Fig. 2: The phenotype of COTL1high NK population in HCC tumours.
a, Scatter plots showing the DEGs between COTL1high NK cells and other NK populations in the tumours. b, The frequencies of positive cells for selected functional genes across six NK clusters from each HCC tumour (n = 4) analysed using scRNA-seq. Data are presented as median ± interquartile range, with individual samples (dots). KIRs, killer cell immunoglobulin-like receptors. c, The t-distributed stochastic neighbour embedding map plots showing the seven NK clusters defined by 25 protein markers. The black arow marks the COTL1high NK cluster. cNK, conventional NK cells; lrNK, liver-resident NK cells. d, A heat map showing the protein expression used in the clustering across seven NK subtypes defined by CyTOF data. e, Bar plots showing the positive rate of CD11b, CD27, granzyme B and IFN-γ in the four tumour-enriched subtypes. f–h, A cytometry analysis of NK cells from tumour tissue of patients with HCC (n = 14) expressing PD-1 (f) (P = 0.0034), IFN-γ (g) (P = 0.0001) and granzyme K (h) (P = 0.0012). i, A violin plot showing the expression distribution of ten-gene IFN-γ-related signature score in COTL1high NK cells from pretreated and post-treated data (GSE235863). j, The RNA-seq data analysis showing the average MHC-I gene expression of paired pretreated and post-treated tumours (EGAD00001010132, n = 5 versus 11; responder, pre versus post, P = 0.0079; non-responder, pre versus post, P = 0.3248). k, The enrichment of IFN-γ response pathways in matched samples with or without MHC-I increase (EGAD00001010132). (with MHC-I increase, pre versus post, P = 0.0009; without MHC-I increase, pre versus post, P = 0.4518). l, The enrichment of IFN-γ downstream JAK–STAT signalling pathway in matched samples with or without MHC-I increase (EGAD00001010132) (with MHC-I increase, pre versus post, P = 0.0001; without MHC-I increase, pre versus post, P = 0.8383). m, Representative mIHC staining (left) and statistical results (right) depicting the tumour MHC-I expression of paired pretreated and post-treated specimens (n = 5 versus 5). Scale bar, 250 μm. (responder, pre versus post, P = 0.0021; non-responder, pre versus post, P = 0.7990). n, The spatial transcriptomics analysis of post-treated samples showing the MHC-I expression, COTL1high NK cell positive spot and IFN-γ response score in responders and non-responders (GSE238264). P values were determined by paired two-sided Mann–Whitney test in f–h and j–m. P values were determined by unpaired two-sided Mann–Whitney test in i. *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001; n.s., not significant.
