BMS 545 Immunology Lecture Notes PDF

WELCOME! BMS 545 IMMUNOLOGY SEPTEMBER 27, 2023 ANNOUNCEMENT S  Office Hours  Tuesday 4-5 pm virtual  Thursday 4-5 pm 316J  No homework until Module 3, but I would recommend working ahead if you have free time   OBJECTIVES  Compare & contrast phagocytosis & macropinocytosis (aga...

WELCOME! BMS 545 IMMUNOLOGY SEPTEMBER 27, 2023 ANNOUNCEMENT S  Office Hours  Tuesday 4-5 pm virtual  Thursday 4-5 pm 316J  No homework until Module 3, but I would recommend working ahead if you have free time   OBJECTIVES  Compare & contrast phagocytosis & macropinocytosis (again )  Identify & explain the purpose, function, & steps of antigen processing & presentation  Elaborate on steps of both MHC I & MHC II processing/presentation, & compare & contrast  Identify proteins of the peptide-loading complex that aid the assembly and peptide loading with MHC  Compare & contrast MHC I & MHC II processing and presentation  Understand the significance of the invariant chain  Describe the steps of dendritic cell maturation and its importance in antigen presentation  How can a peptide-derived from an intracellular pathogen that circumvents phagolysosome vesicles load into a class II molecule? (Importance of cross presentation) ANTIGEN PRESENTATION- OVERVIEW  T cells are restricted- aka TCR can not bind free antigen in body (aka MHC restriction)  Antigens must first be processed & presented to T cells via antigen presenting cells (APCs)  Either phagocytosis or macropinocytosis  Antigen presentation- process by which protein antigen is presented to lymphocytes in form of short peptide fragments  When ingested proteins are enzymatically degraded & resulting peptide fragments are loaded into MHC class molecules (forming pMHC class I or II)  Activation of naive T cells by antigen 8-1 Dendritic cells carry antigens from sites of infection to secondary lymphoid tissues Dendritic cells take up antigens at an infected skin wound and carry them to the draining lymph node for presentation to naive T cells Figure 8.2 Maturation of dendritic cells changes their form and function  Activation of naive T cells by antigen 8-2 Dendritic cells are adept and versatile at processing pathogen antigens Dendritic cells use several pathways to process and present protein antigens Because they are a nucleated cell they have MHC I, but because they’re an APC they have MHC II, too!  PHAGOCYTOSIS & CLATHRIN 1. Cells, particles, & molecules are captured by PRRs associated with clathrin-coated pits 2. Clathrin-associated membrane invaginates & pinches off to form a phagosome 3. Clathrin is recycled back to the cell membrane to form new coated pits MACROPINOCYTOSIS 1. Cytoplasmic protrusions or ruffles engulf & surround microbes, particles, or molecules 2. Forms a cytoplasmic vesicle 3. Cytoplasmic vesicle fuses with a lysosome to become phagolysosome 4. Phagolysosomes containing enzymatically degraded material fuse with vesicles containing MHC 5. Empty phagolysosomes are recycled back to the cell membrane  Antigen processing and presentation 5-9 MHC class I and class II bind peptides in different intracellular compartments Phagocytosis OR macropinocytosis depending on cell type Figure 5.16 MHC class I and class II load peptides that are produced in different compartments of the cell Black arrows & black-outlined vesicles=  MHC I- Peptides produced by MHC I pathway protein degradation in cytosol Red arrows & red-outlined vesicles= MHC II are pumped into lumen of ER pathway where they are loaded onto MHC class I & taken by exocytic vesicles through Golgi to plasma membrane  MHC II- Pathogens taken up from extracellular fluid are transported via endocytic vesicles to lysosomes, where proteins are degraded to peptides & transported via Cytosol (Cyt) endocytic vesicles to fuse with Nucleus (N) vesicles containing MHC class II. Endoplasmic reticulum (ER) Peptides are loaded onto class Golgi apparatus II molecules & taken to plasma Endocytic vesicles (En) Exocytic vesicles (Ex) membrane Antigen processing and presentation 5-10 Peptides produced in cytosol are transported to endoplasmic reticulum for binding to MHC class I  In all nucleated cells, proteasomes degrade cellular proteins in the cytosol that are poorly folded, damaged, or unwanted into peptides  These peptides are transported from cytosol into lumen of ER by protein called transporter associated with antigen processing (TAP), which is embedded in ER membrane Figure 5.20 Long peptides bound to MHC class I can be shortened from the amino- terminal end ERAP is also referred to as ERAAP endoplasmic Nonamer= reticulum 9 aminopeptidase (ERAP)  Antigen processing and presentation 5-11 MHC class I binds peptides in the context of a highly specific peptide-loading complex Figure 5.21 Proteins of the peptide-loading complex aid the assembly and peptide loading of MHC class I in the endoplasmic reticulum This slide is important Figure 5.22 The peptide-loading complex (Part 1)  MHC class I peptide-loading complex includes the chaperones calreticulin, ERp57, & tapasin  Interactions of these chaperones with TAP & MHC class I occur in endoplasmic reticulum (ER)  Tapasin (turquoise) & ERp57 (brown) form a heterodimer linked by a disulfide bond  Tapasin makes contact with MHC class I that stabilizes empty conformation of peptide- binding groove  Calreticulin (orange) binds to monoglucosylated N-linked glycan (turquoise hexagon) at asparagine 86 of MHC class I heavy chain  Transmembrane region of tapasin connects peptide-loading complex with TAP, bringing empty MHC class I into proximity with peptides transported from cytosol into ER Figure 5.22 The peptide-loading complex (Part 2) Figure 5.23 Tapasin also acts to increase the affinity of peptides bound by MHC class I ANIMATION  https://digital.wwnorton.com/immunesystem5  Antigen processing and presentation 5-13 Invariant chain prevents MHC class II from binding peptides in the endoplasmic reticulum  Structure of invariant chain -> Figure 5.26 Peptides that bind to MHC class II are generated in acidified endocytic vesicles (aka phagosome) Figure 5.27 The invariant chain prevents peptides from binding to MHC class II until the invariant chain:MHC class II complex reaches the site of extracellular protein degradation HLA-DM= membrane protein class II–associated invariant-chain peptide (CLIP) ANIMATION  https://digital.wwnorton.com/immunesystem5  DENDRITIC CELL MATURATION  When an immature dendritic cell senses an invasive threat, it rapidly begins to mature  Threats are detected by PRRs, either directly or indirectly  Direct sensing- engagement of pattern recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs) on viruses, bacteria, fungi, & protozoa  Indirect sensing- Engagement of other receptors (e.g., those that detect antibodies or complement molecules that have bound to microbes) are responsible for perceived threats  Threat sensing causes D.C. to migrate to nearby lymph nodes, decrease their phagocytic & macropinocytic activity, & increase MHC class II synthetic activity  *MHC class II molecules make no distinction between peptides of self & non- self origin  Self antigens displayed on the phagocyte surface usually go unrecognized because most self-reactive CD4+ T cells have been eliminated during development Activation of naive T cells by antigen 8-3 Naive T cells first encounter antigen presented by dendritic cells in secondary lymphoid tissues Naive T cells encounter and respond to specific antigen in secondary lymphoid organs Figure 5.11 Effector T cells function by making contact with other cells Figure 1.25 Activation of adaptive immunity in a draining lymph node 1. Pathogens & antigens (& dendritic cells carrying pathogens & antigens) arrive at a lymph node in afferent lymph draining the infected tissue 2. Pathogens & debris are removed by macrophages 3. Dendritic cells become residents & move to T-cell areas, where they encounter small lymphocytes that have entered LN from blood (green) 4. Dendritic cells orchestrate division & differentiation of small pathogen- specific lymphocytes into effector cells (blue)  Some helper & cytotoxic T cells leave in efferent lymph & travel to infected tissue  Other helper T cells stay in LN to stimulate division of pathogen-specific B cells & their differentiation into plasma cells (yellow) (B cell follicles → germinal centers) 5. Plasma cells move into medulla of lymph node, where they secrete pathogen-specific antibodies  Other plasma cells leave LN & travel to bone marrow, where they secrete pathogen-specific antibody in quantity 6. Antibodies travel to infected tissue by efferent lymph & blood WHAT ABOUT INTRACELLULAR PATHOGENS?  I just read that the TCRs of CD4+ T cells recognize pMHC class II complexes of exogenous origin. How can a peptide derived from an intracellular pathogen that circumvents phagolysosome vesicles load into a class II molecule?  Some intracellular antigens are broken down & their peptide fragments are loaded into MHC class I (forming pMHC class I) molecules  To avoid detection by the adaptive immune system, some pathogens employ a “stealth mechanism” by circumventing phagolysosome vesicles altogether. Others may enter the cell in phagosomes but are able to leave them and enter the cytoplasm. But their ruse is not perfect, as some infected cells die, prompting dendritic cells to take up dead cells and cellular debris by either phagocytosis or macropinocytosis. The proteolytic peptides are then displayed in class II molecules. Mystery solved!  Cross-presentation- ability of certain professional antigen-presenting cells (mostly dendritic cells) to take up, process and present (typically) extracellular antigens with MHC class I molecules to CD8 T cells (cytotoxic T cells)  Antigen processing and presentation 5-14 Cross-presentation enables extracellular antigens to be presented by MHC class I  Molecular pathway of cross-presentation is still ???  One route could involve translocation of ingested proteins from phagolysosome into cytosol, where they undergo degradation by proteasome, enter ER via TAP, & be loaded on to nascent MHC class I in usual way?  Another route could involve transport of antigens directly from phagolysosome into a vesicular compartment (without passage through cytosol) where peptides are allowed to bind to mature MHC class I molecules?  Pathways of cross-presentation (red arrows)  Normal pathway of presentation of intracellular antigen by MHC class I (blue arrows) ANTIGEN PROCESSING SUMMARY SLIDES JUST ANOTHER VISUAL PRESENTATION OF EVERYTHING YOU’VE LEARNED IN THE ABOVE SLIDES!  PRESENTATION BY MHC CLASS I- INTRACELLULAR 1. Proteasome-generated peptide fragments within cytoplasm are transported into endoplasmic reticulum (ER) by gatekeeper TAP-1 & TAP-2 heterodimers 2. Calnexin (chaperone molecule) binds to newly synthesized MHC class I molecules to allow β2 microglobulin to form a MHC class I:β2 complex 3. Calnexin is replaced by calreticulin (chaperone molecule) 4. Tapasin (chaperone molecule) associated with TAP heterodimer assists loading the peptide into MHC class I:β2 complex  MHC class I:β complex rapidly disintegrates if 2 a suitable peptide is not loaded 5. Exocytotic vesicles containing new pMHC class I complexes bud off from ER & transported for display on cell surface by CD8+ T cells with appropriate TCR  PRESENTATION OF MHC  Antigens of extracellular origin (L) or of CLASS self originII- (R)EXTRACELLULAR are degraded within phagolysosomes  MHC class II αβ heterodimers + invariant chain are assembled in the endoplasmic reticulum (ER)  Vesicles containing MHC class II + invariant chain bud off from the ER to fuse with peptide-rich vesicles that bud off from phagolysosome  Acidic environment of the fused vesicle causes the invariant chain to disintegrate, allowing peptides to occupy peptide-binding groove of MHC class II molecule  Invariant chain-lacking MHC class II molecules that do not bind a peptide disintegrate in the acidic environment of the vesicle  Exocytotic vesicle containing pMHC class II fuse with cell’s plasma