Lecture 13 Immunology and disease: parasite antigenic diversity

Today: Benefits and mechanisms of antigenic variation Antigenic variation that allows pathogens to persist in the individual host they’ve infected Antigenic variation that allows pathogens to infect hosts with prior exposure

Benefits of antigenic variation 1.Persist in infected host Let’s look at some experimental results…

Experimental evolution Manipulates 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 We’ll 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 1-27 The two main classes of MHC molecules present antigen from cytosol (MHC class I) and vesicles (MHC class II) Review

Figure 3-23 MHC class I molecule presenting an epitope

Figure 1-30

CTL escape CTL 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/transport A 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/transport fmr mcf

CTL escape: interfering with processing/transport Proteasomes 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/transport Changing 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 binding Several 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 binding Lymphocytic 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 binding Later, 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 binding SIV/macaques is used as a model system for HIV since you can’t 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 binding Ten 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 binding The 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 system’s ability to see that epitope

Benefits of antigenic variation 2. 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 3 In the simplest case, each antigenic variant acts like a separate parasite that doesn’t cross-react with other variants

Figure 11-1 part 2 of 3

Figure 11-1 part 3 of 3

Benefits of antigenic variation 2. Infect hosts with prior exposure 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

Figure 11-2 part 1 of 2

Figure 11-2 part 2 of 2

Benefits of antigenic variation 2. Infect hosts with prior exposure Antigenic drift is caused by point mutations in the hemagglutinin and neuraminidase genes, which code for surface proteins Every 2-3 years a variant arises that can evade neutralization by antibodies in the population Previously immune individuals become susceptible Most individuals still have some cross-reactivity and the ensuing epidemic tends to be relatively mild (but still kills 100s of thousands per year!)

Benefits of antigenic variation 2. Infect hosts with prior exposure Antigenic shift brings in an all-new hemagglutinin or neuraminidase gene to a naïve population Can lead to severe infections and massive pandemics like the Spanish flu of 1918.

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?