1. The branch that breaks Is called rotten, but Wasn’t there snow on it? Bartolt Brecht Haiti after a hurricane

2. Your body has evolved complex mechanisms of recognizing “non- self” and fighting against it

3. The Immune System is the Third Line of Defense Against Infection

4. Antibodies are Produced by B Lymphocytes (B cells to their friends)

5. T Lymphocytes (T cells) provide “cell based” immunity

6. Lymphocyte Origins 16-22

7. Let’s start with the role of B cells and antibodies in the immune response

8. Some definitions are in order Antigen A substance produced by a pathogen (e.g., protein, complex sugar) capable of producing an immune response

9. Some definitions are in order Antibodies Protein molecules (immunoglobulins) produced by B lymphocytes to help eliminate an antigen

10. Molecular Biology of the Cell Alberts et al B cells Make Antibodies In response to antigens

11. Molecular Biology of the Cell Alberts et al These antibodies can bind to and “neutralize” Viruses or can direct immune attack of virus-infected cells

12. Molecular Biology of the Cell Alberts et al Antibodies can also direct phagocytosis of pathogens

13. Cytotoxic (Killer) T Cells Recognize, Attack and Kill Virus-Infected Cells CELLS alive!

14. Let’s focus first on antibodies Molecular Biology of the Cell Alberts et al

15. Antibodies are proteins that have evolved to recognize molecules from pathogens

16. These molecules from pathogens are called Antigens

17. Molecular Biology of the Cell Alberts et al The variable and constant regions of antibodies are related = Ig domains

18. Constant Region Hypervariable Region Light Chain Heavy Chain Antigen Binding Region Let’s use as an example an antibody that recognizes a protein on the surface of flu (influenza) virus courses.washington.edu/medch401/pdf_text/401_07_lect2.ppt

19. Hemagglutinin Here is the antibody Bound to the “antigen” = influenza hemagglutinin Human antibody

20. Rotate ~90  Add all atoms The antibody recognizes the antigen by a lock-and-key fit

21. Antigen residues at the interface = epitope Epitopes are typically ~5 residues long This interaction is VERY specific

22. hemagglutinin antibody Space-filling mode Grey now = mainchain of hemagglutinin Epitopes reside in turns and loops This interaction is VERY specific

23. You can generate antibodies against HIV like you do against other viruses

24. Molecular Biology of the Cell Alberts et al Given thousands of pathogens each of which is constantly evolving how do we generate antibodies against each?

25. Molecular Biology of the Cell Alberts et al We cannot dedicate all 25,000 genes in the genome just to make antibodies. What’s the solution?

26. Molecular Biology of the Cell Alberts et al We cannot dedicate all 25,000 genes in the genome just to make antibodies: What’s the solution? Put antibodies together by a mix-and match approach!

27. Molecular Biology of the Cell Alberts et al requires rearranging the DNA

28. Molecular Biology of the Cell Alberts et al requires rearranging the DNA

29. Molecular Biology of the Cell Alberts et al The result: An antibody light chain

30. Since there are multiple types of each gene segment, there are thousands of possible V-D-J combinations Each B cell gets a unique combination

32. Other mechanisms further increase antibody diversity Molecular Biology of the Cell Alberts et al

33. When a pathogen enters the body it stimulates proliferation of the specific B Cells that recognize its Antigens

34. Once you are exposed to an antigen your B cells “remember” this

35. CELLS alive! OK, that explains antibodies and B cells but what about us?

36. Molecular Biology of the Cell Alberts et al T cells carry antibody-related proteins on their plasma membranes called T cell receptors

37. Molecular Biology of the Cell Alberts et al T cell receptors are also assembled by gene rearrangement, creating great diversity

38. However, T cell receptors cannot recognize antigens from pathogens alone

39. Molecular Biology of the Cell Alberts et al T Cells Only Recognize Antigen when it is presented by another cell

41. Antigen presentation is done by another family of proteins called MHC proteins

42. Molecular Biology of the Cell Alberts et al Viral or bacterial proteins are digested by Cellular proteases inside the cell and pieces of them bind the MHC proteins

43. Molecular Biology of the Cell Alberts et al This allows T cells to recognize HIV infected cells, for example, and even internal proteins like reverse transcriptase can serve as antigens

44. Molecular Biology of the Cell Alberts et al Here is where our old friend CD4 comes into the picture

45. Let’s come back to the immune response to HIV

46. People initially mount a strong immune response

47. However, this response ultimately fails for five reasons

48. Antigenic escape Inaccessible epitopes Downregulating MHC Destruction of CD4+ T cells Integration and latency

49. We already discussed two of these Antigenic escape Inaccessible epitopes Downregulating MHC Destruction of CD4+ T cells Integration and latency

50. First, the ability to integrate into the host genome allows HIV to lurk undetected

51. Second, by killing CD4+ Helper T Cells HIV ultimately disables both antibody production and Killer T cells

52. What about the other three means HIV uses for immune evasion? Antigenic escape Inaccessible epitopes Downregulating MHC Destruction of CD4+ T cells Integration and latency

53. One way HIV “hides” is by hiding its most “antigenic” regions Antigenic escape Inaccessible epitopes Downregulating MHC Destruction of CD4+ T cells Integration and latency

54. Most antibodies against the virus do not block viral entry

55. Why not?

56. Regions of gp120 and gp41 key for viral entry are hidden until after the shape change we discussed

57. Natural selection also shapes the sequence of viral proteins Antigenic escape Inaccessible epitopes Downregulating MHC Destruction of CD4+ T cells Integration and latency

58. Remember that while reverse transcriptase is an amazing Enzyme, there was something it lacks—which was….

59. Remember that while reverse transcriptase is an amazing Enzyme, there was something it lacks—which was….

60. This has major consequences RT makes 1 error /10,000 bp =1 error per replicated genome And since the viral generation time Is 2.5 days and one infected cell produces ~10 10 –10 12 new VIRIONS each day…..

61. Do the numbers!

62. Given that billions of cells are infected per day There will be thousands of copies of EVERY possible mutation Present in the gene pool!!

63. Recombination adds to the amount of variation Many cells are co-infected by two or more viral variants and RT can switch between viral templates when copying the genome

64. Remember these sequence based “trees” we used to study the evolution of different HIV and SIV strains?

65. We can use the same approach to study the evolution of a single virus after it infects a single person

66. Viral diversity in 9 AIDS patients HIV rapidly evolves into different “strains” after the initial infection

67. How could That happen?

68. Can you say Natural selection?

69. We start with the tremendous amount Of viral variation caused by RT errors

70. Now we add the selective pressure Exerted by the immune response +

71. In response to antibody selection Mutations accumulate in gp120 and gp41

72. T cell selection selects for changes in peptide “epitopes” so they no longer bind to MHC proteins

73. The result: despite high levels of anti-HIV antibodies viral variants escape from the immune response

74. HIV also has one more trick Antigenic escape Inaccessible epitopes Downregulating MHC Destruction of CD4+ T cells Integration and latency

75. Remember our discussion of Long-term non-progressors: Some are infected with a mutant HIV virus lacking the accessory gene Nef

76. What does Nef do?

77. Nef prevents infected cells from putting MHC proteins on their cell surface!

78. Without MHC proteins infected cells become Invisible to T cells

79. Molecular Biology of the Cell Alberts et al This allows T cells to recognize HIV infected cells, for example, and even internal proteins like reverse transcriptase can serve as antigens This formidable array of defense mechanisms Allows HIV to avoid being suppressed by our immune system Antigenic escape Inaccessible epitopes Downregulating MHC Destruction of CD4+ T cells Integration and latency