T Cell Differentiation

For Immunology Chapter 11 Day 2

  1. What are the three features that define helper T cell subsets?
  2. Figure 11-9 is confusing. Redraw it with a separate pair of DCs and naïve T cells.  In other words, draw DC/T cell interaction for Th1 and a separate DC/T cell interaction for Th2.  Add in the relevant information from 11-9 for each DC/T cell pair.
  3. Th1 polarizing cytokines prevent Th2 differentiation. Th2 polarizing cytokines prevent Th1 differentiation.  Explain how this happens at both the “master regulator” and the “effector cytokine” functional levels.
  4. Why do IL-12(p40) KO mice have neither Th1 nor Th17 cells?
  5. The book points out that there is some overlap in the Th17 and Treg cell polarizing cytokines (such as TGFbeta). What example situation did they suggest would lead toward Th17 polarization rather than Treg polarization?
  6. What types of immune responses lead to the tuberculoid and the lepromatous form of leprosy (Hanson’s disease)? Compare the pathology of these two forms of the disease.

B Cell Life after Split with T Cell

For Immunology Chapter 12 Day 2

  1. Activated B cells depart from their interaction with T cells at the T cell/B cell boundary and head either to the extrafollicular area to immediately begin developing into plasma cells or to the germinal centers (GC) where they go on to interact with FDC and TFH. Explain which activated B cell fate produces either the soluble IgM or the soluble IgG during the primary response (see first half of figure 12-16).  Why do they make the Ab isotypes?
  2. Draw a GC with a surrounding follicular mantle. What cell type(s) would be expected in the mantle, the dark zone of the GC, and the light zone of the GC.  Compare the activities of the B cells in the light and dark zones.
  3. Activation-induced cytodine deaminase (AID or AICD) is involved in what GC process(es)? Deamination of a deoxycytodine results in the creation of what dNTP?
  4. Draw an AID mutational hotspot that has the sequence DGYW and the antisense sequence WRCH. Where would AID make a mutation? What region of the Fab contains high numbers of these sequences?
  5. What are the possible outcomes when DNA repair machinery “fixes” the base pair mismatch caused by AID? What happens if DNA repair machinery doesn’t get involved?
    1. Uridine glycosylation + short-patch base excision repair
    2. Mismatch repair
    3. No repair
  6. What effect does having many WGCW sequences (antisense = DGCD) in the “switch” regions of the heavy chain locus when AID is active?

Bonus: How is this related to genomic editing with CRISPR?

  1. A B cell cannot switch from expressing IgE antibodies to IgG1 antibodies. Why?
  2. Why, in figure 12-16, is the response to 2o Ag so different than 1o antigen?

B Cells Meet T Cells in the Middle

For Immunology Chapter 12 Day 1

  1. What were some of the important ideas MacFarlane Burnett put forth in this “Clonal Selection Theory” publication?
  2. When B cells interact with CD4+ T cells that recognize the same antigen, there are three signals. Describe signals 1, 2, and 3 as well as the purpose of each of these signals.
  3. B cells can respond to antigen independently of T cells in two ways. Briefly compare TI-1 (involves PRRs) and TI-2 (involves C3d and multiple Ig receptors) initiated responses.
  4. How are antigen-displaying B cells controlled to stick around the boundary between the B cell and T cell area?
  5. What are some “big picture” differences between the fates of activated B cells that enter primary foci compared to those that enter a germinal center?
  6. Many different routes can be taken to providing naïve B cells antigen in the lymph node. Describe a couple of them.
  7. Membrane spreading…what is it and what purpose does it serve?
  8. For B cells, some antigen is taken up into clathrin-coated pits and some remains on the B cell’s surface. What main role do these two pools of antigen have?

T Cell and APC Signals 1, 2, and 3!

For Immunology Chapter 11 Day 1

  1. “Signal 1” occurs when a TCR recognizes antigen within an MHC molecule on an antigen presenting cell. Then, transcription of IL-2 and CD25 occur.  What is the significance of the upregulation in these two genes?
  2. What molecular interactions would you expect to find in cSMACs and pSMACs? What purpose do these interactions serve?
  3. We have been saying that “signal 2” occurs when CD28 molecules on T cells interact with CD80/CD86 molecules on APCs. Describe the outcomes of these other types of signal 2 interactions.
    1. ICOS and ICOS-L
    2. CTLA-4 and CD80/86
    3. PD-1 and PD-L1/L2
  4. What professional APCs would you most likely find in secondary lymphoid organs? Where in the SLO would they be and why would they be there?
  5. Do superantigens simulate signal 1, 2, or 3? How?
  6. Mosmann and Coffman studied clonal CD4+ T cells to look for heterogeneity in a polyclonal T cell culture. They found that the 50 clones that they studied fell into two groups based on cytokine production.  What did they call these two groups?  What appeared to be the general purpose for each group?

Wrapping Up T Cell Development with a Discussion of Death (or Not)

For Immunology Chapter 9 Day 3

  1. During the selection process in the thymus, thymocytes mature from CD4+ CD8+ (DP) cells to being single positive (SP) for either CD4 or CD8. Briefly describe the following:
    1. Instructive model
    2. Stochastic (random) model
  2. The kinetic signaling model is the currently accepted idea for explaining why cells commit to a CD4+ vs. CD8+ lineage. Which lineage is the default?  What happens when the TCR signal is interrupted on its way to the default lineage?
  3. Why would individuals that are lymphopenic have a higher percentage of recent thymic immigrants relative to typical levels?
  4. Thinking back to the two-step model for T cell activation (TCR/peptide/MHC interaction + CD28/CD80 or CD86 interaction), describe how recognition (in peripheral tissues) of a self peptide in an MHC molecule may not lead to T cell activation.
  5. Discuss two mechanisms (out of four that the book describes) for how TREG cells prevent autoimmunity. Can you think of an example of when a drug that inhibits these regulatory cells would be useful?
  6. What are some characteristics you would detect in a cell undergoing the apoptotic version of programmed cell death? How do these differ from the characteristics of a necrotic cell?
  7. T cells and thymocytes often die via apoptosis as an infection is controlled and during selection, respectively. Which of these situations is more likely to use the “extrinsic” (from outside the cell) pathway?  How does the extrinsic pathway differ from the intrinsic pathway?
  8. Certain types of B cell leukemia can be caused by translocations of chromosomes. Why would translocation of the bcl-2 gene next to an immunoglobulin heavy chain promoter be “BAD!”?

T Cell Development – Selection and More Selection

For Immunology Chapter 9 Day 2

  1. After jumping through the hoops necessary to make functional α and β chains of their TCRs, ~95% of CD4+CD8+ (DP) thymocytes die from what? Because of this fact, why are quotes necessary when someone says thymocytes “learn” or are “educated” in the thymus?
  2. What stages of T-cell development (DN1, DN2, DN3, DN4, DP, CD4 SP, or CD8 SP) would be affected in mice with the following genetic modifications? Justify your answers.
    1. Mice that do not express MHC class II
    2. Mice that do not express AIRE.
    3. Mice that do not express the TCRα chain.
  3. You stain thymocytes with PE-conjugated anti-CD3 and FITC-conjugated anti-TCRβ. Most cells stain with both.  However, you find a proportion of cells that stain with neither antibody.  You also find a small population that stain with anti-CD3, but not with anti-TCRβ.  What thymocyte populations might each of these populations represent?
  4. The overview figure for this chapter (9-1) shows that “Positive and negative selection” occurs in the thymic cortex and that “Negative selection” occurs in the thymic medulla. Compare and contrast the two forms of negative selection.  (Hint: In which negative selection step does “AIRE” play a role?)
  5. Describe the experiments where Hogquist and colleagues made use of 1) the fetal thymic organ culture (FTOC) system and 2) mice deficient in TAP-1. From these experiments, what is the estimated difference in binding affinity between cells that are negatively vs. positively selected?