1. Microbiology 204: Cellular and Molecular Immunology Class meets MWF 1:00-2:30PM (*exceptions: no class Fri Oct 9; Wed Nov 25 will be moved to 11/24 or 11/23) Lectures are open to auditors “Flipped sessions” are open to auditors Discussions are restricted to those enrolled in class (Cliff Lowell (clifford.lowell@ucsf.edu)) Problem sets and review sessions every other week by our TA: John Gagnon( john.gagnon@ucsf.edu ) john.gagnon@ucsf.edu

2. Microbiology 204: Cellular and Molecular Immunology Course web site: http://immunology.ucsf.edu/Micro204schedule Recommended textbook : Janeway’s Immunobiology; OR Abbas and Lichtman Cellular and Molecular Immunology; OR DeFranco, Robertson, and Locksley Immunity; ALSO TRY TO READ 3 PAPERS PER LECTURE Grades: 2/3 take-home final and 1/3 participation in discussions My office hours: Mondays 3-4PM HSE1001E or by arrangement (anthony.defranco@ucsf.edu)

3. What does the immune system do? It protects us from infections with: –208 viruses –538 bacteria –317 fungi –287 worms – 57 parasitic protozoa (CDC numbers) It promotes normal functioning of the body (tissue cleanup, wound repair) It removes abnormal cells including malignant ones But the immune system can also cause disease when it is not doing the right thing (allergies, autoimmunity, transplant rejection, etc.)

4. The players Sentinel cells in tissues –Dendritic cells, macrophages, mast cells Circulating phagocytes and granulocytes –Neutrophils, monocytes, eosinophils, basophils Lymphocytes: cells which can recognize particular pathogens (but also can cause allergies and autoimmune diseases) –B lymphocytes: antibodies –T lymphocytes: cell-mediated immunity –(also innate lymphoid cells, NK cells, etc.) Tissue cells (epithelial cells, endothelial cells, etc.)

5. Immune sentinel cells in the tissues: dendritic cells Langerhans cells (epidermal dendritic cells) in the skin WJ Mullholland et al. J. Invest. Dermatol. 126: 1541, 2006. Green= dendritic cells Blue= nuclei of all cells

6. TNF or dendritic cell Inflammatory mediators: -Lipids (prostaglandins, etc.) -Proteins (cytokines/chemokines) Others Inflammatory mediators are made in response to detection of infection or injury

7. Cytokines “Cytokines”: soluble protein mediators secreted by immune cells (mostly) and act on other cells (“cyto”) to regulate their activity (“kine”) Name of a cytokine often doesn’t reflect its most important function (example: TNF stands for “tumor necrosis factor”) many cytokines are called “interleukins” (IL-1, IL-2, etc.) Cytokines that direct migration of cells are called “chemotactic cytokines” or “chemokines”

8. Cytokines and Inflammation Pro-inflammatory cytokines are many, but especially important: TNF, IL-1, and IL-6 TNF and IL-1 signal to endothelial cells to make them: –Leaky to fluid (influx of plasma; containing antibodies, complement components, etc.) –Sticky for leukocytes, leading to influx of leukocytes IL-6 promotes adaptive immune responses; systemic effects

9. Leukocyte recruitment to sites of inflammation or DC

10. The neutrophil is the immune system’s first responder Neutrophils are typically the first white blood cells to come into a site of acute inflammation (PLAY MOVIE HERE): Lammermann et al. Nature 498: 371-5, 2013.

11. Phagocytosis and Killing of Microbes Abbas et al. Fig. 2-17

12. Innate Immunity vs. Adaptive immunity Innate immunity utilizes evolved recognition mechanisms and is surprisingly effective, but changes little based on life experience In innate immunity, limited numbers of distinct receptors; recognize highly conserved features of classes of microbes. Adaptive immunity learns from previous experience and hence can protect better upon a second infection by the same agent. Adaptive immunity has a very large number of distinct “antigen receptors” of T and B lymphocytes; generated by DNA rearrangements in each developing lymphocyte; clonal selection of lymphocytes that recognize an infecting agent

13. Many different antibodies are created by combinations of gene segments

14. Adaptive Immunity: Antibodies I A molecule that induces the production of an antibody is called an “antigen” A few B cells that recognize the infectious agent become activated, each multiply to form a “clone”. These progeny then become antibody-secreting factories.

15. Generation of lymphocytes of many specificities Clonal deletion to remove self- reactive lymphocytes Clonal selection to expand pathogen-reactive lymphocytes during an immune response The Clonal Selection Hypothesis

17. Antibody responses proceed in two phases Goodnow et al, Nature Immunol. 2010

18. Adaptive Immunity: Antibodies II Rapid production of lower affinity antibody made by short- lived plasma cells Slower “germinal center response”  selection for higher affinity  gives rise to long-lived plasma cells Rational design of the “conjugate vaccines” (starting in the 1990s)

19. Antibodies bind antigens Two protein components: heavy chain and light chain; can come in 5 varieties of heavy chains: IgM, IgG, IgA, IgE, IgD

20. Antibodies can be directly protective or can promote immune protective mechanisms via other cells or molecules neutralizationactivation of complement

21. Adaptive Immunity: Antibodies III “Active immunity” (infection, vaccination) “Passive immunity”: maternal transfer of IgG across placenta; injection of antibodies to protect against infections, toxins; IVIG for immunodeficiency “Monoclonal antibodies” for passive immunity, therapy, diagnosis. All identical  more standardized therapeutic or diagnostic. To work well as therapy, need to make as human as possible; many new MAb therapeutics in the last 10 years. Most are to treat cancers or to suppress immune responses

22. Monoclonal antibodies used in medicine Standardized, unlimited reagents for diagnosis or therapy Some representative examples. This list is rapidly expanding in recent years

23. 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

24. The TCR of CD4+ and CD8+ T cells recognizes MHC- bound peptide + portions of the MHC. Other T cells (  T cells, NKT cells) recognize non- peptide antigens Recognition of antigen by the TCR

25. Peptides are bound to MHC molecules and presented to T cells MHC=major histocompatability complex. HLA=human leukocyte antigen

26. Killer T cells and Helper T cells killing cytokines helper Microbe evades Killing

27. Adaptive Immunity: Anatomy of the response Naïve T cells and B cells recirculate between lymph nodes, spleen, and the blood. Antigen is taken to the lymph node either by the flow of lymph or is carried by a maturing dendritic cells that migrate along the lymphatics. The dendritic cell presents antigen to naïve T cells in the lymph node.

28. Role of costimulation in T cell activation

29. Immune responses are tailored to the type of infection Defense against extracellular microbes: IgM, IgG and Th17 Defense against microbes that survive and replicate inside phagocytes (macrophages and monocytes): “type 1 immunity” (Th1) Defense against viruses: –early defense: innate mechanisms that restrict virus replication (interferon, etc.) –Adaptive immune defense: antibodies which block virus infection of cells (“neutralizing antibodies”) plus cytotoxic T cells Defense against worms and biting insects: “type 2 immunity” (IgE, Th2), Manifestations include: sneezing, coughing, itching, diarrhea, tears, etc. (allergies and asthma mostly involve this type of immune response)

30. Innate Lymphoid Cells: Parallels to T cell subsets Spits and DiSanto, Nature Immunology 12: 21-27, 2011 IL-5

31. Immune system and chronic inflammation Sterile inflammation (tissue injury but no infectious agent present): innate recognition of tissue damage Chronic inflammation: if antigen persists, antigen- reactive T cells can drive continued inflammation, which can cause tissue damage (autoimmune diseases and inflammatory diseases) Likely important role of inflammation in pathogenesis of chronic diseases: atherosclerosis, type 2 diabetes, probably Alzheimer’s disease, cancer (can be positive or negative)