MHC II Antigen Presentation Pathway

• The immune system defends the body against pathogens, toxins, and altered cells

Phases of the Immunological Response

• Recognition of pathogen or danger signals
• Alerting and mobilization of immune components
• Elimination of the pathogen

Immune Recognition

• The immune system differentiates between self and non-self (foreign material, pathogens)
• Continuous monitoring and presentation of antigens is essential to avoid destructive immune responses against self-antigens, as the immune system normally remains tolerant to them
• Immune responses are classified as immunogenic or tolerogenic
• Antigens are classified as immunogenic or tolerogenic based on the response they trigger

Antigens

• Antigens are entities specifically recognized by B and T lymphocytes through antigen receptors, and the recognition includes pathogens and self-derived materials
• A vast variety of antigenic peptides (10^15-17) pair with highly specific antigen receptors
• The immune system has up to 10^7-9 receptors
• Antigen specificity relies on the ability of highly specific receptors to bind to a material or structure
• Even small chemical an antigen can render it unrecognizable
• The immune system can produce a vast variety of highly specific receptors in the order of billions
• Receptor diversity is achieved via molecular genetic mechanisms
• Each individual cell produces only one type of antigen-specific receptor
• One lymphocyte is specific to one type of antigen

PAMPs vs Antigens

• PAMPs (pathogen-associated molecular patterns) are recognized by pattern recognition receptors (PRRs) on various cell types
• Antigens are structures recognized by lymphocytes with their antigen-specific receptors
• First recognition of pathogens and danger signals is mediated by PRRs
• Fine recognition and distinction between self, non-self, and modified self-molecules are mediated by lymphocytes with antigen receptors
• Molecules recognized by antigen receptors can trigger a specific response (tolerance or destruction)
• B lymphocytes carry receptors to recognize only one type of antigen
• Billions of B and T cells can recognize billions of different structures

B Lymphocytes vs T Lymphocytes

• T lymphocytes recognize peptide antigens
• B cells recognize peptides, proteins, nucleic acids, polysaccharides, lipids, and small chemicals
• T cell-mediated immune responses are induced by protein antigens, and humoral immune responses are seen with protein and nonprotein antigens
• B cells recognize antigens via cell surface antigen receptors (immunoglobulins), and express many membrane-bound immunoglobulins
• Detection of antigens activates B cells which then differentiate into plasma cells
• Plasma cells do not carry cell surface immunoglobulins, but produce antibodies
• Antibodies recognize antigens of pathogens and bind to them, to mark (opsonization) or neutralize them

Types of T cells

• Cytotoxic T cells kill infected or tumor cells
• Helper T cells facilitate immune responses and their regulation and enhance cytotoxic T cell responses
• Helper T cells help macrophages destroy microbes and support B cell antibody production
• Cytotoxic T cells express CD8, and helper T cells express CD4 cell surface receptors
• Thus, cytotoxic T cells are CD8+ and helper T cells are CD4+
• Freshly generated, "naïve" T and B lymphocytes from primary lymphoid organs are not fully functional until maturation/activation in secondary organs to differentiate into effector cells

Naive T cells

• Naive T cells are primarily activated in secondary lymphoid organs
• Naive T cells haven't met their specific antigen and are activated mainly by dendritic cells
• Dendritic cells express MHC molecules and cell surface molecules that stimulate naive T cells
• Activated naive T cells proliferate and differentiate into effector T cells

T cell recirculation

• CD4+ and CD8+ naive T cells enter circulation and migrate to secondary lymphoid organs to "screen" local antigen-repertoire
• A continuous recirculation of T cells occurs until a T cell finds its specific antigen, which induces activation, clonal expansion, and differentiation into effector T cells
• T cells that fail to find a specific antigen undergo apoptosis in a few weeks
• In most cases, antigens for naïve T cells are transported to the lymph node by dendritic cells from the tissues, after pathogen recognition
• Processing of the pathogen-derived antigen results in peptide fragments that are presented on MHC molecules
• Initial activation of T cells occurs in the lymph node, with clonal expansion of antigen-specific T cells
• In the periphery, cytotoxic T cells (Tc) recognize their specific peptide fragment (antigen) presented by cells expressing MHC I molecules, and may be infected or tumor cells
• Helper T lymphocytes (Th cells) are activated by professional antigen-presenting cells expressing cell surface MHC II molecules

MHC

• MHC (Major Histocompatibility Complex, HLA in humans) include genes with the highest polymorphism in the human population that are codominantly expressed
• MHC molecules with the same function are slightly different from each other
• MHC molecules present peptide fragments from various antigens to T cells
• One MHC molecule presents 1 peptide, but one cell presents many different peptides
• MHC molecules can present microbial, altered, or foreign peptides
• T cells "check" peptides bound to MHC molecules and search for pairings that activate them

MHC Genes

• Individuals express the alleles inherited from each parent for a given MHC gene
• Maximizes the number of MHC molecules available for presenting peptides to T cells
• The structure of Class I MHC is a chain-like structure made up of the polypeptide chains
• The structure of Class II are anchored inside the cell membrane

MHC features

• Each MHC molecule comprises of an extracellular peptide-binding cleft, followed by immunoglobulin (Ig)-like domains, transmembrane and cytoplasmic domains
• Class I molecules consist of one polypeptide chain encoded in the MHC
• Class II molecules are made up of two MHC-encoded polypeptide chains
• The polymorphic amino acid residues are located in and adjacent to the peptide-binding cleft
• This cleft is formed by paired a-helices above an eight-stranded |-pleated sheet
• Polymorphic resides are the amino acids that vary between MHC alleles
• CD4 and CD8 bind to nonpolymorphic Ig-like domains of MHC molecules, as expressed on distinct T lymphocyte subpopulations
• CD4 binds selectively to class II MHC molecules, CD8 binds to class I molecules
• CD4+ T cells recognize peptides displayed by class II molecules, CD8+T cells recognize peptides presented by class I molecules
• CD4+T cells function as helper cells, and many CD8+cells are CTLs (cytotoxic T lymphocytes)
• Class I MHC has an MHC-encoded α chain (44-47 kD) plus a non-MHC-encoded 12 kD subunit called ~2-microglobulin
• Class II MHC has two noncovalently associated polypeptide chains, a 32-34 kD α chain and 29-32 kD ~chain

MHC-peptide complex

• Binding is a noncovalent interaction mediated by residues of both the peptides and in the clefts T cell recognition involves an MHC molecule binding and displaying a peptide, along with a T cell receptor recognizing residues of both the MHC molecule and the peptide

Antigen presentation

• The binding of peptides involves a flexible conformation before the peptide binding, with the peptide bond triggering a conformational change
• The bound peptide contributes to stabilizing the conformation of the MHC+peptide complex
• The amino acid residues of a peptide contain side chains that fit into pockets may bind with complimentary amino acids in the MHC
• Peptides can only bind one peptide at a time, but each MHC can bind many different peptides

Protein Antigen Processing

• Protein antigens are proteolytically cleaved in antigen-presenting cells (APCs)
• The resulting peptides bind to the clefts of MHC molecules in a n extended conformation
• Bound peptides + water fill the clefts, contacting residue w/ amino acid residues that form the floor’s ß-strands
• ß-strands in the floor contain "pockets" and anchor residues contribute most of the binding interactions
• The immune system response is affected by which MHC alleles are expressed

MHC I

• Expressed on all cells with nuclei (except red blood cells)
• Linked to peptides (8-10 amino acids) degraded from proteins (intracellular, endogenous) in cell cytoplasm
• Abnormal proteins from tumors can be present
• Presentation of the internal environment of the call is for CD8+ cytotoxic effector T cells
• Is the antigen presenting mechanism
• Will presents any protein (no selection)

MHC II

• Presentation is specific to professional antigen presenting cells
• DCs, Macrophages and B lympocytes are considered professional antigen presenting cells
• These cells all utilize endocytosis of exogenous antigens of 10-20 amino acids long
• This is the main antigen presenting machanism
• Will present a antigen the cells external enviornment

MHC I antigen presentation

• Involves any protein located in the cytosol (self / non-self) whether it is derived from a pathogen or not. Can be on the cells own proteins, or from intracellular bacteria or viral peptides
• The process:
  • Peptides are put in the cytosol
  • A proeasome cleaves proteins in to peptide fragements that are 8-10 amino acids long
  • These generated peptides are transported via TAP ( transporter protein complex) and then ER ( endoplasmic reticulum)
  • Once there, they will bind to MHC I molecules
  • The bound MHC I travels through the golgi and appears on the cell surface

MHC II Antigen Presentation

• MHC II molecules exhibit a restricted expression pattern, primarily on professional antigen-presenting cells (APCs)
• Macrophages and dendritic cells use MHC II to present extracellular/exogenous peptides ingested from the extracellular space
• Following phagocytosis or endocytosis, exogenous antigens enter the endosome and fuse with lysosomes to create endolysosomes containing proteolytic enzymes
• 10-20 amino acids long peptides typically bind to MHC II molecules Invariant chain li, prevents binding of endogenous peptides and blocks the molecule
• Invariant Enzymes degrade the chain makin ght binding site available for peptides that have been derived from extracellular antigens

Antigen Presenting Cells

• Antigen-presenting cells (APCs) capture microbial and other antigens, display them to lymphocytes, and provide signals for lymphocyte differentiation and proliferation
• APC usually refers to a cell that displays antigens to T lymphocytes, where the major APC initiating T cell response being dendritic cells
• Macrophages present antigens to T cells during cell-mediated immune responses
• B lymphocytes function as APCs for helper T cells during humoral immune responses
• Follicular dendritic cells (FDCs) display antigens to B lymphocytes

Dendritic Cells

• Play key roles in capturing antigen and production of T lympocytes
• Are derived from bone marrow
• Sample extracellular environment by pinocytoiss and phagocytosis
• Express surface Toll like receptiors

Mononuclear Phagocytes

• Act as an APC for adaptive/innate immmunity
• Macrophages display microbial antigens to differentiated effector T cells which activate the macrophages to kill the intracellular microbes (major mechanism of cell-mediated immunity)
• -Also participate in the adaptive immune response with foreign antigens

Follicular Dendritic Cells

• Are specialized to collect large anitgen complexes of activated B cells
• Are not dirived from bone marrow
• Antigens on T lympocytes are trapped by these

T Cells and Coordination

• Helper / Th cells do not kill pathogens but coordinate other immnoucyte
• Antigen-specific activation via CD4 causes expression of surface molecules resulting in cytokine production
• Synthesize/degrade cellualtr proteins
• Peptides from these proteins transport cell surface and show complex with MHC I
• Th cells recognize/presented/kill antigens

T Cell Activation Inhibition

• Virus's/pathogens may have developed ways to evade immune responses
• Several viral genes may encoded proteinis
• Some proteins will then start the process of inhiting the presentation of viral antigens to T cells

E1A Protein and MHC

• The E1A protein inhibits MHC and transcription of the class I genes
• Prevents capture/transport of cytotoxic peptides
• E3 Protien prevents molecules from exiting their peptide cargo

US2 and US11 Protien functions

• Causes cells for non coding sequences
• Prevents cells from loading up on peptides or undergoing degredation

Vpu / Nef protien functions

• Inhibits infection related classes of sequences / molecules.
• This is done by force internalized I molecule surface.
• New sythensized proteins break down I molecules.

Explore the MHC II antigen presentation pathway, including the role of the invariant chain (Ii), MHC II molecule encounters with processed peptides, and T cell-mediated immune responses. Understand the characteristics of the peptide-binding groove of MHC II molecules and the key differences between B cell and T cell antigen recognition.