Figure 5.
scTCR-seq of CD4 TRM reveals clonal sharing between organs. (A) UMAP plot split by tissue (lung or NT) and colored according to clone size for CD4 TRM in IAV-infected mice. Clones were binned into single clones (1 member; light blue), small (2 to 5 members; red), medium (6 to 19 members; green), and large (over 20 members; gold). Light grey dots represent cells where TCR clonotype could not be assigned. (B) UMAP plot split by tissue (lung or NT) and antigen specificity (I-Ab NP306–322 tetramer or I-Ab HA91–107 tetramer) and colored according to clone size for CD4 TRM in IAV-infected mice. Clones were binned into single clones (1 member; light blue), small (2 to 5 members; red), medium (6 to 19 members; green), and large (over 20 members; gold). Light grey dots represent cells where TCR clonotype could not be assigned. (C) Bar plot characterizing the top 34 most expanded clones. The y axis reports CDR3 sequences of TCRαβ, while the bar graphs show the number of cells divided according to cluster distribution, I-Ab NP306–322 tetramer+ or I-Ab HA91–107 tetramer+, and organ specificity. n.d., not determined. (D) Tile plot indicating paired TRAV and TRBV genes usage split by tissue (lung or NT) and antigen specificity (I-Ab NP306–322 tetramer or I-Ab HA91–107 tetramer) in CD4 TRM of IAV- infected mice. The size of the tile is proportional to TRAV usage frequency. (E) Graph showing clonal relationship between lungs and NT from PR8 IAV-infected mice. Each circle indicates one clonal family, and size of the circle defines the size of the clonal family. Color of the circle denotes the antigenic specificity against I-Ab NP306–322 tetramer and against I-Ab HA91–107 tetramer. n.d., not determined. (F) Clonotype bias plot for clones with at least 6 cells. Clonotypes are colored according to predominant cluster. The red line highlights the null distribution (background distribution) for each clone size. The clones to the right of the red line are biased clones. (G) UMAP plot, split by tissue (lung or NT), depicting two biased clones. Cells belonging to the clonal family are colored according to the cluster, while other cells are in light grey. (H) UMAP plot, split by tissue (lung or NT), depicting the two most expanded clones. Cells belonging to the clonal family are colored according to the cluster, while other cells are in light grey. Refer to the image caption for details. Panel A shows U M A P plots of C D 4 T R M colored by clonal family size across nasal tissue and lungs. Panel B shows U M A P plots of antigen specific C D 4 T R M colored by clonal size for N P and H A specificity. Panel C shows bar plots of expanded clonotypes with distribution across cell types specificity and organ compartments. Panel D shows tile plots of T C R V gene usage patterns across nasal tissue and lungs with antigen specificity. Panel E shows scatter plots of clonal family sizes comparing nasal tissue and lung distributions with antigen specificity. Panel F shows scatter plots of clonotype bias relative to clone size highlighting biased expanded clones across cell types. Panel G shows UMAP plots of representative biased clones across nasal tissue and lungs within clustered C D 4 T R M. Panel H shows UMAP plots of most expanded clones across nasal tissue and lungs showing clonal expansion patterns.

scTCR-seq of CD4 TRM reveals clonal sharing between organs. (A) UMAP plot split by tissue (lung or NT) and colored according to clone size for CD4 TRM in IAV-infected mice. Clones were binned into single clones (1 member; light blue), small (2 to 5 members; red), medium (6 to 19 members; green), and large (over 20 members; gold). Light grey dots represent cells where TCR clonotype could not be assigned. (B) UMAP plot split by tissue (lung or NT) and antigen specificity (I-Ab NP306–322 tetramer or I-Ab HA91–107 tetramer) and colored according to clone size for CD4 TRM in IAV-infected mice. Clones were binned into single clones (1 member; light blue), small (2 to 5 members; red), medium (6 to 19 members; green), and large (over 20 members; gold). Light grey dots represent cells where TCR clonotype could not be assigned. (C) Bar plot characterizing the top 34 most expanded clones. The y axis reports CDR3 sequences of TCRαβ, while the bar graphs show the number of cells divided according to cluster distribution, I-Ab NP306–322 tetramer+ or I-Ab HA91–107 tetramer+, and organ specificity. n.d., not determined. (D) Tile plot indicating paired TRAV and TRBV genes usage split by tissue (lung or NT) and antigen specificity (I-Ab NP306–322 tetramer or I-Ab HA91–107 tetramer) in CD4 TRM of IAV- infected mice. The size of the tile is proportional to TRAV usage frequency. (E) Graph showing clonal relationship between lungs and NT from PR8 IAV-infected mice. Each circle indicates one clonal family, and size of the circle defines the size of the clonal family. Color of the circle denotes the antigenic specificity against I-Ab NP306–322 tetramer and against I-Ab HA91–107 tetramer. n.d., not determined. (F) Clonotype bias plot for clones with at least 6 cells. Clonotypes are colored according to predominant cluster. The red line highlights the null distribution (background distribution) for each clone size. The clones to the right of the red line are biased clones. (G) UMAP plot, split by tissue (lung or NT), depicting two biased clones. Cells belonging to the clonal family are colored according to the cluster, while other cells are in light grey. (H) UMAP plot, split by tissue (lung or NT), depicting the two most expanded clones. Cells belonging to the clonal family are colored according to the cluster, while other cells are in light grey.

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