Thymic epithelial cells undergo apoptosis during aGVHD. Thymic sections from unconditioned BDF₁ mice were analyzed 2 weeks after infusion of T cells from allogeneic B6.CD45.1 mice (b→bd, A-D) or syngeneic BDF₁ mice (bd→bd, E-H). TUNEL⁺ cells among total thymic cells are shown in green (40×/0.75 numerical aperture [NA] objective). For TEC analysis, thymic sections were stained for the intracellular cytokeratin K18²⁵  (shown in red). aGVHD in this nonirradiated model results in severe morphologic alterations in the thymic stromal microenvironment, with a loss in regular organization among K5⁻K18⁺, K5⁺K18⁻ and K5⁺K18⁺ TECs (Figure S3 and Rossi et al²⁵ ). The colocalization of TUNEL and K18 denotes apoptotic TECs (yellow, arrows in insets panels C and D; original magnification × 160 for panels D and H) whose detection depends also on the orientation of the epithelial cell. Areas of elevated epithelial density and TUNEL⁺ TECs were not seen in thymi of mice receiving syngeneic transplants. The relatively low frequency of apoptotic TECs was consistent with the established efficiency of the thymic microenvironment to remove apoptotic-cell debris and also with the high turnover of epithelial cells in situ.^40,41  Four individual experiments were performed, with 2 to 4 animals per group and experiment. Because these experiments yielded comparable results, a representative photomicrograph is shown for each group.