Extended Data Fig. 11: HR deficiency impacts myeloid cell phenotypes.

a, Estimated effects of mutational signature on dendritic and macrophage cell cluster compositions using GLM. b, Left, intra-sample diversity of myeloid cell clusters in adnexal and non-adnexal samples estimated by Shannon entropy, with samples grouped by mutational signature (patient and sample counts shown). Right, intra- and inter-patient dissimilarity in myeloid cell cluster composition, with samples grouped by mutational signature, estimated using the Bray–Curtis distance. Pairwise dissimilarity is shown for all pairs of sites (patient and sample pair counts shown) excluding ascites (top) and for adnexal versus non-adnexal pairs of sites (bottom). c, Fraction of macrophages expressing CD274 (PDL1) and CXCL10 and JAK-STAT pathway activity with respect to mutational signature. d, Spatial density of CD68⁺PDL1⁺ macrophages in adnexal and non-adnexal mpIF samples as a function of distance to the tumour-stroma interface, grouped by mutational signature. Counts within 10 μm distance bands are grouped across FOVs from each mutational signature subtype, and are normalized by the total number of CD68⁺ cells. Error bars denote the standard error of the proportion (Methods). e, Site and signature-specific enrichment of coarse-grained myeloid cell clusters using GLM. Colour gradient indicates log₂ odds ratios and sizes indicate the Bonferroni-corrected −log₁₀(P value). f, Dimensionality reduction of the dissimilarity in myeloid cluster composition between pairs of samples using NMDS (Methods). Convex hulls highlight differences between samples based on the anatomic site and mutational signature. g, Spatial density of CD68⁺ macrophages in adnexal and non-adnexal samples as a function of distance to the tumour-stroma interface, grouped by mutational signature. Counts within 10 μm distance bands are grouped across FOVs from each mutational signature subtype, and are normalized by the total number of cells. Error bars denote the standard error of the proportion (Methods). h, Correlation between the fraction of dendritic cells expressing interferon regulating factors and JAK-STAT signaling scores in cancer cells, T cells and macrophages. In b and c, brackets indicate two-sided Wilcoxon pairwise comparisons. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.