1. Chapter 3: Antigen Recognition by T lymphocytes TCR T H 1 - T Helper cell type 1 T H 2 - T Helper cell type 2 T C or TCL - cytotoxic T cell

2. Mechanism of Self-tolerance Positive selection = bind to self Double selection = bind to strongly to self

3. Two Types 1) TCR  and TCR   T cells  TCR  and TCR   T cells Antigen Binding site - V  and V  Similar to Fab fragment T-cell Receptor

4.  T cells - Recognize MHC:peptide complex - Diverse Functions A) Stimulate other immune cells B) Cytotoxic - kill infected host cells - Cell:cell interactions  T cells - Dominant T-cell in epithelial tissue (only 1-5% in circulation) - Recognizes more than MHC:peptide - Not well characterized Functions and Properties of T Cells

5. Antigen-Recognition site = Peptide:MHC Recognition site Single V region - CDR1-3 for each chain All TCRs on a single T cell are the same Different T cells express different TCRs Diversity mechanisms like BCRs

6. Figure 3-3   No Ds in V  gene DJ first then VDJ in  gene rearrangement Occurs in the Thymus

7. Figure 3-8  -chain locus is within  -chain locus Fewer V segments then  and  Two D segments can be incorporated

8. Functional T-cell Receptor Complex Core complex CD3 complex:  ,   (zeta) chain Function of CD3 and  : Transport Signal Transduction Invariant Chains Avidity

9. PROPERTYB CELLST CELLS Initial DevelopmentBone MarrowThymus Pre-antigen Diversity YES Post antigen Diversity YESNO Single antigen specificity YES Antigen recognizedVarietyPeptide:MHC Secreted form of Receptor YesNo Invariant signaling subunits Yes Comparison of B and T cells

10. SCID - severe combined immunodeficiency disease - Many causes but a rare disease - Classified according to lymphocyte profile (T B NK) - Bone Marrow transplant can cure Omenn syndrome - RAG proteins have reduced activity - Patient is: T+ B- NK+ CD3  and CD3  deficiency diseases - Mutations in some CD3 genes - Patient is: T+/TCR- B+ NK+ or T- B+ NK+ Immunodeficiency diseases

11. How do T cells recognize antigens? Antigen Processing Antigen Presentation Antigen Presenting Cell (APC) Professional APC

12. MHC class I communicates with Tc cells

13. MHC class II communicates with T H cells

14. IR to Extracellular Pathogens (CD4-MHC II) 1.Antibodies needed 2.Pathogen recognition/internalization by professional APCs a. B cells b. Macrophages c. Dendritic cells 3.Phagolysosome degrades proteins to peptides 4.Peptides:MHC II complex transported to surface 5.Professional APC contacts CD4 T cells 6.CD4 T H cells secrete cytokines to signal B cell maturation

15. IR to Intracellular Pathogens (CD8-MHC I) 1.Antibodies ineffective 2.Pathogen replicates in the cell and proteins are degraded in the cytoplasm of the cell 3.Peptides are transported into ER and bind MHC I and transported to the surface 4.MHC I expressing cells present to CD8 T cells 5.CD8 T cells (cytotoxic T cell, CTL) kills host cell

16. Figure 3-11

17. Structures involved in MHC Presentation TCR CD4 and CD8 MHC1 and MHCII

18. T cell Co-Receptors Binds MHC I Binds MHC II THTH TCTC

19. Figure 3-13 part 1 of 2 Variable Invariant

20. CD8-MHC ICD4-MHC II CD8-  3 CD4-  2

21. Figure 3-15 ClosedOpen 8-10 amino acids 13-25 amino acids Degenerate binding specificity

22. Figure 3-16

23. Proteosome=Shredder Transporter associated with antigen processing Peptide Degradation and Transport

24. Chaperones Calnexin Calreticulin Tapasin

25. Bare lymphocyte syndrome -TAP deficiency -Viral infections

26. Figure 3-19 Acidic process Golgi Transport Vacuolar Transport

27. CLIP - class II-associated invariant-chain peptide Prevention of Peptide:MHC II formation in ER Invariant Chain (li) - Prevent peptide binding in ER - Deliver to vesicles HLA-DM - Release of CLIP, peptide loading

28. Figure 3-21 part 2 of 3 TCR binds MHC and peptide CDR3 binds peptide CDR2 binds MHC CDR1a binds N-terminal CDR1b bind C-terminal

29. Cytokines can regulate expression Interferon  induces MHC II expression

30. T-cell Diversity - Recombination - Structure of TCR and associated molecules - Immunodeficiency diseases Antigen Processing and Presentation - Intracellular vs Extracellular - MHC structure

31. INTRA Proteasome TAP MHC I Golgi Calnexin Calreticulin Tapasin CD8 T C EXTRA Li MHC II Golgi Vesicle CLIP HLA-DM CD4 T H Summary

32. Alleles: different forms of one gene Allotypes: different forms of one protein (isoforms) Polymorphic: alternative forms of one gene = Many alleles Oligomorphic: a few forms of one gene = Few alleles Monomorphic: no polymorphism Homozygous: same allele on both inherited chromosomes Heterozygous: different allele on both inherited chromosomes MHC in humans is called HLA (human leukocyte antigen complex)

33. Figure 3-13 part 1 of 2 Variable Invariant No rearrangements or somatic changes Diversity is derived from 1) Gene families 2) Genetic polymorphism

34. HLA-A,B,C -present peptide antigens to CD8 Tcells and interact with NK-cells HLA-E,G -interact with NK-cells HLA-F -? HLA-DP,DQ,DR - present peptide antigens to CD4 Tcells HLA-DM,DO -regulate peptide loading of DP,DQ,DR Human leukocyte antigen complex Abs used to ID MHC molecules react with leukocytes not RBCs

35. Figure 3-24 part 1 of 2  Heavy Chain

36.  Heavy Chains

37.  2 -microglobulin on chr15  and  chain = GeneA and GeneB Haplotype - combination of alleles inherited from Chr6 2% meiotic recombination rate generates population diversity Crossover: Haplotypes, normally, are inherited intact and hence antigens encoded by different loci are inherited together (e.g., A2; B27; Cw2; DPw6; DQw9; DRw2). However, on occasions, there is crossing over between two parental chromosomes resulting in new recombinant haplotypes. Thus, any one specificity encoded by one locus may combine with specificities from other loci. This results in vast heterogeneity in the MHC make-up in a given population. Chr6 Chromosome Organization of HLA complex

38. Cytokines (Interferons) coordinately regulate the group of genes - class I heavy chain and other associated genes TAP transporter, Tapasin, Proteasome subunits - LMP2 and LMP7 ---> all proteins involved in Antigen Processing

39. Interferon , , and  ----> Class I ,  2 M, TAP, LMP2, LMP7 Interferon  ----> CIITA transcription factor ---> MHC class II transactivator (CIITA) - deficiency leads to bare lymphocyte syndrome HLA II genes, li chain

40. MHC I (single peptide binding chain  ): 3 genes to present antigen HLA-A, HLA-B, HLA-C MHC II (two chains,  and  ): 3 genesb to present antigen HLA-DQ, HLA-DP, HLA-DR Each MHC II locus encodes a gene for the  chain and a gene for the  chain: e.g. HLA-DQA, HLA-DQB => MHC II isoforms HLA-DPA, HLA-DPB => MHC II isoforms HLA-DRA, HLA-DRB => MHC II isoforms

41. Maternal: 3 MHC I genes HLA-A M, HLA-B M, HLA-C M Paternal: 3 MHC I genes HLA-A P, HLA-B P, HLA-C P Maternal: 3 MHC II genes HLA-DPA M, HLA-DPB M HLA-DQA M, HLA-DQB M HLA-DRA M, HLA-DRB M Paternal: 3 MHC II genes HLA-DPA P, HLA-DPB P HLA-DQA P, HLA-DQB P HLA-DRA P, HLA-DRB P 6 different MHC I proteins on all cells 6 different MHC II proteins on all cells (some individuals have 8 due to two HLA-DRB genes) Heterozygous

42. Homozygous = one DR type Heterozygous = up to four DR combinations, but only 3 types can be made by one person HLA-DRA P, HLA-DRB1 P HLA-DRA P, HLA-DRB3 P HLA-DRA P, HLA-DRB4 P

43. Figure 3-34 Red – heterozygous for all the highly polymorphic HLA I & II Yellow - Homozygous for one locus Blue - Homozygous for two or three loci Correlation is mainly with HLA class I - consistent with killing of virus infected cells Seroconversion - when antibodies have first been detected

44. Figure 3-28 part 1 of 2 MHC One MHC isoform can bind multiple peptides Contact residues - the MHC amino acid residues that interact with TCR or the bound peptide

45. Figure 3-28 part 2 of 2 Error in the textbook on HLA-DR (oligomorphic vs invariant)  chain  chain HLA-DR

47. Figure 3-29 Peptide binding motif - combination of anchor residues Anchor residues (green) - peptide amino acids interacting with MHC

48. Figure 3-30 Co- MHC restriction - TCR recognizes the complex of both the peptide and MHC by interacting with exposed amino acid residues

49. Figure 3-31 Large circles- total # antigenic peptides that can be presented via MHCI & MHCII small circles- total # antigenic peptides that can be presented via an individual MHCI & MHCII haplotype Balancing Selection Favors multiple alleles

50. Figure 3-32 part 1 of 2 Advantages for heterozygous for the MHC

51. Figure 3-32 part 2 of 2

52. Different mechanism from recombination - DNA is exchanged between alleles and copied in one direction to generation new MHC allele HLA B*5301- Found in African populations and associated with resistance to severe malaria

53. Figure 3-33 part 2 of 2 HLA B*4601- Found in southeast Asian populations and associated with susceptibility to nasopharyngeal carcinoma. Recombination between alleles of a different gene Generation of new MHC alleles

54. MHC selection by Infectious Disease Pathogens adapt to avoid MHC - recent MHC isoform may provide a survival advantage (hence higher frequency level) Epidemic diseases place survival advantages on those who can best present pathogenic peptides Only a minority of HLA alleles are common to all humans - most are recent and specific to ethnic groups

55. HLA Type and Disease Susceptibility Ankylosing spondylitisB27 IDDMDR4/DR3 Multiple SclerosisDR2 NarcolepsyDR2 Rheumatoid arthritisDR4 Lupus (SLE)DR3 AIDS (rapid)HLA-A29, HLA-B22 HLA-C16, HLA-DR11 AIDS (slow)HLA-B14, B27, B57 HLA-C8, C14

56. MHC polymorphism and Organ Transplants Developing T cells that recognize complexes of peptide and MHC molecules on HEALTHY tissue (self- peptides presented by self MHC) are DESTROYED This results in the preservation of T cells that recognize non-self MHC (allogeneic MHC). These are alloreactive T cells and are 1-10% of total T-cell repertoire Immune system is primed for rejection of foreign organs that express allogeneic MHC THIS IS WHY YOU WANT TO MATCH HLA TYPE