Fig. 2: Subclustering of MNs, immune, endothelial and stromal cells.
a, UMAP visualization showing all MNs (n = 49,633) present in the snRNA-seq dataset from all conditions. b, Dot plot showing marker genes of MN clusters. c, Compositional analysis of type 1 MNs (P(CTRL-IBM) = 2.1 × 10−2; P(CTRL-IMNM) = 1.8 × 10−2), type 2 MNs (P(CTRL-IBM) = 6.1 × 10−3; P(IMNM-IBM) = 6.1 × 10−3), reactive MNs (P(CTRL-IBM) = 9.3 × 10−4; P(CTRL-IMNM) = 2.4 × 10−2; P(IMNM-IBM) = 6.1 × 10−3) and damaged MNs (P(CTRL-IBM) = 5.2 × 10−3; P(IMNM-IBM) = 1.7 × 10−2) in CTRL, IMNM and IBM (CTRL, n = 7; IMNM, n = 4; IBM, n = 8). d, UMAP visualization showing all immune cells (n = 20,620) present in the snRNA-seq dataset from all conditions. e, Dot plot showing marker genes of immune cell clusters. f, Compositional analysis of MΦ1 cells (P(CTRL-IBM) = 1.0 × 10−1, P(CTRL-IMNM) = 1.4 × 10−1), MΦ2 cells (P(CTRL-IBM) = 1.1 × 10−2), cDC1 cells (P(CTRL-IBM) = 5.4 × 10−3; P(IMNM-IBM) = 2.4 × 10−2) and CTLs (P(CTRL-IBM) = 2.7 × 10−2; P(IMNM-IBM) = 4.2 × 10−2) in CTRLs, IMNM and IBM (CTRLs, n = 7; IMNM, n = 4; IBM, n = 8). g, UMAP visualization showing all endothelial–stromal cells (n = 22,781) present in the snRNA-seq dataset from all conditions. h, Dot plot showing marker genes of identified endothelial–stromal cells. i, Compositional analysis of COL15A1-expressing FAPs (P(CTRL-IBM) = 2.8 × 10−2), CD55-expressing FAPs, EC-C cells (P(CTRL-IBM) = 9.3 × 10−4; P(IMNM-IBM) = 6.1 × 10−3) and pericytes in CTRL, IMNM and IBM (CTRL, n = 7; IMNM, n = 4; IBM, n = 8). Box plots in c, f and i show the median and interquartile range (IQR) of cell/nuclei-type proportions, with whiskers extending to the largest and smallest values within 1.5× the IQR range. Two-tailed, pairwise Wilcoxon’s rank-sum tests with Benjamini–Hochberg correction to account for multiple comparisons or Tukey’s HSD test were performed between conditions in c, f and i. *P < 0.05, **P < 0.01, ***P < 0.001.
