Antigen processing and presentation II

• Describe the structure of MHC-II

  MHC-II is a dimer composed of 2 transmembrane glycoprotein chains: alpha and beta. Alpha1 and beta1 comprise the peptide binding cleft, which is left open at each end and allows MHC II to bind to longer peptides. Polymorphisms in alpha1 and beta1 subunits define binding in the peptide binding cleft. The alpha2 and beta2 chains are conserved across all MHC II molecules.
• Describe MHC II gene expression

  Alpha and beta genes are co-dominantly expressed from both the maternal and paternal chromosome. These maternal and paternal chains can pair up between chromosomes and with chains expressed on the same chromosome to produce:

  • Up to 4 DP, DQ and DR chains (n/b not 8 DRs since the alpha chain is monomorphic)
• Describe peptide binding in MHC II

  The peptide binding cleft is open ended, allowing long peptides between 10-30 amino acids to bind. The ends of the peptides are not bound in the groove and the peptide lies in an extended conformation. The peptide is bound by hydrogen bonds distributed along the length of the peptide and held by interactions with both polymorphic amino acids in the groove and conserved side chains of invariant amino acids that line the peptide binding groove.
• Describe sequence specificity of MHC II binding peptides

  Since the peptide ends protrude from the MHC, any length of peptide is possible. Therefore, long peptides are trimmed by peptidases to make them 13-17 amino acids long. These peptides must exhibit similar properties but not necessarily the same sequences as the peptide binding cleft. These similar residues are known as anchor residues, which bind to polymorphic residues in the MHC.
• Describe the generation of MHC II peptides

  Extracellular proteins are internalised via endocytosis or phagocytosis. Internalised proteins are degraded by acid proteases and acidification of vesicles triggers fusing with lysosomes. Macrophage and DC activation makes endosomal acidification and lysosomal fusion more efficient. MHC II is loaded with peptides in the vesicles before being transported to the cell membrane.
• Describe the proteases used for peptide processing

  Cathepsins are cysteine endopeptidases.

  • Cathepsin S and L are important for peptide processing for MHC II
• What is GILT?

  GILT reduces and degrades disulphide bonds before pathogenic peptides are digested and processed. GILT is localised in endosomal compartments.
• What is the invariant chain?

  The invariant chain, also known as the Li chain, inhibits peptide binding by sitting in the peptide binding groove. This prevents MHC class II from prematurely binding to peptides before entering the endosomal compartment. Calnexin stabilises the assembly of the Li-MHC complex. Li chain targets the MHC complex for delivery to low pH endosomal compartments, via transmembrane segment signalling.
• How is the Li chain cleaved from the MHC II?

  The Li chain is cleaved from MHC II in the MHC II compartment by proteases:

  • Cathepsin L: in thymic epithelial cells
  • Cathepsin S: in APC

  This produces the class II associated invariant chain peptide (CLIP)
• Describe the HLA-DM molecule

  HLA-DM is responsible for removing CLIP from MHC II and enables binding of peptides. It closely resembles MHC II with both an alpha and beta chain. HLA-DM also performs peptide editing by removing unstably bound peptides from the MHC-II complex and enables long lasting expression of MHC II peptide complexes on the cell surface.
• Describe the action of HLA-DO

  HLA-DO counteracts HLA-DM, which traffics up from the ER with HLA-DM to ensure that APCs do not have high levels of MHC II on their surface. Cytokines upregulate HLA-DM, to tip the balanced with HLA-DO.
• Describe MARCH-1

  Immature DCs: MARCH-1 promotes degradation of MHC-II by ubiquitylating proteins and targeting them to the proteasome.

  Activated DCs: MARCH-1 expression is suppressed and MARCH-1 is quickly degraded due to its short half life. This leads to improved expression of MHC II peptide complexes to ensure that DCs can optimally interact with CD4+ T cells during an immune response.
• Describe the importance of presentation of endogenous antigens by MHC II

  10-30% of peptides presented by MHC II in B cells and DCs are from intracellular proteins. This is so that MHC II can produce a broader response by activating different types of CD4+ T cells in response to intracellular pathogens.
• Describe the action of Autophagy in expression of cytosolic antigens on MHC II

  Autophagy can occur in B cells, DCs and macrophages. IFN-gamma can stimulate Autophagy, which mediates uptake of cytosolic pathogens and presentation on MHC II to enable CD4+ T cell response. Autophagosomes intersect with endosomes and phagosome to incorporate MHC II pathway. This pathway is very important in thymic selection.
• Describe how TCRs interact with MHC II molecules outside of the peptide cleft

  TCRs have to be able to interact with the scaffold and MHC molecule. Polymorphic residues are also present at the top of the alpha helices that lines the peptide binding groove, and these residues interact with TCR.
• Describe MHC interactions with T cell co-stimulatory molecules

  The MHC molecule invariant regions interact with CD4 and CD8 molecules associated with the TCR. CD4 and CD8 molecules localise intracellular signalling kinases to the TCR to amplify the T cell response.