lecture 11 immunology and disease: parasite antigenic diversity

Lecture 11

Immunology and disease: parasite antigenic diversity

RNAi interference video and tutorial (you are responsible for this material, so check it out.)

http://www.pbs.org/wgbh/nova/sciencenow/3210/02.html

http://www.nytimes.com/2006/10/03/science/03nobel.html?em&ex=1160107200&en=7cbf3cd9027a96ea&ei=5087%0A

Benefits of antigenic variationTo understand why parasites vary in the ways they do, it helps to break down the potential benefits provided by variation

But first, what about the potential disadvantages?(think in terms of trade-offs)

So, what are the benefits?

Benefits of antigenic variation

Why, fundamentally, is it of benefit to a parasite to extend the length of infection or re-infect hosts with prior exposure?

Benefits of antigenic variationExtend the length of infection

Initial infection stimulates immune response against dominant antigens

In some cases (e.g. measles virus) this response is sufficient to clear infection

If the parasite can evolve new variants, it can stay one step ahead of the immune response and maintain a vigorous infection

The host must generate a new response against each escape mutant (parasite with altered genotype that allows for immune escape)


There are a variety of mechanisms parasites use to generate novel antigens or evade immune response:

-Mutation

-Recombination

-Differential expression of archived variants

-Latency

-Subversion of immune response


Some viruses, like HIV, escape by changing their dominant epitopes to evade CTL response.

Even though such changes may arise only rarely in each replication, the huge population ensures that the epitope space is efficiently explored

Both mutation and recombination may play a role in immune escape. Well explore HIV evolution in detail later

Figure 11-29

Experimental evolutionManipulates the environment of a population and then looks at the resulting patterns of evolutionary change

Allows for the direct study of the selective forces that shape antigenic diversity

Well focus on CTL escape, which gets us down to the level of single amino acids changes that can mean life or death for both hosts and parasites

Figure 1-27The two main classes of MHC molecules present antigen from cytosol (MHC class I) and vesicles (MHC class II)

Review

Figure 3-23MHC class I molecule presenting an epitope

Figure 1-30

CTL escapeCTL pressure favors escape mutants, pathogens with amino acid substitutions in their epitopes that make them escape recognition. Substitutions can lead to escape in three ways.

They can interfere with processing and transport of peptides.

They can reduce binding to MHC molecules.

And they can reduce the affinity of TCR receptor binding.

CTL escape: interfering with processing/transportA study of murine leukemia virus showed that a single amino acid substitution in a viral peptide can alter the cleavage pattern, and hence epitope presentation, and hence CTL response

MuLV is an oncogenic retrovirus

There are two main types (MCF and FMR)

Both types are controlled in large part by CTL responses, but with different immunodominant epitopes

The immunodominant CTL epitope for MCF is KSPWFTTL

CTL escape: interfering with processing/transportfmrmcf

CTL escape: interfering with processing/transportProteasomes are hollow multiprotein complexes. They are like meat-grinders for pathogen proteins found in the cytosol

Cellular proteasomes continuously chop up proteins into smaller peptides, for presentation by MHC

Proteasomal cleavage patterns determine which bits of pathogen peptides get to the cell surface

CTL escape: interfering with processing/transportChanging KSPWFTTL to RSPWFTTL introduces a new cleavage site (the proteasome likes to chop after R)

Viruses with RSPWFTTL are cleaved right within what would otherwise be a great epitope, leading to a huge reduction in the abundance of the R-containing epitope available for MHC presentation

Inspection of the nucleotides reveals that this escape is mediated by a single point mutation!

End result: that epitope is unavailable to MHC and the CTL response to FMR type is weak

CTL escape: reducing MHC bindingSeveral studies report mutations that reduce peptide-MHC binding

This can either prevent MHC from dragging the peptide successfully to the cell surface, or from holding on to it once there

CTL escape: reducing MHC bindingLymphocytic choriomeningitis virus (LCMV) is an RNA virus that naturally infects mice

Infection can be controlled or eliminated by a strong CTL response

Puglielli et al. used an LCMV system with transgenic mice that expressed an MHC molecule that binds a particular epitope of LCMV (GP33-43)

After infection, an initial viremia was beaten down by CTL pressure

CTL escape: reducing MHC bindingLater, virus titers increased. Were escape mutants to blame?

The late viruses indeed had a V to A substitution at the 3rd site of the epitope.

This substitution nearly abolished binding to the MHC molecule expressed by the mice

CTL escape: reducing MHC bindingSIV/macaques is used as a model system for HIV since you cant experimentally infect humans to study the arms race between HIV and humans

Escape from CTLs appears to be a key component of the dynamics and persistence of infection within hosts

Allen et al. (2000) studied 18 rhesus macaques infected with SIV

CTL escape: reducing MHC bindingTen of the monkeys expressed a particular MHC, and these all made CTLs to an epitope in the Tat protein in the acute phase of infection

Shortly after, the frequency of these Tat-specific CTLs dropped off

Sequencing showed that a majority of these animals had mutations in the Tat viral epitope that destroyed binding to the MHC

There was little variation outside of the epitope

End result: positive selection to block MHC binding

CTL escape: reducing TCR bindingThe LCMV system also shows examples of single amino acid changes that can lead to a decline in affinity for the TCR

Tissot et al (2000) showed that a Y to F substitution in one immunodominant epitope obtained during experimental evolution in vivo caused a 100-fold reduction in affinity for the TCR

End result: escape mutation that destroys the immune systems ability to see that epitope


Other viruses, like hepatitis C virus, escape by evading the host antibody response

In most cases, a persistent infection is established, with high variability in the envelope protein indicating positive selection

Both HIV and HCV make use of high mutation rates to stay ahead of the adaptive immune responses in the host-parasite arms race


Antigenic variation in trypanosomes allows them to escape immune surveillance

Trypanosoma brucei, the agent of sleeping sickness changes its dominant antigenic surface glycoprotein about once every hundred cell divisions

This occurs not through mutation, but through differential expression of a huge pool of variant genes already present in the genome

The surface of a trypanosome is covered with variant-specific glycoprotein (VSG)There are about 1000 different VSG genesUpon initial infection, antibodies are raised against the VSG initially expressed

A small number of trypanosomes spontaneously change VSG via gene conversion, and the new variant growsAs the new variant grows, the whole cycle is repeated, leading to successive waves of parasitemia and clearanceWears out your immune system and leads to coma


Several other important pathogens also sample from a pool of archival genomic variation

Borrelia hermsii, the spirochete that causes relapsing fever, swaps expression sites of a surface lipoprotein leading to waves of fever

Plasmodium falciparum expresses the var gene within erythrocytes. The gene product is expressed on cell surface influencing recognition by host immunity. Clones switch between pool of var variants


Some viruses persist in vivo by ceasing to replicate until immunity wanes

During latency the virus is not transcriptionally active, and causes no disease

Because its not producing viral peptides, it cannot be disposed of because it cannot be recognized

Figure 11-4 Initial infection by herpes simplex virus in the skin is cleared by an effective immune response

But residual infection persists in sensory neurons

When the virus is reactivated, the skin is re-infected. This can be repeated endlessly

Benefits of antigenic variation1. Extend the length of infection

Why do sensory neurons remain infected?First, because the virus remains quiescent, few viral proteins are produced and hence there are few virus-derived proteins to present on MHC class ISecond, neurons carry low levels of MHC class I molecules making it harder for CTLs to recognize and kill them.

Why would neurons have low MHC I expression?


Low level of MHC I expression may be beneficial to the host since it reduces the risk that neurons, which cannot regenerate, will be attacked inappropriately by CTLs.


Some pathogens resist destruction by host defense mechanisms or even exploit them

Mycobacterium tuberculosis, for example, is taken up by macrophages but prevents the fusion of the phagosome with the lysosome, effectively hiding from antibody-mediated immunity

Many viruses, particularly DNA viruses, subvert various arms of the immune system

How would you do this if you were a virus?


One way is through inhibiting MHC class I synthesis or assembly

Figure 11-5 part 3 of 3

Benefits of antigenic variation2. Infect hosts with prior exposure

Hosts often maintain memory against prior infections, generating a selective pressure for parasites to vary

Cross-reaction occurs when the host can use its specific recognition from a prior exposure to fight against a later, slightly different antigenic variant

Good vaccines are ones that have excellent cross-reactivity (e.g. measles virus)

Figure 11-1 part 1 of 3In the simplest case, each antigenic variant acts like a separate parasite that doesnt cross-react with other variants


A more dynamic mechanism of antigenic variation is seen in influenza virus

Antigenic drift is caused by point mutations in the genes encoding surface proteins

Antigenic shift is caused by reassortments leading to novel surface proteins


Antigenic drift is caused by point mutations in the hemagglutinin and neuraminidase genes, which code for surface proteinsEvery 2-3 years a variant arises that can evade neutralization by antibodies in the populationPreviously immune individuals become susceptibleMost individuals still have some cross-reactivity and the ensuing epidemic tends to be relatively mild (but still kills 100s of thousands per year!)


Antigenic shift brings in an all-new hemagglutinin or neuraminidase gene to a nave population

Can lead to severe infections and massive pandemics like the Spanish flu of 1918.

lecture 11 immunology and disease: parasite antigenic diversity

Documents

kspwfttlctl escape

escape mutant parasite

new response

ctl responses

ctl responsemulv

potential benefits

cytosol mhc class

antigenic diversitywell