Fig. 5

Transcriptional and clonal diversity of CD8 T lymphocytes between pCR and non-pCR patients. a tSNE of cells from total samples colored by cell type based on scRNA-seq, b Expressions of selected canonical marker genes in each major cell population based on scRNA-seq, c tSNE of CD8 T lymphocytes from total samples colored by cell type based on scRNA-seq, d Expressions of selected canonical marker genes in each major CD8 T lymphocytes populations based on scRNA-seq, e abundance of major CD8 T lymphocytes populations in each tissue sample based on scRNA-seq, f Heatmap and abundance of major CD8 T lymphocytes populations in all primary tumors based on cyTOF data, g validation of CDKN1A+ CD8 T lymphocytes score in pCR and non-pCR patients based on RNA-seq data. h Volcano plot showing differentially expressed genes between CDKN1A+ CD8 T lymphocytes and CDKN1A- CD8 T lymphocytes, i External validation of CDKN1A+ CD8 T lymphocytes in BioKey, j External validation of CDKN1A+ CD8 T lymphocytes in GSE246613, k Venn plot of the shared TCR clonetypes of CD8 T lymphocyte between primary lesions and lymph nodes, l Shannon Index of TCR in tumor, peripheral blood and lymph nodes between pCR and non-pCR patients, m Gini Simpson index of TCR in tumor, peripheral blood and lymph nodes between pCR and non-pCR patients, n TCR clonality in tumor, peripheral blood and lymph nodes between pCR and non-pCR patients. tSNE t-Distributed Stochastic Neighbor Embedding, pCR pathological complete response. E, T cell expansion. NE, no T cell expansion