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Updated: Jun 28, 2026

Preparation and Applications of Organotypic Thymic Slice Cultures
Published on: August 6, 2016
Clonal deletion of thymocytes can occur in the cortex with no involvement of the medulla
Tom M McCaughtry1, Troy A Baldwin, Matthew S Wilken
1Center for Immunology, Laboratory Medicine, and Pathology, University of Minnesota, Minneapolis, MN 55454, USA.
Insights
Self-reactive T cells are deleted in the thymic cortex, not just the medulla. Cortical epithelial cells activate T cells, but rare dendritic cells are key for eliminating self-reactive thymocytes.
Area of Science:
- Immunology
- T cell development
- Thymic selection
Background:
- The thymic medulla is traditionally considered the primary site for negative selection of T cells.
- The role of the thymic cortex in negative selection, particularly concerning ubiquitous self-antigens, remains controversial.
- Cortical epithelial cells are known to be crucial for positive selection.
Purpose of the Study:
- To investigate the site and mechanism of negative selection for self-reactive thymocytes encountering ubiquitous self-antigens in the thymic cortex.
- To determine the specific antigen-presenting cells responsible for inducing apoptosis during negative selection in the cortex.
Main Methods:
- Utilized the HY(cd4) mouse model with timed T cell receptor (TCR) expression and a ubiquitous self-antigen.
- Analyzed the location and kinetics of clonal deletion (apoptosis) in vivo.
- Investigated the role of cortical epithelial cells and CD11c(+) cortical dendritic cells in TCR activation and apoptosis.
Main Results:
- Demonstrated that clonal deletion of self-reactive thymocytes occurs unambiguously in the thymic cortex.
- Found that apoptosis was activated asynchronously relative to TCR activation.
- Cortical epithelial cells efficiently induced TCR activation but not apoptosis; rare CD11c(+) cortical dendritic cells were preferentially associated with deleted thymocytes.
- Elimination of these dendritic cells impaired thymocyte deletion.
Conclusions:
- Negative selection of self-reactive thymocytes can occur in the thymic cortex.
- Cortical epithelial cells are involved in TCR activation, but cortical dendritic cells play a critical role in mediating apoptosis during negative selection.
- This finding refines our understanding of T cell development and self-tolerance induction within the thymus.
Abstract:
The thymic medulla is generally held to be a specialized environment for negative selection. However, many self-reactive thymocytes first encounter ubiquitous self-antigens in the cortex. Cortical epithelial cells are vital for positive selection, but whether such cells can also promote negative selection is controversial. We used the HY(cd4) model, where T cell receptor for antigen (TCR) expression is appropriately timed and a ubiquitous self-antigen drives clonal deletion in male mice. We demonstrated unambiguously that this deletion event occurs in the thymic cortex. However, the kinetics in vivo indicated that apoptosis was activated asynchronously relative to TCR activation. We found that radioresistant antigen-presenting cells and, specifically, cortical epithelial cells do not efficiently induce apoptosis, although they do cause TCR activation. Rather, thymocytes undergoing clonal deletion were preferentially associated with rare CD11c(+) cortical dendritic cells, and elimination of such cells impaired deletion.
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