Human thymopoiesis produces polyspecific CD8+ α/β T cells responding to multiple viral antigens
- Sorbonne Université, INSERM, Immunology‐Immunopathology‐Immunotherapy, France
- AP‐HP, Hôpital Pitié‐Salpêtrière, Clinical Investigation Center for Biotherapies (CIC‐BTi) and Immunology‐Inflammation‐Infectiology and Dermatology Department (3iD), France
- Université Paris Cité, Institut Cochin, CNRS, INSERM, France
- ILTOO pharma, Statistical department, France
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, France
- Center of Life Sciences, Skoltech, Russian Federation
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, France
Figures
Figure 1 with 3 supplements
Thymocyte differentiation produces clustered CDR3s with high generation probability and preferential TRB VJ gene combinations.
(A) Representation of βCDR3aa networks from DPCD3−, DPCD3+, and CD8+. Each dot represents a single CDR3. Dots are connected (forming clusters) by edges defined by Levenshtein distance of ≤1 (one AA …
Figure 1—figure supplement 1
Dotplot of thymocytes sorting.
(A) Dotplot of thymocytes sorting. Cells from the different patients were sorted according to their phenotypes: CD3+CD4CD8+ for ThyCD8, CD3+CD4+CD8+ for DPCD3+ and CD3−CD4+CD8+ for DPCD3−. (B) …
Figure 1—figure supplement 2
Properties of thymocytes’ TCRs.
βCDR3 network during thymopoiesis. Representation of the 18,000 most frequent βCDR3 networks from DPCD3+ and CD8+ thymocytes of eight donors (Pn).
Figure 1—figure supplement 3
Properties of thymocytes’ TCRs.
(A, B) Clustered αCDR3s from DPCD3+ and CD8+ thymocytes. Analyses were performed on the first 18,000 most frequent αCDR3s per sample (n=6 for DPCD3+ and n=10 for CD8+ thymocytes). (A) Percentage of …
Figure 2 with 1 supplement
Thymocyte differentiation produces clustered CDR3s with high publicness.
Mean percentages of public (black) or private (gray) βCDR3s in all, dispersed or clustered nodes (****p<0.0001, Mann–Whitney test, mean ± s.e.m, n=13). (B) Enrichment of public βCDR3s in the CD8+ …
-
Figure 2—source data 1
Enrichment of public βCDR3s in CD8+ thymocytes versus DPCD3+.
- https://cdn.elifesciences.org/articles/81274/elife-81274-fig2-data1-v1.docx
Figure 2—figure supplement 1
Publicness of thymocytes’ CDR3s.
(A) βCDR3 sharing between individuals. Pie charts represent the sharing between individuals before (DPCD3+) and after thymic selection (CD8+). Colours represent the dispersed (gray) or clustered …
Figure 3 with 3 supplements
Clustered public TCRs are enriched for virus-specific TCRs.
(A) Barplots showing the mean percentages of CDR3s associated with pathogens within DPCD3+ and ThyCD8 cells and for dispersed or clustered CDR3s. (B) Mean generation probability of virus-specific …
-
Figure 3—source data 1
Enrichment of virus-specific βCDR3s from databases in clustered CD8+ thymocytes.
- https://cdn.elifesciences.org/articles/81274/elife-81274-fig3-data1-v1.docx
Figure 3—figure supplement 1
Virus specificities of thymocytes’ CDR3s.
(A) Enrichment of virus-specific βCDR3s in the CD8+ thymocyte repertoire. Representation of the generation probability as a function of βCDR3 connections in individuals (Pn). The contour plots …
Figure 3—figure supplement 2
Sharing of virus specific thymocytes’ CDR3s.
(A) Network of clustered nodes from the first top ranking 18,000 CDR3s. For each individual, we plot CDR3s as viral-associated (red) either if they are in the public database (lines 1 and 2) or if …
Figure 3—figure supplement 3
Binding properties of single-cell TCRs.
(A) Network of tetramer-binding CDR3s from public database (VDJdb) identifying CDR3s with multiple viral specificities. Each dot represents a single CDR3. Dots are connected by an edge defined by a …
Figure 4 with 2 supplements
Identification of polyspecific TCRs.
(A) Analysis of shared T-cell specificities with the GLIPH2 algorithm. 216,000 CDR3β sequences from the CD8 thymocytes and 32,496 sequences from VDJdb that are tetramer specific were analysed to …
-
Figure 4—source data 1
List of peptides represented on the chord plot from Figure 4C.
- https://cdn.elifesciences.org/articles/81274/elife-81274-fig4-data1-v1.docx
Figure 4—figure supplement 1
Binding patterns to A*03 and A*11 dextramers.
(A) Heatmap of the binding score for different dextramers of different TCRs using the same CASSIRSSYEQYF βCDR3, in two donors. The recognition properties are remarkably similar whatever the βCDR3. …
Figure 4—figure supplement 2
Single-cell gene expression analysis.
(A) Six of the most expanded clonotypes were selected from the single-cell data set, of which three were specific to the Influenza_A0201 GILGFVFTL dextramer (A02_GILG9 specific), and the other three …
Figure 5 with 2 supplements
Polyreactivity of polyspecific TCRs.
(A) Schematic representation of the in vitro cross-activation experiment. (B) In vitro activation of polyspecific T cells. Percentage of IFNγ producing emCD8+ cells after activation with …
-
Figure 5—source data 1
List of the sequences of individual TCRs expressed and analyzed in vitro in Figure 5.
- https://cdn.elifesciences.org/articles/81274/elife-81274-fig5-data1-v1.docx
Figure 5—figure supplement 1
Gating strategy for sorting effector memory (emCD8) Dextramer positive cells.
(A, B) CD8 were previously enriched from cytapheresis PBMC. Gating strategy of the sorting of Cytomegalovirus (A) or Epstein-Barr virus (B) dextramère positive effector memory CD8 (emCD8) from CD8 …
Figure 5—figure supplement 2
Polyspecific properties of anti-CMV cytotoxic cells.
(A) PBMC were stimulated in vitro using Peptivator CMV pp65 (that consists mainly of 15-mer peptides with 11-amino acid overlap, covering the complete sequence of the pp65 protein) and cultured for …
Author response image 1
Author response image 2
Author response image 3
multi-GIL are multi-specific clonotypes with the highest specificity being towards the A02-GIL dextramer.
Multi-other refers to multi-specific clonotypes without any differentially high binding to any of the dextramers. Finally, uni-GIL are uni-specific clonotypes that exclusively bind the A02-GIL …
Author response image 4
