Fig. 4: Distinct genes are associated with clonal expansion in autoimmune follicular T cells.

a Clone size mapped onto UMAP visualization of transcriptomic data of individual follicular T cells from WT (left) or mixed 564Igi (right) mice. Clonotypes are defined by paired full length TCRα and TCRβ sequences and clone sizes are number of individual cells within a given clonotype. b Scatter plot comparing clone size between WT and mixed 564Igi chimeras. Clonotypes are colored according to preferential expansion (absolute log₂FC > 3 and clone size >10) in WT (black) or mixed 564Igi (red) chimeras and sized according to number of samples in which the given clonotype is observed. c Volcano plots of differentially expressed genes between cells belonging to clonotypes preferentially expanded in mixed 564Igi versus WT chimeras indicated in (b). Adjusted P-value <0.01 and log₂FC > 0.2 shown in red. Differential expression computed by MAST and adjusted for multiple comparison based on Bonferroni correction. d Expression of indicated genes in cells belonging to preferentially expanded clonotypes in WT (gray) or mixed 564Igi (red) chimeras. e Rank order plot of Spearman’s correlation coefficients of each gene with clone size across all cells. f Scatter plots comparing correlation coefficients of each gene with clone size between WT and mixed 564Igi chimeras within assigned clusters. Correlation coefficients >0.05 are indicated in black (correlated in both conditions), red (correlated in mixed 564Igi chimeras only), or red (correlated in WT chimeras only). g Average expression of indicated gene amongst all cells belonging to individual clonotypes versus clone size. Clonotype color indicates sample condition (black, WT; red, 564Igi).