Microbiology 204: Cellular and Molecular Immunology

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1 Microbiology 204: Cellular and Molecular Immunology Class meets MWF 1:00-2:30PM (*exceptions: no class Fri Sept 23, Fri Oct 14, Nov 11, or Wed Nov 23) Lectures are open to auditors and will be live-streamed to Mission Bay and will be recorded Flipped sessions are open to auditors (not recorded or streamed) Discussions are restricted to those enrolled in class (Cliff Lowell Problem sets and review sessions every other week by our TA: Carlos

2 Microbiology 204: Cellular and Molecular Immunology Course web site: Recommended textbook : Janeway s Immunobiology; OR Abbas Pillai, and Lichtman Cellular and Molecular Immunology; 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

3 Microbiology 204: Cellular and Molecular Immunology 1) Keep up! 2) Prepare for the interactive sessions - Flipped classroom sessions: view background lecture in advance; some sessions may have additional preparation required -Discussions: read paper carefully, check assignment page to see if you have a specific assignment or if there are recommended issues to think about in advance 3) Read some original papers beyond the discussions

4 Microbiology 204: Cellular and Molecular Immunology 1) Keep up! 2) Prepare for the interactive sessions - Flipped classroom sessions: view background lecture in advance; some sessions may have additional preparation required -Discussions: read paper carefully, check assignment page to see if you have a specific assignment or if there are recommended issues to think about in advance 3) Read some original papers beyond the discussions 4) Optional TA sessions every other week; first one will get everyone up-to-speed with flow cytometry; last one will give you some tips for take-home exam; in between there are some problem sets ; opportunity to discuss the material.

5 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.)

6 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.)

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

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

9 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

10 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

11 Leukocyte recruitment to sites of inflammation or DC

12 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.

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

14 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

15 Many different antibodies are created by combinations of gene segments

16 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.

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

18

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

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

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

22

23 Antibodies can be directly protective or can promote immune protective mechanisms via other cells or molecules neutralization activation of complement

24 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 à 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

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

26 Monoclonal antibodies used in medicine Genentech s plant in Vacaville, CA for producing Herceptin to treat breast cancer

27 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

28 Recognition of antigen by the TCR The TCR of CD4+ and CD8+ T cells recognizes MHCbound peptide + portions of the MHC. Other T cells (γδ T cells, NKT cells) recognize nonpeptide antigens

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

30 Killer T cells and Helper T cells killing helper Microbe evades Killing cytokines

31 Capture and presentation of antigens by dendritic cells Abbas et al. Basic Immunology Antigens and naïve T cells come together in lymphoid organs

32 Role of costimulation in T cell activation

33 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)

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

35 Immune system and chronic inflammation Sterile inflammation (tissue injury but no infectious agent present): innate recognition of tissue damage Chronic inflammation: if antigen persists, antigenreactive 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)

36 Does inhibition of inflammation protect against heart attacks and/or strokes? From: Yousuf et al. J. Amer. Coll. Cardiol. 65 (5): , 2013 Canakinumab: monoclonal antibody that binds IL-1β and blocks function methotrexate: immune suppressant used to treat some inflammatory diseases (rheumatoid arthritis, etc.)

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