1. Microbiology 204: Cellular and Molecular Immunology Class meets MWF 11-12:30 Lectures are open to auditors Discussions are restricted to those enrolled in class (or by permission) Textbook recommended: Janeway et al Immunobiology or Abbas and Lichtman Cellular and Molecular Immunology

2. Microbiology 204: Cellular and Molecular Immunology Grades: 2/3 take-home final and 1/3 participation in discussions My office hours: Mondays 4-5PM HSE1001F (defranco@cgl.ucsf.edu)

4. The central questions How does the immune system respond to different infections? –Microbes are recognized by two mechanisms, evolved broad recognition mechanisms (innate immunity), and by highly specific lymphocyte antibodies and T cell receptors (adaptive immunity) –Different types of microbes are eliminated by different effector mechanisms, which are designed to best combat each type of microbe Why does the immune system not respond to self antigens? What are the pathogenic mechanisms and clinico- pathologic consequences of abnormalities in the immune system?

5. Cells of the immune system Lymphocytes –Mediators of adaptive immune responses; only cells with specific receptors for antigens Antigen-presenting cells (APCs) –Specialized to capture, concentrate, and display antigens for recognition by lymphocytes –Dendritic cells; macrophages, B cells; follicular dendritic cells –Different APCs serve different roles in adaptive immune responses Effector cells –Function to eliminate microbes; include lymphocytes, granulocytes (neutrophils, eosinophils), macrophages

6. Cells of the myeloid lineages

7. Innate vs. Adaptive Immunity

8. Examples of Innate Immune Recognition

9. Principal mechanisms of defense against microbes Antibodies PhagocytesT cells (CTLs) ( may work with antibodies, T cells) All microbes Intracellular microbes, esp. viruses

11. Pathogen recognition by adaptive immunity: great variety, selectivity

12. Great variability of antigen recognition is created by combination of gene segments during lymphocyte development

13. Two types of T cells

14. CD Nomenclature Structurally defined leukocyte surface molecule that is expressed on cells of a particular lineage (“differentiation”) and recognized by a group (“cluster”) of monoclonal antibodies is called a member of a cluster of differentiation (CD) CD molecules (CD antigens, CD markers) are: Identified by numbers Used to classify leukocytes into functionally distinct subpopulations, e.g. helper T cells are CD4+CD8-, CTLs are CD8+CD4- Often involved in leukocyte functions Antibodies against various CD molecules are used to: Identify and isolate leukocyte subpopulations Study functions of leukocytes Eliminate particular cell populations

15. Two types of MHC Coordination of properties with functions of two types of T cells: source of peptide and cells expressing

16. Two types of T cells: coordination of function with properties of antigen-presentation CD4 T cells. Help other immune cells Recognize peptide + MHC II MHC II is expressed primarily on immune cells Peptides are from endocytosed antigen CD8 T cells. Kill virus-infected cells Recognize peptide + MHC I MHC I is expressed on all nucleated cells Peptides are from cytosolic antigen

17. Generation of lymphocytes of many specificies Clonal deletion to remove self-reactive lymphocytes Clonal selection to expand pathogen-reactive lymphocytes during an immune response

18. Anatomy of the lymphoid system

19. Anatomy of a lymph node Naïve lymphocytes circulate between blood and lymphoid tissues; antigen in tissue arrives at draining lymph node via lymph flow and being carried by dendritic cells

20. Applies to B cells and T cells For T cells: costimulatory molecules include B7-1 and B7-2 on dendritic cells Mechanism for directing the immune response against microbes and not against self, food, etc.

21. Sequence of Events in an Immune response

23. Stages of lymphocyte activation Naïve lymphocytes –Mature lymphocytes that have not previously encountered antigen; function -- antigen recognition –Preferential migration to peripheral lymphoid organs (lymph nodes), the sites where immune responses start Effector lymphocytes –Activated lymphocytes capable of performing the functions required to eliminate microbes (‘effector functions”) –Effector T lymphocytes: cytokine secretion (helper cells), killing of infected cells (CTLs) –B lymphocytes: antibody-secreting cells (e.g. plasma cells) Memory lymphocytes –Long-lived, functionally silent cells; mount rapid responses to antigen challenge (recall, or secondary, responses)

26. Immune responses often can be characterized as type 1 or type 2 Type 1 immune responses: Killing microbes –Pro-inflammatory; neutrophils and macrophages –Antibody classes involved in phagocytosis and complement activ. –Macrophage activation Type 2 immune responses: Defense at epithelium –Allergic inflammation: eosinophils, basophils –Antibody classes: IgE and IgG1 (mast cell activation) –Expulsion type reactions (diarrhea, coughing, sneezing, etc.).

27. Congenital immunodeficiency diseases are often caused by blocks at different stages of lymphocyte maturation LYMPHOCYTE DEVELOPMENT

28. The Immunoglobulin Superfamily (a few examples)

29. Integrins: Regulated Cell-cell and cell- ECM adhesion

31. Cytokine receptor families

33. Chemokines: lymphoid or homeostatic chemokines