytoplasmic or secreted
Examples include membrane bound Toll-like receptors (TLRs) and cytoplasmic NOD-like receptors (NLRs), RIG-1 like receptors (RLR) and protein kinase R (PKR)
intrinsic responses: MAMP
Microbe associated molecular patterns
Macromolecules that are shared among groups of microorganisms and recognized as foreign to the host
Examples of MAMPs include dsRNA peptidoglycan, LPS, flagellin, viral proteins
intrinsic responses: MAMP + PRR result
- leads to signalling events that ultimately activate transcription factors such as NFkB and the interferon regulatory factors IRFs
- results in expression of cytokine genes such as the inflammatory cytokines and Type I Interferon (IFNs)
RIG1 + MDA5
intracellular viral PRRs: intrinsic response
Cytoplasmic RNA helicases that function as RNA sensors
RIG1: detects 5’ triphosphate RNA without 5’ cap
Mechanism
1) RIG1 held in inactive conformation via intramolecular interactions (phosphorylated)
2) in addition to dephosphorylation by PP1, RIG1 is activated by ubiquitylation of its CARD protein at the C-terminal domain, ubiquitinated RIG1 binds to MAVS (which are receptors on mitochondria)
3) the RIG complexes that are ubquitinated induces expression of activators that enter the nucleus and promote expression of IFNs and pro-inflammatory cytokines to induce antiviral state
MDA5: detects dsRNA
Mechanism
1) in uninfected cells, CARD domains on MDA5 are phosphorylated: inactive conformation
2) binding of viral RNA, CARDs are dephosphorylated by specific phosphatases; active conformation
3) in their active conformations, RIG-1, MD5 are targeted to the mitochondrial antiviral signalling protein (MAVS)
What examples of how viruses evade RIG1 and MDA5 responses
1) sequestration or modification of viral RNA ligands
2) manipulation of post-translational modifications on RIG1, MDA5, MAVS
3) cleavage of RIG1, MDA5, MAVS
4) sequestration or delocalization of RIG1, MDA5
protein kinase R (PKR)
intracellular viral PRRs: intrinsic response
Sensor for viral dsRNA, inhibits cap-dependent translation by eIF2
eiF2 brings in initiator methionine in a GTP bound form to initiate translation then changes conformation to GDP and releases so cycle can start again
Translation arrest by the dsRNA-activated protein kinase PKR
When PKR binds to viral dsRNA, it undergoes dimerization and autophosphorylation which leads to its activation
Activated PKR phosphorylates the alpha-subunit of eIF2 which causes it to remain in an inactive GDP-bound form (blocks translation)
Inactive GDP-bound eIF2 is not able to recruit Met-tRNA leads to an arrest of translation, translation arrest may lead to apoptosis
Examples of how viruses evade PKR responses
Some viruses may also use of eIF2 independent translation mechanisms
Viral proteins may promote activation of protein phosphatase = keeps eIF2 in a non-phosphorylated state
Viral protein PKR antagonists will inhibit PKR which will activate translation
cGAS
intracellular viral PRRs: intrinsic response
Mechanism
1) cyclic GMP-AMP synthase binds to viral dsDNA in the cytoplasm (host knows dsDNA shouldn’t be in cytoplasm)
2) following DNA binding, cGAS generates cyclic GMP-AMP (cGAMP)
3) cGAMP binds and activates STING which is located on the ER, STING dimerizes and is further activated by ubiquitylation
4) activated STING translocates to perinuclear structures where it promotes expression of Type 1 IFNs and pro-inflammatory cytokines
What are some examples of how viruses evade these responses
1) viral manipulation of STING post-translational modifications
2) cleavage of STING
3) prevent/limit cGAS sensing of nucleic acid ligand
innate response: complement system
the complement system consists of a series of serum proteins that circulate in the blood in inactive forms and are activated in a sequential manner when there is an infection to promote pathogen cytolysis and inflammation
Serum proteins activate each other to do 3 things:
1) opsinin: substance that binds microbial surface that enhances uptake by phagocytic cells
2) formation of membrane attack complex: pore within membranes which leads to lysis
3) inflammation: production of cytokines and recruitment of immune cells to the site of infection
innate immune response: NK cells, progenitors, activity, virus modulation of NK activity
Hematopoietic stem cells (HSC)
* lymphocytes are derived from precursor cells known as HSCs in the blood in bone marrow where they mature through hematopoiesis
Natural killer cells
* Front line of innate defence, ready to recognize and kill infected cells by releasing perforins and granzymes that generate pores in the target cell membrane which leads to caspase-mediated cell death
* don’t recogize antigens, recognize MHCs
Normal cell: MHC I on normal cell is recognized by NOK inhibitory receptor = no cell death
Infected cell: lack of MHC I on infected cell can’t stimulate an inhibitory signal = cell death
Virus encoded mechanisms for modulation of NK cell activity
* expression of viral protein similar MHC I
* activation receptor antagonist
* stimulating cytokines by binding of viral factor or functioning as a receptor antagonist
innate + adaptive immunity: protection vs eradication strategies
Innate immunity + protection against infection = antiviral state
Innate immunity + eradication of established infection = killing of infected cell
Adaptive immunity + protection against infection = neutralization
Adaptive immunity + eradication of established infection = killing of infected cell
major cells of adaptive immune response
lymphocytes: B + T cells
B cells and T cells have receptors that recognize foreign antigens
Each lymphocyte has a unique antigen receptor, meaning that they each recognize a specific antigen
Interaction of antigen with its corresponding antigen receptor initiates signalling cascades within the lymphocyte, that promotes cell proliferation, differentiation and activation of effector functions of the lymphocyte in order to defend against the foreign invader
**dendritic cells **
bridge the innate and adaptive response they are phagocytic cells and present antigen to T cells in order to initiate the adaptive response, they are called antigen presenting cells (APCs)
lymphoid progenitor -> cells for adaptive response -> B cells
myeloid progenitor -> most cells in innate response
adaptive immunity: progenitor -> activated lymphocytes
- Each lymphoid progenitor gives rise to a large number of lymphocytes each bearing a distinct antigen receptor (different kinds of T cells = dif receptors)
- Some of the lymphocytes react with self antigens (autoimmune disease)
- but are normally eliminated before they become fully mature ensuring tolerance to self antigens
- When a foreign antigen interacts with the receptor on a mature naive lymphocyte that cell is activated and starts to divide and creates many identical progeny all of whose receptors bind the same antigen
- Antigen specificity is thus maintained as the progeny proliferate and differentiate into effector cells
- when antigen is eliminated by effector cells some lymphocytes are retained to mediate immunological memory but most will lyse
how are adaptive immune responses initiated (dendritic cells)
requires antigens to be presented by antigen presenting cells (APCs), ie dendritic cells, to specifically T cells
- immature dendritic cell is phagocytic and will uptake antigens then process them into peptides that will be loaded onto MHC molecules that hold foreign pathogen peptides
- dendritic cells will take info (peptide) and present it to the adaptive response as an antigen (it is now mature dendritic cell)
- MHC presentation of antigen triggers cytokine secretion as a result (cytokines can activate T cell differentiation/polymerization as well)
- the mature dendritic cell (no longer phagocytic) migrates to the lymph node as it displays peptide loaded MHC molecules and can now bind to/activate naive T cell
- TCR-MHC-peptide engagement leads to T cell activation and differentiation
ensuring migration to the physical location of lymph node ensures interaction between naive T cells and dendritic cells
dendritic cells: class 1 vs class 2 MHC pathway
- Class 1 MHC pathway
- Antigens found in the cytosol of the APC bind to MHC class 1 molecules
- MHC1 complexes are recognized by receptors on the CD8 + T cells
- antigen proteins are endocyzed into immature dendritic cells -> cytosolic protein is tagged -> proteasome breaks down protein into peptides -> peptides enter ER vis TAP and interact with MHC via TAP -> MHC1+antigen are brought to membrane and are placed in PM of APC)
- Class 2 MHC pathway
- Antigen peptides found within intracellular vesicles of the APC bind to MHC class 2 molecules
- Peptide MHC class 2 complexes are recognized by antigen receptors on the CD4 + T cell
- Endocytosis of extracellular antigen protein into vesicle -> protease found within vesicle break it down -> ER releases MHC2 and invariant chains into protease vesicle where antigen peptides and MHC2 interact -> vesicle binds to PM and presents MHC2+antigen extracellularly
T cell co-receptors
The T cell co-receptors are required for T cell signalling
The T cell co-receptors are CD4 and CD8
They are transmembrane glycoproteins that bind to MHC molecules on APCs and facilitate T cell signalling
Mature T cells express either CD4 or CD8 (they don’t express both)
CD4 cells only bind to MHC2
CD8 cells only bind to MHC1
Each type has specific effector function
adaptive immunity: cell mediated
Cell mediated immunity
Mediated by cytotoxic T cells and NK cells
defends against intracellular pathogens in non-phagocytic cells
Helper T cells are CD4 and interact with MHC2 APCs
cytotoxic T cells are CD8 and interact with MHC1 APCs
Tc cells:
infected non-phagocytic cells (epithelial cells) will present antigens via the MHC1 pathway -> Tc cell CD8 interacts with MHC1 -> will release granuoles that cause the host cell to undergo apoptosis
NK cells:
natural tendency is to kill cells (even if not infected), have activate and inhibit receptors, 2 ways to interact (kill or not kill)
not kill: activatory receptor + host ligand as well as inhibitory receptor + MHC1 -> if sense MHC1 will disengage
kill: if MHC1 is absent NK cells will be triggered to release cytokines that cause apoptosis of host -> that way if virus tricks Tc cells by downregulating MHC1 it will still be killed, and if it is infected and is presenting normal amounts of MHC1 then Tc cells will eventually recognize it
adaptive immunity: T cell roles in mediated vs humoral
Naive T cells undergo development in the thymus (no interaction with foreign antigen yet), will become mature in thymus
(when introduced first to APC with MHC1 then become Tc cells (increases CD8), MHC2 becomes helper T cells (increase CD4))
humoral
CD4 T cells are important in humoral immunity bc when interact with B cells causes change in B cells (which release antigens that inhibit cytoplasmic pathogens) AND release of cytokines
Cytokines will activate the maturation of CD8 cells in the lymph node
T cells humoral
cytoxic T cells (CD8) will activate via the cytokines from CD4 T cell activation as well as the direct interaction with MHC1s on non-phagocytic cells (ie. epithelial cells) and cause apoptosis of the infected host cell to kill intracellular pathogens
CD8 vs CD4 effector mechanism
CD8 T cells effectors
* Engagement of CD8 Tcell via interaction with MHC1 causes direct release of granuoles that have perforin (forms pores), granzymes (proteasome that targets BID and pro-caspase 3) and serglycin
* granuole binds to host cell releasing enzymes
* granzyme cleaves BID causing mitochondrial disruption and cleaves the inhibitor of the DNAse
* host DNA chewed up by DNase
* cleaved DNA causes release of cytochrome C into cytosol which activates apoptosis
CD4 T cell effector functions
CD8 does most of the antiviral work but requires CD4 to activate via cytokines
CD4 subset important for establishing viral defence (also roles in activating macrophages)
B cell antibody isotopes, roles, variation
Different antibody isotopes serve different roles in the humoral immune response
Different antibodies have different isotypes
Fab = antigen binding fragment (recognizes the antigen)
Fc = crystallizable fragment (interacts with cells)
When B cells interact with helper T cells and cytokines it causes differentiation into plasma cell and antibody secretion
Antibodies allow neutralization (prevents adherence), opsonization (promotes phagocytosis) and complement activation (enhances opsonization and lyses bacteria)
Antigenic variation inhibits:
antigen processing
complement system
innate immunity
viral patterns of infection
Acute (short term infection)
Virus particles produced, symptoms appear, infection is cleared
Persistent (latent)
Periodic episodes of acute infections followed by quiescent phase (no detection of viral particles), reactivation stimulated throughout host life (may result in virus particle production)
Persistent (asymptomatic)
Virus production continues for the life of the host or in tissues where immune cells do not often patrol
Persistent (pathogenic)
Period of years separates primary infection and fatal appearance of symptoms, production of virus particles may be continuous or not detectable throughout life (HIV, rabies)
Incubation period
period of time before symptoms of disease appear following initial infection
During this period viral genomes may be replicated and innate immune responses initiates production of cytokines
Incubation periods can vary depending on the virus
acute infection
Pattern of infection whereby virus particles produce rapidly and infection is resolved relatively quickly by the immune system (short term infection)
Antibodies and memory lymphocytes produced during the adaptive response provide lasting protection to subsequent infections
Adaptive immune responses are intimated if infection reaches a certain threshold
Threshold level of virus required to activate adaptive immune response
persistent infection
- viral infection is not cleared by the immune system (long-term infection)
- While there is no single mechanism for a persistent infection, when viral cytopathic effects are minimized and host defences are suppressed a persistent infection may be likely
- a feature of establishing persistent infection is the reduction of host defences ie. modulation of the adaptive immune response may perpetuate a persistent infection
- ex. Viral gene products may block presentation of viral peptides within MHC 1 complexes at several steps within the pathway (ie. lowering expression of MHC1 genes, proteasome-derived viral peptides, and transport to cell surface)
- Initial infection site can differ from where pathogenesis is (ie. rabies)
latent herpes simplex virus
human herpesvirus
* Enveloped viruse
* dsDNA genome
* Transmission saliva, sexual content, maternal-neonatal
* Primary site of infection; epithelial mucosal cells, latency established in sensory ganglia
*
* latency:
* Viral genome persists within the infected cell to ensure productive infection may be initiated at a later time, ensures that virus progeny may be transmitted to new hosts
* Viral gene products may not be continuously synthesized (or synthesized in small quantities)
* Cells that contain the viral genome may be poorly recognized by the immune system
* viral genome may be a non replication chromosome in non dividing cell, autonomous replicating chromosome in dividing cells or integrated into host chromosome
*
* Reactivation depends on specific virus
herpes virus latency mechanism
- Infection in epithelial cells at mucosal surfaces
- Virus enters sensory neurons, transported to the neuronal cell body via microtubule-based systems
- Viral DNA is released into the neuronal nucleus and circularizes
- Circular viral DNA in the neuronal cells nucleus expresses mRNA -> latency associated transcript (LAT) that inhibit host lytic genes
- LATs allow latent infection by blocking transcription of lytic genes which contributes to gene silencing to maintain latent site
After immune response controls the epithelial infection the virus persists in latent state in the sensory neurons
Factors such as hormonal changes environmental stress may reactivate the virus
Virus can then travel down the axons of the sensory neurons and re-infects the epithelial tissues
Immune responses are re-activated and controls local infection by killing epithelial cells producing a new sore
