Figure S7.

Mtb-Imprinted HSCs Have Impaired Engraftment for up to at Least 1 Year Post-exposure, Related to Figure 7

(A-K) Mixed chimeric mice were generated as described in Figure 7A. At 4-week intervals post-reconstitution, peripheral blood was sampled. Percentages of CD45.1⁺ versus CD45.2⁺ leukocytes (A), Ly6C^hi monocytes (B), neutrophils (C) or T cells (D) in the blood. At 16 weeks post-reconstitution, BCG:Mtb mixed chimera mice were sacrificed. Frequency of total BM CD45 (E), CCR2⁺ monocytes (F), or neutrophils (G), as well as pulmonary leukocytes (H), CCR2⁺ monocytes (I), neutrophils (J) and macrophages (K). (L-R) Secondary engraftment experiments were performed as in Figure 7K. Mtb CFU in the BM cells prior to secondary engraftment (L). In the peripheral blood, total cell counts of CD11b⁺ cells (M), Ly6C^hi monocytes (N) and neutrophils (O), as well as BM LKS (P), LT-HSC (Q) and CMP (R) frequencies. (S-T) UMAP dimensionality reduction plots for LKS and myeloid progenitor cells, respectively, for the serial engraftment experiment. (U) Schematic hematopoietic tree diagram showing the approximated position of the different clusters identified (cluster specific color code common to panels S-T). (V) Average expression of cell-type markers across clusters. (W) Correlations between genome-wide expression patterns of our myeloid progenitor data and results published by Paul et al. (2015). In each column, Spearman correlations are normalized to cover the range [0-1]. Blue boxes mark the best fit (i.e., candidate identity match) for each of our clusters. (X) Expression patterns across clusters for some marker genes associated to commitment to the different lineages characterized in this study. (Y) Genome wide correlation of Mtb versus BCG effect sizes (logFC) in each cluster. Differences measured via Two-Way ANOVA followed by Sidak’s Multiple Comparison Test (A-D), Student’s Two-tailed T-Test (E-K) and One-Way ANOVA followed by Tukey’s Multiple Comparisons Test in (M-R). In A-D, only significant differences at 16 weeks were labeled.