Extended Data Fig. 11: Myeloid cell heterogeneity and spatial mapping in human myocardial infarction.

a, UMAP embedding of integrated snRNA-seq and snATAC-seq data coloured by patient contribution, region, modality and clusters (resolution= 1). b, Marker dot plot showing the DEGs for each fibroblast state. c, Gene expression of MRC1, ITGAX, FLT3 and CD163. Colors refer to gene-weighted kernel density as estimated by using R package Nebulosa. d, Bar plots visualizing myeloid cell sub-population proportion per patient. e, Gene expression of MRC1, ITGAX, SPP1, CCL18, FLT3, ZBTB46 in an external dataset of ischaemic patients. Colors refer to gene-weighted kernel density as estimated by using R package Nebulosa. f, Comparison of myeloid cell proportion between patient groups. P-values were calculated using Wilcoxon Rank Sum test (unpaired, two-sided) (n = 13 for myogenic, n = 8 for ischaemic, and n = 5 for fibrotic group). g, In situ hybridization of CCR2, SPP1 and TREM2 on human myocardial infarction section IZ. Arrows point to phagocytotic vacuoles in the magnification. h, In situ hybridization of SPP1, POSTN and CD163 on human myocardial infarction section IZ. Note that SPP1+ macrophages colocalized in distinct tissue regions and appeared to have an enlarged cell-size. i, In situ hybridization quantification of cell type proportion per tissue section. n=7 patient tissues. Adjusted P-values were calculated using Wilcoxon signed-rank test. j, Median standardized importances (>0) of the cell-state scores of myeloid cells within the spot in the prediction of other myeloid cell-state scores in spatial transcriptomics. k, Mean pearson correlation between myeloid cell’s state scores across all spatial transcriptomics slides. Data in f, i are represented as boxplots where the middle line is the median, the lower and upper hinges correspond to the first and third quartiles, the upper whisker extends from the hinge to the largest value no further than 1.5 × IQR from the hinge (where IQR is the inter-quartile range) and the lower whisker extends from the hinge to the smallest value at most 1.5 × IQR of the hinge, while data beyond the end of the whiskers are outlying points that are plotted individually.