1. T Cell Development Amy Lovett-Racke, PhD Associate Professor
Department of Microbial Infection and Immunity
Reading: The Immune System 3rd Edition, Peter Parham, Chapter 7

2. At the end of this module, you will:
Learning Objectives
At the end of this module, you will:
Understand
the significance and purpose of thymic education and the potential deficits that can occur if this process is ineffective.
Describe
thymus anatomy and the stages of T cell development that associate with different thymic compartments.
the process of positive- and negative-selection.

3. The primary purpose of T cell development is to generate a diverse repertoire of T cells that distinguishes between self and non-self.
Thymic Education

4. Thymus – Primary lymphoid organ
The thymus is considered a primary lymphoid organ because it is the site of T cell development. The bone marrow is the other primary lymphoid organ. The bone marrow and thymus are considered primary lymphoid organs because they are the site at which progenitor cells become different immune cell types. The thymus is located just above the heart. Lymphoid progenitor cells migrate from the bone marrow to the thymus via blood. These lymphoid progenitor cells will undergo a maturation process, called thymic education or T cell development. At the end of this process, naive mature T cells will be released from the thymus via the blood where they will migrate to secondary lymphoid tissues., such as the spleen lymph nodes. and gut associated lymphoid tissues. Secondary lymphoid tissues are sites of lymphocyte activation. The term "T cell" originated from thymus-dependent lymphocytes that was shortened to T lymphocyte and now T cell.
Thymus-dependent lymphocytes → T lymphocytes → T cells

5. Structure of the Thymus
Flat, bilobed organ situated above the heart. Each lobe is surrounded by a capsule and is divided into lobules, which are separated from each other by strands of connective tissue called trabeculae. Each lobule is organized into two compartments: the cortex (outer compartment) the medulla (inner compartment).

6. The Thymus
The thymus is composed of epithelial cells (thymic stroma) that form a network surrounding developing lymphocytes.
Dendritic cells and macrophages in the thymus are critical for T cell selection.
Patient who fail to develop a thymus are severely immunocompromised (DiGeorge’s syndrome).

7. Involution of the Thymus
3 days old
70 year old

8. Involution of the Thymus
3 days old
70 year old
Are bone marrow transplants more successful in children or adults?

9. Involution of the Thymus
3 days old
70 year old
Bone marrow transplants are more successful in children!

10. Cell Surface Markers Associated with T Cell Development
CD34+ progenitor cells enter the thymus via blood vessels.
On interaction with stromal epithelial cells, the cells divide and differentiate.
Stem cell markers are down-regulated (CD34 and CD44) and T cell-specific markers are upregulated.
IL-7 produced by stromal cells is a critical initial step to thymocyte differentiation.
Mutations in IL-7 receptor results in no T cell development.
Cell Surface Markers Associated with T Cell Development

11. Cell Surface Markers Associated with T Cell Development
CD34+ stem cells enter the thymus via blood vessels.
On interaction with stromal cells, the stem cells divide and differentiate.
Stem markers are down-regulated (CD34 and CD44) and T cell-specific markers are upregulated.
IL-7 produced by stromal cells is a critical initial step to thymocyte differentiation.
Mutations in IL-7 receptor results in no T cell development.
Cell Surface Markers Associated with T Cell Development
What class of disease would mutations in the IL-7 receptor cause?

12. Cell Surface Markers Associated with T Cell Development
CD34+ stem cells enter the thymus via blood vessels.
On interaction with stromal cells, the stem cells divide and differentiate.
Stem markers are down-regulated (CD34 and CD44) and T cell-specific markers are upregulated.
IL-7 produced by stromal cells is a critical initial step to thymocyte differentiation.
Mutations in IL-7 receptor results in no T cell development.
Cell Surface Markers Associated with T Cell Development
What class of disease would mutations in the IL-7 receptor cause?
Severe Combined Immunodeficiency Syndrome (SCID)

13. Double-negative T-cell progenitor
A common progenitor gives rise two lineages of T cells.
Double-negative refers to the absence of CD4 and CD8.
Each T cell receptor has two chains.

14. Double-negative T-cell progenitor
A common progenitor gives rise two lineages of T cells.
Double-negative refers to the absence of CD4 and CD8.
Each T cell receptor has two chains.
IL-7 receptor signaling

15. IL-7 receptor signaling
A common progenitor gives rise two lineages of T cells.
Double-negative refers to the absence of CD4 and CD8.
Each T cell receptor has two chains.
IL-7 receptor signaling

16. Uncommon double-negative positive thymocyte
A common progenitor gives rise two lineages of T cells.
Double-negative refers to the absence of CD4 and CD8.
Each T cell receptor has two chains.
The generation of a T cell Receptor is vital to T cell development. The T cell receptors are generated from different gene segments that combine, somewhat randomly, to form new genes. This rearrangement process occurs at the DNA level, so that rearrangements within the DNA of a specific T cell is permanent and unique for that particular T cell. This is the same process that occurs in B cells for B cell receptors which results in immunoglobulin or antibody production. This process is unique for B cells and T cells, and is critical to generating a population of adaptive immune cells that can recognize many different pathogens. Gamma, delta and beta chain genes go thru a rearrangment process first. If the gamma and delta genes rearrange successfully before the beta chain, this T cell will express a gamma delta T cell receptor and this T cell is mature, yet naive. It is naive because it has not encountered antigen. However, most T cells will rearrange the beta chain successfully first. If this happens, gene rearrangement ceases. This initiates the expression of the co-receptors CD4 and CD8. These cell are referred to as double-positive T cells.

17. Gene rearrangements
A common progenitor gives rise two lineages of T cells.
Double-negative refers to the absence of CD4 and CD8.
Each T cell receptor has two chains.

18. Committed alpha-beta T cell
A common progenitor gives rise two lineages of T cells.
Double-negative refers to the absence of CD4 and CD8.
Each T cell receptor has two chains.

19. Gamma-delta T cells Comprise only 1-5% of total T cells
Do not required MHC presentation of antigens
Express less T cell receptor diversity
Function similar to cells of the innate immune response in that they can traffic to site of inflammation due to specific chemokine receptor expression.
Bridge between the innate and adaptive immune responses

20. Positive Selection 1. Positive selection only occurs for αβ T cells.
2. It occurs in the cortex of the thymus.
3. Only ~2% of double-positive thymocytes have T cell receptors that can recognize the MHC expressed by that individual.
4. Positive selection retains T cells that recognize self-MHC.
Positive Selection

21. Positive Selection
Cortical epithelial cells express self-peptides on their surface to double-positive thymocytes.
If the TCR can not bind to the MHC/peptide complexes, no signal is sent and the thymocyte dies.
If the TCR can bind effectively to the MHC/peptide complexes, a survival signal is sent and the T cell lives.

22. Peptide Presentation
The number of different peptides that can be presented by a specific MHC molecule is ~10,000.
If an individual is heterozygous for the six major HLA genes, ~120,000 peptides could be expressed.
The number of unique T cell receptors is ~25,000,000.
Only ~2% of double-positive thymocytes express αβ TCR that will recognize self-MHC.

23. Positive Selection
Positive selection also down-regulates either CD4 or CD8, depending on whether the TCR interaction with peptide occurred in the context of MHC class I (CD8) or class II (CD4), resulting in single positive T cells.
Positive selection retains T cells that recognize self MHC.

24. Positive Selection
Positive selection also down-regulates either CD4 or CD8, depending on whether the TCR interaction with peptide occurred in the context of MHC class I (CD8) or class II (CD4), resulting in single positive T cells.
Positive selection retains T cells that recognize self MHC.
What happens if an individual does not express MHC class I or II molecules?

25. Positive Selection Bare Lymphocyte Syndrome
Positive selection also down-regulates either CD4 or CD8, depending on whether the TCR interaction with peptide occurred in the context of MHC class I (CD8) or class II (CD4), resulting in single positive T cells.
Positive selection retains T cells that recognize self MHC.
What happens if an individual does not express MHC class I or II molecules?
Bare Lymphocyte Syndrome

26. Negative selection Negative selection deletes self-reactive T cells.
If T cells have TCR that bind tightly to MHC/peptide complexes, a signal results in apoptosis of the T cell.
This occurs in the cortico-medullary junction in the thymus.
Dendritic cells and macrophages are the primary antigen presenting cells that mediate negative selection.
Negative selection deletes self-reactive T cells.

27. Negative selection
How do T cells that recognize antigens unique to specific tissues (brain, muscle, etc) get eliminated in the thymus?
Autoimmune regulator (aire) is a transcription factor expressed in the thymus that promotes the expression of many genes in the thymus at very low levels.

28. Negative selection
How do T cells that recognize antigens unique to specific tissues (brain, muscle, etc) get eliminated in the thymus?
Autoimmune regulator (aire) is a transcription factor expressed in the thymus that promotes the expression of many genes in the thymus at very low levels.
What happens if someone has a mutation in the Aire gene?

29. Negative Selection
How do T cells that recognize antigens unique to specific tissues (brain, muscle, etc) get eliminated in the thymus?
Autoimmune regulator (aire) is a transcription factor expressed in the thymus that promotes the expression of many genes in the thymus at very low levels.
What happens if someone has a mutation in the Aire gene?
Autoimmune Polyendocrinopathy-Candidiasis-Ectodermal Dystrophy

30. Apoptotic T-cells
Thymocytes die via apoptosis at each stage of development, but most T cell death occurs in the cortex by thymocytes that fail to generate a functional TCR or do not get selected.
Apoptotic T cells are engulfed and degraded by macrophages.

31. TCR
Figure 5-6
TCR are generated from numerous germline gene segments that recombine to form unique TCR genes.
Heterogeneity in αβ TCR is generated by
Multiple V, D (β), and J segments.
Addition or deletion of bases during gene rearrangement.
Pairing of α and β genes.
Thymic negative selection deletes T cells that have generated TCR that recognize self-peptides with high affinity.
Human genome contains about 25,000 genes, yet generates at least 25,000,000 unique TCR.

32. TCR
Figure 5-6
TCR are generated from numerous germline gene segments that recombine to form unique TCR genes.
Heterogeneity in αβ TCR is generated by
Multiple V, D (β), and J segments.
Addition or deletion of bases during gene rearrangement.
Pairing of α and β genes.
Thymic negative selection deletes T cells that have generated TCR that recognize self-peptides with high affinity.
Human genome contains about 25,000 genes, yet generates at least 25,000,000 unique TCR.

33. TCR
Figure 5-6
TCR are generated from numerous germline gene segments that recombine to form unique TCR genes.
Heterogeneity in αβ TCR is generated by
Multiple V, D (β), and J segments.
Addition or deletion of bases during gene rearrangement.
Pairing of α and β genes.
Thymic negative selection deletes T cells that have generated TCR that recognize self-peptides with high affinity.
Human genome contains about 25,000 genes, yet generates at least 25,000,000 unique TCR.

34. TCR
Figure 5-6
TCR are generated from numerous germline gene segments that recombine to form unique TCR genes.
Heterogeneity in αβ TCR is generated by
Multiple V, D (β), and J segments.
Addition or deletion of bases during gene rearrangement.
Pairing of α and β genes.
Thymic negative selection deletes T cells that have generated TCR that recognize self-peptides with high affinity.
Human genome contains about 25,000 genes, yet generates at least 25,000,000 unique TCR.

35. TCR
Figure 5-6
TCR are generated from numerous germline gene segments that recombine to form unique TCR genes.
Heterogeneity in αβ TCR is generated by
Multiple V, D (β), and J segments.
Addition or deletion of bases during gene rearrangement.
Pairing of α and β genes.
Thymic negative selection deletes T cells that have generated TCR that recognize self-peptides with high affinity.
Human genome contains about 25,000 genes, yet generates at least 25,000,000 unique TCR.

36. Basic Overview of T Cell Development
1. CD34 goes does 2. IL-7R goes up
3. TCR β,γ,δ chains rearrange
4. CD4+CD8 up
5. TCR α,γ,δ chains rearrange
Lymphoid prgenitor cells enter the sub-capsular region of thymic cortex. They mature from CD34+ cells to T cell receptor expressing cells.
In the cortex, the cells expressing αβ TCRs interact with thymic epithelial cells expressing peptides via MHC. MHC class I results in CD8+ T cells. MHC II results in CD4+ T cells.
Lymphoid progenitor cells enter the thymus via blood and naïve mature T cells exit the thymus via blood.
In the cortico-medullary junction, T cells interact with DC expressing MHC molecules containing self-peptides. T cells with TCRs with high avidity for MHC/self-peptides die.
Mature, naïve, self-tolerant T cells exit through venules in the medulla.

37. Basic Overview of T Cell Development
1. CD34 goes does 2. IL-7R goes up
3. TCR β,γ,δ chains rearrange
4. CD4+CD8 up
5. TCR α,γ,δ chains rearrange
Lymphoid prgenitor cells enter the sub-capsular region of thymic cortex. They mature from CD34+ cells to T cell receptor expressing cells.
In the cortex, the cells expressing αβ TCRs interact with thymic epithelial cells expressing peptides via MHC. MHC class I results in CD8+ T cells. MHC II results in CD4+ T cells.
Lymphoid progenitor cells enter the thymus via blood and naïve mature T cells exit the thymus via blood.
In the cortico-medullary junction, T cells interact with DC expressing MHC molecules containing self-peptides. T cells with TCRs with high avidity for MHC/self-peptides die.
Mature, naïve, self-tolerant T cells exit through venules in the medulla.

38. Basic Overview of T Cell Development
1. CD34 goes does 2. IL-7R goes up
3. TCR β,γ,δ chains rearrange
4. CD4+CD8 up
5. TCR α,γ,δ chains rearrange
Lymphoid prgenitor cells enter the sub-capsular region of thymic cortex. They mature from CD34+ cells to T cell receptor expressing cells.
In the cortex, the cells expressing αβ TCRs interact with thymic epithelial cells expressing peptides via MHC. MHC class I results in CD8+ T cells. MHC II results in CD4+ T cells.
Lymphoid progenitor cells enter the thymus via blood and naïve mature T cells exit the thymus via blood.
In the cortico-medullary junction, T cells interact with DC expressing MHC molecules containing self-peptides. T cells with TCRs with high avidity for MHC/self-peptides die.
Mature, naïve, self-tolerant T cells exit through venules in the medulla.

39. Basic Overview of T Cell Development
1. CD34 goes does 2. IL-7R goes up
3. TCR β,γ,δ chains rearrange
4. CD4+CD8 up
5. TCR α,γ,δ chains rearrange
Lymphoid prgenitor cells enter the sub-capsular region of thymic cortex. They mature from CD34+ cells to T cell receptor expressing cells.
Lymphoid progenitor cells enter the thymus via blood and naïve mature T cells exit the thymus via blood.
In the cortex, the cells expressing αβ TCRs interact with thymic epithelial cells expressing peptides via MHC. MHC class I results in CD8+ T cells. MHC II results in CD4+ T cells.
In the cortico-medullary junction, T cells interact with DC expressing MHC molecules containing self-peptides. T cells with TCRs with high avidity for MHC/self-peptides die.
Mature, naïve, self-tolerant T cells exit through venules in the medulla.

40. T Cell Development Quiz

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