Fig. 4: Single-cell expression and bulk TCR analysis of resected tumours from patients treated with neoadjuvant ICB. | Nature Communications

Fig. 4: Single-cell expression and bulk TCR analysis of resected tumours from patients treated with neoadjuvant ICB.

From: Neoadjuvant immune checkpoint blockade in women with mismatch repair deficient endometrial cancer: a phase I study

Fig. 4

a Paired dot plot of bulk TCR CDR3 sequencing from pre- and post-treatment biopsy tissues (n = 8). Individual patients are annotated by their pathologic and radiologic response. b Heatmap showing correlation between TCR CDR3 sequences in post-treatment biopsies and resection specimens (n = 6), corresponding to those used for IHC in Fig. 3. c UMAP visualization of 11,870 T cells with identical CDR3 TCRs present in bulk TCR sequencing data from the same patient. Clusters are colour-coded by inferred identity. d Bubble plot showing expression and abundance of key canonical marker genes for T cell clusters. e Bar graph of cell subset fractions within significantly expanded and non-expanded populations as determined by bulk TCR sequencing. f Bar graph of clone sizes within expanded and non-expanded populations from bulk TCR sequencing. g UMAP visualization of 199 significantly expanded CD4 T cells, colour-coded by inferred identity. h Circle plot showing shared full-length TCR sequences between significantly expanded CD4 T cells from different clusters. i UMAP visualization of 3014 CD8 T cells with significantly expanded CDR3 TCRs from pre- vs post-treatment bulk TCR sequencing. Clusters are colour-coded by inferred identity. j Bubble plot of marker gene expression and abundance differentially expressed among CD8 T cell subsets. k Scatter plot showing clonal diversity as a function of clone size for significantly expanded CD8 T cells, colour-coded by most abundant cluster. l Bar graph of cell subset fractions within the most abundant ( > 10 identical TCRs) expanded CD8 T cell clones, with each bar representing an individual clone. m Bar graph showing inferred identity of cycling T cells within individual expanded CD8 T cell clones, with each bar representing cycling T cells from an individual clone. Abbreviations: MPR major pathological response, pPR partial pathological response, PR partial response, SD stable disease. Source data are provided as a Source Data file.

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