1. General information 455 LSA, Tuesday 11 to noon Anytime after class email: lcoscoy@berkeley.edu Use MCB150 as subject line Please only quick (yes/no) questions

2. Bone marrow Thymus Spleen Lymph nodes T-cell precursors Naive T-cells (CD8 or CD4) Cell mediated immunity

3. Bone marrow Thymus Spleen Lymph nodes T-cell precursors Naive T-cells (CD8 or CD4) Cell mediated immunity Infection Dendritic cells Antigens

4. Bone marrow Thymus Spleen Lymph nodes T-cell precursors Naive T-cells (CD8 or CD4) Cell mediated immunity Infection Dendritic cells Antigens Effector T-cells Memory T-cells

5. B Cell T Cell APC Antigen Recognition by B and T lymphocytes

6. CellsMHC Class IMHC Class II T cells+++- B cells++++++ Macrophages++++++ Dendritic cells++++++ - MHC Expression APCs

7. APC Naïve CD8 T-cell Naïve CD4 T-cell A simple view of T-cell mediated immunity Key APCs are activated Dendritic cells in 2' immune organs After initial activation, T cells differentiate into effector cells and can be activated in lymphoid organs and periphery.

8. APC Naïve CD8 T-cell Naïve CD4 T-cell Effector CD4 T-cell Effector CD4 T-cell Macrophage B-cell Activation Memory CD4 T-cell A simple view of T-cell mediated immunity APCs still activate effector Th cells. APCs still activate effector Th cells.

9. APC Naïve CD8 T-cell Effector CD8 T-cell Infected cell Naïve CD4 T-cell Killing Memory CD8 T-cell A simple view of T-cell mediated immunity Target cells activate effector CD8 + Tc (CTLs). Target cells activate effector CD8 + Tc (CTLs). ( Target cells can be any Class I MHC expressing cell.) ( Target cells can be any Class I MHC expressing cell.)

11. Antigen Processing and Presentation Laurent Coscoy MCB 150

12. Activation of T cells APCs determine which peptides will be presented on Class I and Class II MHC during initial activation. APCs determine which peptides will be presented on Class I and Class II MHC during initial activation. T cells need to be able to distinguish between external antigens (taken up by APCs) and internal antigens (infected cell). T cells need to be able to distinguish between external antigens (taken up by APCs) and internal antigens (infected cell).

13. What is Antigen Processing? Enzymatic process of degrading proteins through proteases into antigenic peptides. Enzymatic process of degrading proteins through proteases into antigenic peptides. Antigen processing requires energy (ATP) and movement of endocytic vesicles. Antigen processing requires energy (ATP) and movement of endocytic vesicles. Cell fixation experiments demonstrated that antigen processing was an active process. Cell fixation experiments demonstrated that antigen processing was an active process.

14. Cellular Compartments Exogenous Antigens vs Endogenous Antigens Endogenous proteins in cytosol or in secretory vesicles. Exogenous proteins come in through endosomes.

15. Two Antigen Processing Pathways Endogenous antigens in cytosol presented on class I MHC molecules to CD8 + T cells. Endogenous antigens in cytosol presented on class I MHC molecules to CD8 + T cells. Exogenous antigens in endosomes presented on Class II MHC molecules to CD4 + T cells. Exogenous antigens in endosomes presented on Class II MHC molecules to CD4 + T cells.

16. Endogenous Antigens Cytosolic Pathway

17. Endogenous Antigens Generation of Class I MHC Peptides Endogenous antigens are from proteins produced inside the cell. Endogenous antigens are from proteins produced inside the cell. These includes self protein antigens and foreign protein antigens. These includes self protein antigens and foreign protein antigens. Class I MHC antigens activate cytotoxic CD8 T cells for killing infected cells and tumor cells. Class I MHC antigens activate cytotoxic CD8 T cells for killing infected cells and tumor cells.

18. Endogenous Antigens Cytosolic Pathway Covalent conjugation to Ubiquitin Ubiquitin targets proteins to Proteasome Ubiquitin proteasome pathway for cytosolic protein degradation in general.

19. Endogenous Antigens Proteasome The proteasome is a cylindrical shaped catalytic protease complex of 28 subunits for cytosol ic protein degradation. The proteasome unfolds proteins and then cleaves proteins into peptides and amino acids. Conserved throughout the eukaryotes and the archaebacteria

20. Endogenous Antigens LMP2 and LMP7 LMP2 and LMP7 are proteasome subunits that are encoded within the MHC. LMP2 and LMP7 are proteasome subunits that are encoded within the MHC. Interferons (IFNs) increase expression of LMP2 and LMP7. Interferons (IFNs) increase expression of LMP2 and LMP7. LMP2 and LMP7, along with LMP 10, appear to have specialized role for increasing the production of peptides that have the preferred sequence for Class I MHC binding. e.g. 7-10 amino acids with a hydrophobic carboxy residue. LMP2 and LMP7, along with LMP 10, appear to have specialized role for increasing the production of peptides that have the preferred sequence for Class I MHC binding. e.g. 7-10 amino acids with a hydrophobic carboxy residue. How many peptides are generated in a cell?

21. Endogenous Antigens Generation of Class I MHC Peptides

22. Endogenous Antigens TAP proteins TAP proteins (Transporters associated with Antigen Processing) TAP 1 and TAP 2 form heterodimer in membrane of ER to facilitate selective transport of peptides from cytoplasm into lumen of ER. TAP pump preferentially transport peptides with a length of 8–15 amino acids

23. Endogenous Antigens Generation of Class I MHC Peptides

24. Calnexin is a chaperone protein that binds to newly synthesized  - chain Class I MHC and retains the Class I MHC until Beta 2- microglobulin binds.

25. Tapasin and Calreticulin both bind to the newly formed Class I MHC complexes, Tapasin forms a bridge between connecting the TAP proteins with the Class I MHC molecules. Endogenous Antigens Generation of Class I MHC Peptides

27. Endogenous Antigens Peptides Required for Class I MHC Stability Peptides bind to the Class I MHC molecules and allow release from tapasin and calreticulin. Peptides bind to the Class I MHC molecules and allow release from tapasin and calreticulin. Peptide binding provides stability for Class I MHC to allow transfer to surface. Peptide binding provides stability for Class I MHC to allow transfer to surface. Do you remember how peptides bind MHC-I molecules

28. Endogenous Antigens Peptide Trimming After Proteasome Though a majority of Class I peptides are ready after leaving proteasome as much as 15% still need trimming. Though a majority of Class I peptides are ready after leaving proteasome as much as 15% still need trimming. Cytosolic proteases have been identified that can trim NH 2 terminal after proteasome. Cytosolic proteases have been identified that can trim NH 2 terminal after proteasome. Recent data indicate that peptides can be trimmed in ER to fit in Class I MHC pocket. Recent data indicate that peptides can be trimmed in ER to fit in Class I MHC pocket.

29. How do internal membrane proteins or secretory proteins enter Class I MHC pathway? Membrane or secreted proteins can be presented in Class I MHC but must be degraded in the cytosol. Membrane or secreted proteins can be presented in Class I MHC but must be degraded in the cytosol. Membrane-bound proteins after synthesis directly into ER can return through retrograde translocation to the cytosol for degradation. Membrane-bound proteins after synthesis directly into ER can return through retrograde translocation to the cytosol for degradation.

30. CD8+ T c Activated by Endogenous or Intracellular Antigens Effector CD8+ T c (CTLs) are primarily needed for killing in infected cells. Effector CD8+ T c (CTLs) are primarily needed for killing in infected cells. CTLs can also be activated against cancer cells (tumor) targets. CTLs can also be activated against cancer cells (tumor) targets.

31. CTL Killing of Infected Target Cells Viruses must replicate inside cells and many bacteria and parasites live inside host cells. Viruses must replicate inside cells and many bacteria and parasites live inside host cells. Therefore antigens for stimulating CTLs come from inside the cell because they signal an intracellular infection. Therefore antigens for stimulating CTLs come from inside the cell because they signal an intracellular infection.

32. RMA-S TAP Deficient Cell Line RMA-S Mouse tumor cell line found to have mutation in TAP and resultant decreased Class I MHC expression and resistance to CTL killing. RMA-S Mouse tumor cell line found to have mutation in TAP and resultant decreased Class I MHC expression and resistance to CTL killing. In absence of TAP Class I MHC molecules are unstable and translocated back to cytosol and degraded. In absence of TAP Class I MHC molecules are unstable and translocated back to cytosol and degraded. Class I MHC expression and killing restored by addition of exogenous peptide or transfection with TAP. Class I MHC expression and killing restored by addition of exogenous peptide or transfection with TAP.

33. CTL Lysis of RMA-S Cells 0 10 20 30 40 50 60 70 Normal RMA-S TAP Transfection of TAP back into RMA-S Cells (RMA-S +TAP ) restores killing of RMA-S targets by tumor specific CTLs. Can also be restored with addition Of exogenous peptide % lysis 30:1 10:1 3:1 1:1 CTL:Target Ratio

34. TAP Deficient Humans Nonsense mutation in TAP-2 gene inherited with MHC haplotype. MHC haplotype. Results in low Class I MHC expression. "Tatiana" was homozygous for MHC alleles. How is CD8 T-cells count affected? MHC-I

35. Immune Evasion Viruses interfere with Class I MHC expression to escape killing by CTLs Herpes Simplex Virus (HSV) protein ICP47 can selectively bind to TAP and inhibit the transfer of peptides into ER. Herpes Simplex Virus (HSV) protein ICP47 can selectively bind to TAP and inhibit the transfer of peptides into ER. Transfection of ICP47 alone caused decreased Class I expression. Transfection of ICP47 alone caused decreased Class I expression. Hill et al 1995 Nature 375:411 Fruh et al 1995 Nature 375:415

36. Exogenous Antigen Pathway Endocytic processing pathway

37. Cellular Compartments Exogenous Antigens vs Endogenous Antigens Endogenous proteins in cytosol. Endogenous proteins in cytosol. Exogenous proteins come in through endosomes. Exogenous proteins come in through endosomes.

38. Peptides bound to MHC Class II molecules are derived from engulfed pathogens (also self proteins and internalized TM proteins) Acidification of endocytic vesicles activates proteases that degrade proteins into fragments. These peptide fragments are loaded onto MHC class II molecules How are peptides generated?

39. Trafficking of MHC class II molecules What prevents MHC class II from binding peptides in the ER? MHC class II  and  chains associate in the ER In the trans golgi network, MHC class II is sorted into vesicles These vesicles deliver MHC class II to specialized compartments where peptide loading occurs

40. Exogenous Pathway Invariant chain Invariant chain (Ii) binds to Class II MHC molecules in ER to prevent endogenous peptide binding. Invariant chain (Ii) binds to Class II MHC molecules in ER to prevent endogenous peptide binding. Ii is cleaved to leave a peptide fragment (CLIP) in the binding groove. Ii is cleaved to leave a peptide fragment (CLIP) in the binding groove. CLIP (CLass II associate Invariant chain Peptide).

41. Ii is cleaved to leave CLIP peptide in Class II MHC Groove Ii binds to Class II MHC molecules in the ER to prevent peptide binding. Signals in the cytoplasmic tail of Ii lead to proper sorting of MHC class II CLass II Associated Invariant Chain Peptide (CLIP) How is CLIP peptide removed?

42. Exogenous Pathway HLA-DM HLA-DM (H-2M in mice) is a Class II like MHC molecule that binds to and stabilizes empty Class II molecules. HLA-DM (H-2M in mice) is a Class II like MHC molecule that binds to and stabilizes empty Class II molecules. HLA-DM helps in the release of CLIP fragment so that antigenic peptide can bind. HLA-DM helps in the release of CLIP fragment so that antigenic peptide can bind.

43. Ii Chain Prevents Newly synthesized self proteins from binding Class II MHC groove until Class II MHC is in endosomes. What would an HLA-DM deficient cell look like?

44. Exogenous Pathway Class II MHC Peptide Loading Class II MHC loading takes place in endosomes where acidic pH is required for exchange of peptides. Class II MHC loading takes place in endosomes where acidic pH is required for exchange of peptides. Invariant Chain is degraded and CLIP is exchanged with foreign peptide. Invariant Chain is degraded and CLIP is exchanged with foreign peptide. Chloroquine can be used to raise vesicular pH and block loading of Class II MHC. Chloroquine can be used to raise vesicular pH and block loading of Class II MHC.

45. CD4+ T h Activated by Exogenous Antigens Foreign antigens/extracellular pathogens need to be taken up by APCs to get noticed by immune system and activate Th cells. Foreign antigens/extracellular pathogens need to be taken up by APCs to get noticed by immune system and activate Th cells. Thus, APCS serve as sentinels or extra barrier to get immune system activated. Thus, APCS serve as sentinels or extra barrier to get immune system activated.

46. Class II Deficiency in Humans Class II deficiency is an autosomal recessive trait caused by defects in transcription factors controlling Class II expression (lack HLA-DR and DQ). Class II deficiency will also reduce number of CD4+ T cells Class II deficiency will also reduce number of CD4+ T cells - Why? And lower levels of antibodies Why?

47. Immune Evasion Class II MHC Viral Inhibition of Class II MHC Adenovirus interferes with Class II upregulation in APCs. Adenovirus interferes with Class II upregulation in APCs. HSV binds Class II HSV binds Class II HIV interference with Class II processing. HIV interference with Class II processing. Pathogens that evade lysosomes Intracellular Leishmania & mycobacteria (tuberculosis) reside in their own vesicles. Intracellular Leishmania & mycobacteria (tuberculosis) reside in their own vesicles.

48. Comparison of Pathways

49. How are T cell antigens kept apart? Location, Location, Accessory Proteins Class I and Class II MHC molecules both traverse through ER to cell surface but load peptides in different cell compartments. Class I and Class II MHC molecules both traverse through ER to cell surface but load peptides in different cell compartments. Control is through accessory proteins. Control is through accessory proteins. Class I requires TAP Tapasin etc control. Class I requires TAP Tapasin etc control. Class II requires low pH for removal of Ii. Class II requires low pH for removal of Ii.

50. CD1 Proteins Class I Like MHC Molecules CD1a-e are nonpolymorphic Class I like molecules that associate with  2m. CD1a-e are nonpolymorphic Class I like molecules that associate with  2m. CD1 present a limited number of bacterial glycolipid antigens to T cells. CD1 present a limited number of bacterial glycolipid antigens to T cells (e.g., mycolic acid from M. tuberculosis).. Bacterial cell wall lipids make excellent innate immune targets because they are not easily mutated. Bacterial cell wall lipids make excellent innate immune targets because they are not easily mutated.

51. CD1 Antigen Presentation CD1 proteins have hydrophobic binding groove for hydrocarbon chains of lipid tails. CD1 proteins have hydrophobic binding groove for hydrocarbon chains of lipid tails. Hydrophilic sugar end or lipid head of antigen available for T cell binding. Hydrophilic sugar end or lipid head of antigen available for T cell binding.

52. CD1 Antigen Processing Jayawardena-Wolf and Bendelac 2001Curr Opin Immunol 13:109 CD1 proteins sample lipid antigens in different compartments. Lipid and glycolipid antigens still require processing.

53. Processing of Class I and Class II vs CD1 Antigens