Fig. 4: Myc expression is elevated in crypt stem cells after allogeneic BMT.

a–d Single cell RNA sequencing of small intestine crypt cells from healthy B6 mice (Naive) or five days after B6-into-B6 syngeneic or B10.BR-into-B6 allogeneic BMT. a GSEA of ISC cluster genes filtered for differential correlation with Stat1 expression in ISCs from syngeneic and allogeneic BMT recipients; NES: normalized enrichment score. b Myc expression in crypt epithelial populations, highlighting Myc upregulation in ISCs after allo-BMT; gene expression imputed using MAGIC; (n = 3685 Naive, 3371 Syngeneic, 4670 Allogeneic cells); E: enterocytes, EEC: enteroendocrine cells, G: goblet cells, I: ISCs, P: Paneth cells, T: tuft cells. The boxplots represent three quartiles, and the whiskers indicate 1.5 times the interquartile range. c Correlation of Myc expression with expression of IFNγ-responsive genes or with expression of Stat1 in ISCs during homeostasis and after syngeneic or allogeneic BMT. d Correlation between average MAGIC-imputed expression of Myc target genes (Hallmark MYC_v1 and v2 pathways) and average imputed cell-cycle-related genes (KEGG cell cycle pathway) in ISCs after allogeneic BMT. The plot shows average gene expression (2nd–98th percentiles). e-f Imaging of full-thickness ileum by 3-D whole mount microscopy four days after B10.BR-into-B6 allogeneic BMT using either TCD BM alone, which does not result in GVHD, or BM and T cells, resulting in GVHD. Shown are 2-D optical slices of the ISC compartment in the lower crypt region (e) or the very base of the crypt (f) from 3-D fluorescent imaging performed after staining with anti-c-Myc (green), anti-Olfm4 (orange glow), and DAPI (blue). Arrows indicate c-Myc⁺Olfm4⁺ ISCs; scale bar: 25 μm.