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. 2022 Jul 13;11:e76339. doi: 10.7554/eLife.76339

Figure 4. Clonal structure of virus-specific CD4+ T cells and clonotype-fate relationship.

(A) Fraction of clonal space occupied by clonotypes with different levels of expansion. For each sample (three replicates for Acute, two replicates for Early Chronic), the plot indicates the number of single cells that belong to clonotypes in one of the five classes of expansion. (B) Number of clones with identical CDR3 nucleotides or amino acid sequence pairs between individual samples among clonotypes with ≥3 cells. (C) Clonotype bias analysis for acute and chronic infection samples. Plots show clonotype bias vs. clonal size for all clones with >10 cells. Clonotypes are colored by predominant T cell subtype (left) or by Z-score of the clonotype functional bias (right). Red line highlights the null distribution (background distribution) for each condition. (D, E) Distribution of cells over the reference map for the (D) four most expanded and (E) four most biased clonotypes in acute and chronic infections. The CDR3 alpha and beta sequences and the clonotype size are indicated for each clonotype.

Figure 4.

Figure 4—figure supplement 1. Repertoire overlap of virus-specific CD4+ T cells and clonotype bias.

Figure 4—figure supplement 1.

(A) Number of clones with identical CD3 nucleotides or amino acid sequence pairs between individual samples among all clonotypes. (B) Clonotype bias analysis for acute and chronic infection samples. A clonotype bias of 1 indicates that a clonotype is composed uniquely of cells from the same subtype, and a clonotype bias of zero corresponds to a clonotype that matches exactly the (random) background subtype distribution. Left plots show clonotype bias colored by sample for all clone with >10 cells. Left plot shows null distribution (background distribution) for each condition. (C) Motif scores calculated on our clonotype data using for significant TCR alpha CDR3 motifs identified by Khatun et al., 2021. Clonotype-biased clones (Zscore >5) are colored according to the dominant CD4 +T cell subtype. (D) Percent and type of biased clones among the top 65% clones as ranked by each of the seven TCR alpha CDR3 motifs. ‘All’ column represents the percent and type of biased clones on all data, regardless of ranking by a specific CDR3 motif.