1. Microbiology 204: Cellular and Molecular Immunology
Class meets MWF 1:00-2:30PM
(*exceptions: no class Fri Oct 10; Wed Nov 26 will be
moved to 11/25 or 11/24)
Lectures are open to auditors
“Flipped sessions” are open to auditors
Discussions are restricted to those enrolled in class (or by permission)
Problem sets and review sessions every other week by our TA: Dan Holohan

2. Microbiology 204: Cellular and Molecular Immunology
Course web site:
Recommended textbook : Janeway’s Immunobiology;
OR Abbas and Lichtman Cellular and Molecular Immunology; OR DeFranco, Robertson, and Locksley Immunity
Grades: 2/3 take-home final and 1/3 participation in discussions
My office hours: Mondays 3-4PM HSE1001E or by arrangement

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
With these mice in hand, we can achieve specific ablation of MyD88 in a cell-type specific way. As mentioned before,
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.

6. 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

7. 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

8. Leukocyte recruitment to sites of inflammation
or DC

9. 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.

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

11. 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

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

13. 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.

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

16. Antibody responses proceed in two phases
Goodnow et al, Nature Immunol. 2010 16

17. 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)

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

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

20. 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

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

22. 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

23. Recognition of antigen by the TCR
The TCR of CD4+ and CD8+
T cells recognizes MHC-bound peptide + portions of the MHC.
Other T cells (gd T cells, NKT cells) recognize non-peptide antigens; these are small cell populations whose function is unclear.

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

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

26. 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.

27. Role of costimulation in T cell activation

28. 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)

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

30. 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)

31. Therapeutics based on the B7:CD28/CTLA-4 family
2. Removing the brakes on the immune response
Anti-CTLA-4 antibody is approved for tumor
immunotherapy (enhancing immune responses against tumors)
Even more impressive results with anti-PD-1 in cancer patients; combination trials recently reported

32. Blocking the PD-1/PDL-1 pathway to enhance tumor immunity