Lecture 11 Immunology and disease: parasite antigenic diversity

1. Lecture 11Immunology and disease: parasite antigenic diversity

2. 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

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

8. Benefits of antigenic variation • To 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?

9. 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?

10. Benefits of antigenic variation • Extend 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)

11. Benefits of antigenic variation • Extend the length of infection • 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

12. Benefits of antigenic variation • Extend the length of infection • 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. We’ll explore HIV evolution in detail later…

13. Figure 11-29

14. 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

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

16. Figure 3-23 MHC class I molecule presenting an epitope

17. Figure 1-30

18. 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.

20. 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

21. CTL escape: interfering with processing/transport mcf fmr

22. 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

23. 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

24. 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

26. 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

27. 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

29. 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

30. 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

31. 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

33. Benefits of antigenic variation • Extend the length of infection • 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

34. Benefits of antigenic variation • Extend the length of infection • 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

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

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

37. Benefits of antigenic variation • Extend the length of infection • 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

38. Benefits of antigenic variation • Extend the length of infection • 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 it’s not producing viral peptides, it cannot be disposed of because it cannot be recognized

39. 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

40. Benefits of antigenic variation 1. 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 I • Second, 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?

41. Benefits of antigenic variation 1. Extend the length of infection • 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.

42. Benefits of antigenic variation 1. Extend the length of infection • 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?

43. Benefits of antigenic variation 1. Extend the length of infection • One way is through inhibiting MHC class I synthesis or assembly…

44. Figure 11-5 part 3 of 3

45. 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)

46. 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

47. Figure 11-1 part 2 of 3

48. Figure 11-1 part 3 of 3

49. 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

50. Figure 11-2 part 1 of 2