Generation of functional thymic epithelium from human embryonic stem cells that supports host T cell development

Abstract

Inducing immune tolerance to prevent rejection is a key step toward successful engraftment of stem-cell-derived tissue in a clinical setting. Using human pluripotent stem cells to generate thymic epithelial cells (TECs) capable of supporting T cell development represents a promising approach to reach this goal; however, progress toward generating functional TECs has been limited. Here, we describe a robust in vitro method to direct differentiation of human embryonic stem cells (hESCs) into thymic epithelial progenitors (TEPs) by precise regulation of TGFβ, BMP4, RA, Wnt, Shh, and FGF signaling. The hESC-derived TEPs further mature into functional TECs that support T cell development upon transplantation into thymus-deficient mice. Importantly, the engrafted TEPs produce T cells capable of in vitro proliferation as well as in vivo immune responses. Thus, hESC-derived TEP grafts may have broad applications for enhancing engraftment in cell-based therapies as well as restoring age- and stress-related thymic decline.

Figure 1. Directed Differentiation of hESCs into TEPs

(A) Schematic of differentiation protocol and marker genes for specific stages. ES, embryonic stem cells; DE, definitive endoderm; AFE, anterior foregut endoderm; VPE, ventral pharyngeal endoderm; TEP, thymic epithelial progenitors; TEC, thymic epithelial cells. (B) Gene expression analysis of day 11 hESCs treated with the indicated factor combinations (conditions 1–7) (n = 4–10). Fetal and adult human thymus samples served as controls. Values are normalized to TBP, relative to undifferentiated hESCs, and shown as mean ± SD. Dash lines correspond to fetal expression levels that were used as a guide to optimize the differentiation protocol (*p < 0.05, **p < 0.01, ***p < 0.001, unpaired Student’s t test, compared to undifferentiated hESCs). (C) Immunofluorescence analysis of stage 4 cultures differentiated with condition 7 for HOXA3 (green) and EpCAM (red) protein expression. Nuclei were stained with DAPI. Scale bar = 50 μm. See also Figure S1.

Figure 2. hESC-Derived TEPs Mature into TECs In Vivo

(A) Gene expression analysis of undifferentiated hESCs (ES, n = 4), hESCs differentiated with condition 7 (TEPs d11, n = 4), and grafts recovered from HFT (n = 5) and TEP (n = 6) recipient nude mice (8–20 weeks after transplantation). Fetal and adult human thymus samples served as controls. Values are normalized to TBP, relative to undifferentiated hESCs, and shown as mean ± SD (*p < 0.05, Mann-Whitney test, compared to TEPs d11). (B and C) Immunofluorescence analysis of HFT and TEP grafts recovered from nude mice (6–8 weeks after transplantation). (B) Epithelial cells within grafts were identified using a wide spectrum cytokeratin antibody (red). hESC-derived tissue is demarcated from the kidney by white dashed lines. Nuclei were stained with DAPI. Scale bar = 100 μm. (C) Cytokeratin 8 (K8) (green) and cytokeratin 5 (K5) (red) staining identify cortical and medullary TECs, respectively, while K5⁺/K8⁺ double positivity (yellow) indicates progenitor cells. Insets display higher magnification of dashed line areas, showing the three cell types in close proximity. Scale bar = 50 μm.

Figure 3. hESC-Derived TECs Support T Cell Development in Athymic Mice

(A) Flow cytometric analysis of cells isolated from peripheral blood of HFT (n = 2–6), TEP (n = 4–10), and control (n = 3–10) nude recipients for the presence of mouse CD4⁺ and CD8⁺ SP T cells. Values are shown as mean ± SD (*p < 0.05, unpaired Student’s t test, compared to control); #, similar to what has been reported with other xenografts in nude animals (Taguchi et al., 1986; Fudaba et al., 2008); mice grafted with HFT started showing signs of autoimmunity and were sacrificed before 15 weeks. (B) Immunofluorescence analysis of HFT and TEP grafts recovered from nude mice for the presence of mouse CD8⁺ (green), CD4⁺ (red) and CD8⁺CD4⁺ DP (yellow) T cells. hESC-derived tissue is demarcated from the kidney by white dashed lines. Nuclei were stained with DAPI. Scale bar = 50 μm. (C–E) Flow cytometric analysis of cells recovered from WT mouse thymus, HFT, TEP, and control grafts for the presence of mouse CD4⁺ (red), CD8⁺ (blue) and CD4⁺CD8⁺ DP (green) T cells. (C) Representative plots from WT mouse thymus and grafts harvested 9 weeks (HFT) or 15 weeks (TEP and control) after transplantation. (D) Quantification of the percentage of mouse DP T cells in WT mouse thymus (n = 5), HFT (n = 5), TEP (n = 6), and control (n = 6) grafts harvested 4–12 weeks (HFT) or 8–22 weeks (TEP and control) after transplantation (*p < 0.05, **p < 0.01, Mann-Whitney test). (E) Cell surface expression of mouse T cell markers CD3 and TCRβ on DP T cells (green), CD4⁺ SP T cells (red), and CD8⁺ SP T cells (blue). See also Figure S2.

Figure 4. New T Cells Are Generated in TEP-Recipient Nude Mice

(A–C) Splenocytes recovered from WT (n = 4), HFT-grafted (n = 8), TEP-grafted (n = 4), control-grafted (n = 7), and nongrafted (n = 5) nude mice were analyzed by flow cytometry for mouse CD4, CD8, TCRβ, and Foxp3 expression. (A) Percentage of CD4⁺ (red) and CD8⁺ (blue) splenocytes. (B) Percentage of CD4⁺TCRβ⁺ (red) and CD8⁺TCRβ⁺ (blue) splenocytes. (C) Percentage of Foxp3⁺ regulatory T cells (purple) among CD4⁺ SP T cells. (p* < 0.05, p** < 0.01, unpaired Student’s t test, compared to control.) (D and E) Assessment of TCR repertoire diversity by spectratype analysis of the CDR3 Vβ regions of mouse T cells recovered from spleens of WT (n = 3), HFT (n = 4), TEP (n = 4), and control (n = 5) recipient nude mice. (D) Representative spec-tratypes from three Vβ families are shown. (E) Spectratype complexity score representing the sum of peaks from each of the 24 Vβ family tested. (p* < 0.05, p** < 0.01, ***p < 0.001, unpaired Student’s t test.)

Figure 5. T Cells Generated in TEP-Recipient Nude Mice Respond To TCR and Allogeneic Stimulation In Vitro

(A) Proliferation of splenic T cells following in vitro TCR stimulation. Splenocytes from WT C57BL/6 (n = 4), HFT (n = 5), TEP (n = 4), and control (n = 6) recipient nude mice were labeled with CFSE and cultured for 3 days in the presence of anti-CD3/CD28. Cells were stained for CD4 and CD8 and gated populations were analyzed by flow cytometry for CFSE levels. Nonstimulated cells are represented by shaded histograms. (*p < 0.05, **p < 0.01, ***p < 0.001, unpaired Student’s t test, compared to control.) (B and C) Proliferation of enriched T cells in response to CD11c⁺ APCs. Enriched T cells from WT C57BL/6 (n = 6–8), HFT (n = 8–10), TEP (n = 8–12), and control (n = 4–8) recipient nude mice were labeled with CFSE and cultured for 4 days in the presence of CD11c⁺ APCs isolated from NOD (B) or nu/+ mice (C). Cells were stained for CD90.2, CD4, and CD8, and gated populations were analyzed by flow cytometry for CFSE levels. Nonstimulated cells are represented by shaded histograms. (*p < 0.05, unpaired Student’s t test, compared to control.)

Figure 6. T Cells Generated in TEP-Recipient Nude Mice Mediate In Vivo Immune Responses

(A) Survival of allogeneic skin grafts (from C57BL/6 mice) in nu/+ (n = 4), HFT (n = 4), TEP (n = 6), and control (n = 9) recipient nude mice. (B) Representative images of allogeneic skin grafts in nu/+, HFT, TEP, and control recipient nude mice at the time of rejection.

Figure 7. Model for the Generation and Maturation of hESC-Derived TEPs in Thymus-Deficient Nude Mice

(1) TEPs are generated from hESCs in vitro using the indicated combination of factors. (2) At the end of stage 4, TEPs are transplanted under the kidney capsule of thymus-deficient nude mice, which allows the in vivo maturation of TEPs into TECs. (3) In the presence of hESC-derived TECs, mouse T cell progenitors from the host can mature from CD4⁻CD8⁻ DN T cells (white) to CD4⁺CD8⁺ DP (green) and SP T cells (blue and red). (4) Functional T cells migrate to the periphery of TEP-grafted mice where they can mediate immune responses such as rejection of allogeneic skin grafts.