Extended Data Fig. 1: MDS stem cells are in two distinct differentiation states.
(a) tSNE maps displaying 5,000 Lin-CD34+ cells from the BM of 122 untreated MDS patients, clustered based on their raw immunophenotypic profiles. Overlaid colors represent the HSPC populations assigned to each cell (left), based on the gating strategy displayed in (b), and the phenotypic group of the corresponding sample of origin of each cell (right). (b) Flow cytometry plots of Lin-CD34+CD38- and Lin-CD34+CD38+ populations in representative CMP-pattern (top) and GMP-pattern (bottom) MDS samples. (c) Frequencies of immunophenotypic MyHPC populations in total BM MNCs from CMP-pattern MDS (left; n=64) and GMP-pattern MDS (right; n=59) samples, compared with those in BM MNCs from HD samples (n=18). Lines represent medians ± IQRs. Statistically significant differences between pairs were detected using two-tailed Mann-Whitney tests (CMP-pattern: *P=0.029, ****P<0.0001, **P=0.003; GMP-pattern: ****P<0.0001, ***P=0.0002). (d) Plating efficiency of colony-forming units (CFUs) derived from CMPs (left), GMPs (center), and MEPs (right) isolated from the BMs of CMP-pattern MDS (CMPs, n=8; GMPs and MEPs, n=6) and GMP-pattern MDS (CMPs, n=11; GMPs and MEPs, n=8), compared with those of HDs (CMPs, n=7; GMPs and MEPs, n=4). Each symbol represents the average of the technical duplicate; lines represent means ± s.d. Statistical significance was calculated using one-way ANOVA and Tukey’s multiple comparisons test (CMPs: ****P=0.0001, *P=0.014; MEPs: P=0.017). (e) Frequencies of CFUs derived from CMPs (left), GMPs (center), and MEPs (right) isolated from CMP-pattern MDS (CMPs, n=8; GMPs and MEPs, n=6) and GMP-pattern MDS (CMPs, n=11; GMPs and MEPs, n=8) samples, compared with those derived from cells isolated from HDs (CMPs: n=6 BFUs-E and GEMMs, n=7 GMs; GMPs and MEPs, n=4). Lines represent means ± SEMs. Statistical significance was calculated using a mixed model analysis with the Geisser-Greenhouse correction for matched values, using type 3 tests of fixed effects (disease x colony lineage in CMPs: F[4, 67]=1.46, P=0.22; GMPs: F[4, 43]=0.97, P=0.43; MEPs: F[4, 43])=5.94, P=0.0007), and Dunnett’s multiple comparison test (CFU-GM: **P=0.0084; CFU-GEMM: **P=0.0028, *P=0.019). BFU-E, burst forming unit-erythroid; GEMM, granulocyte/erythrocyte/monocyte/megakaryocyte; GM, granulocyte/macrophage.
