FLT3-ITDs instruct a myeloid differentiation and transformation bias in lymphomyeloid multipotent progenitors

Abstract

Whether signals mediated via growth factor receptors (GFRs) might influence lineage fate in multipotent progenitors (MPPs) is unclear. We explored this issue in a mouse knockin model of gain-of-function Flt3-ITD mutation because FLT3-ITDs are paradoxically restricted to acute myeloid leukemia even though Flt3 primarily promotes lymphoid development during normal hematopoiesis. When expressed in MPPs, Flt3-ITD collaborated with Runx1 mutation to induce high-penetrance aggressive leukemias that were exclusively of the myeloid phenotype. Flt3-ITDs preferentially expanded MPPs with reduced lymphoid and increased myeloid transcriptional priming while compromising early B and T lymphopoiesis. Flt3-ITD-induced myeloid lineage bias involved upregulation of the transcription factor Pu.1, which is a direct target gene of Stat3, an aberrantly activated target of Flt3-ITDs, further establishing how lineage bias can be inflicted on MPPs through aberrant GFR signaling. Collectively, these findings provide new insights into how oncogenic mutations might subvert the normal process of lineage commitment and dictate the phenotype of resulting malignancies.

Graphical abstract

Figure 1

Mutation of Runx1 in Flt3^ITD/ITD Mice Results in High-Penetrance Aggressive Myeloid Leukemia (A) Leukemia-free survival curves of Flt3^ITD/ITDRunx1^fl/fl mice stratified according to Mx1Cre genotype (n = 50–68 mice of each genotype). (B and C) Low-power (20×; B) and high-power (100×; C) morphology of typical leukemic cells in Flt3^ITD/ITDRunx1^fl/flMx1Cre⁺ mice. (D) Differential morphology results from BM of WT (+/+), Flt3^ITD/ITDRunx1^fl/flMx1Cre⁻, and leukemic Flt3^ITD/ITDRunx1^fl/flMx1Cre⁺ mice; percentage of total BM cells. Mean (SEM) values for 4–11 mice of each genotype. (E) Fluorescence-activated cell sorting (FACS) analysis of PB and BM from an Flt3^ITD/ITDRunx1^fl/flMx1Cre⁺ mouse with myeloid leukemia (representative of 19 further analyzed cases). Error bars represent SEM. See also Figure S1.

Figure 2

Flt3-ITDs Expand Myeloid-Biased MPPs (A) Expansion of LSK cells in 8- to 10-week-old Flt3^ITD/ITD mice (+/+: n = 27; ITD/ITD: n = 23). (B) Expression of CD48 and CD150 on BM LSK cells from Flt3^+/+ and Flt3^ITD/ITD mice. (C) Expansion of LSKCD48⁺CD150⁻ MPPs in 8- to 10-week-old Flt3^ITD/ITD mice (+/+: n = 27; ITD/ITD: n = 23). (D) GSEA demonstrating downregulation of E-affiliated genes in Flt3^ITD/ITD versus Flt3^+/+LSKCD48⁺150⁻ MPPs (n = 4 of each genotype). FDR, false discovery rate; NES, normalized enrichment score. (E) Reduced MkE-affiliated gene expression in LSKCD48⁺150⁻ cells from Flt3^+/+, Flt3^ITD/+, and Flt3^ITD/ITD mice relative to Flt3^+/+ LSK FLT3⁻ cells; p values represent a comparison of Flt3^+/+LSK FLT3⁻ cells versus LSKCD48⁺150⁻Flt3^ITD/ITD cells by unpaired t test (n = 6–8 replicates from 2–3 mice per genotype). Differences among Flt3^+/+, Flt3^ITD/+, and Flt3^ITD/ITD MPPs were not significant. (F) Single-cell Mk potential of Flt3^+/+and Flt3^ITD/ITD LSKCD48⁺150⁻ MPPs in comparison with Flt3^+/+LSKCD48⁻150⁺ HSCs (n = 3 independent experiments). (G) GSEA demonstrating upregulation of myeloid affiliated genes in Flt3^ITD/ITD versus Flt3^+/+LSKCD48⁺150⁻ MPPs (n = 4 of each genotype). (H) Single-cell GM potential of Flt3^+/+and Flt3^ITD/ITD LSKCD48⁺150⁻ MPPs. Open bars show the frequency of clones formed, and closed bars show the frequency of highly proliferative clones (covering >50% of the well; n = 3 independent experiments). (I) GSEA demonstrating downregulation of lymphoid transcriptional program in Flt3^ITD/ITD versus Flt3^+/+ LSKCD48⁺150⁻ MPPs (n = 4 of each genotype). (J) Expression of lymphoid-affiliated genes in LSKCD48⁺150⁻ MPPs from Flt3^+/+, Flt3^ITD/+, and Flt3^ITD/ITD mice (n = 6–8 replicates from 2–3 mice per genotype); p values indicate comparisons of Flt3^+/+ versus Flt3^ITD/+ MPPs, and Flt3^+/+ versus Flt3^ITD/ITD MPPs by unpaired t test (p < 0.001 for all analyses). (K) B cell potential (B220⁺CD19⁺) of Flt3^+/+ versus Flt3^ITD/ITD BM LSKCD48⁺150⁻ MPPs (10 cells/well). Data are mean (SEM) values of 2–3 experiments, with 9–12 replicate wells in each experiment. Error bars represent SEM. See also Figure S2.

Figure 3

Early T and B Cell Progenitors Are Suppressed and Myeloid Biased in Flt3^ITD/ITD Mice (A) Thymic cellularity of Flt3^+/+ and Flt3^ITD/ITD mice at 2–3 and 8–10 weeks (n = 7–10 mice of each genotype at each age). (B) Representative DN staging of Flt3^+/+ and Flt3^ITD/ITD thymocytes from 2-week-old mice; percentages are relative to total thymocytes. (C) Progressive reduction of DN1Kit⁺ cells in Flt3^ITD/ITD thymus. (D) Expression (SEM) of Ccr9 in LSKCD48⁺150⁻ BM cells from 8- to 10-week-old Flt3^+/+ and Flt3^ITD/ITD mice (n = 3–4 mice per genotype, 2–3 separately sorted replicates per mouse). (E) T cell potential on OP9DL1 cells of DN1 cells (10/cells per well) from 2- to 3-week-old Flt3^+/+ and Flt3^ITD/ITD mice (n = 2 mice per genotype, 12 replicate wells per mouse). ND, not detected. (F) Representative staging of early B cell progenitors in Flt3^+/+ and Flt3^ITD/ITD 2- to 3-week-old mice. pre-pro-B cells are identified as Lin⁻B220⁺CD19⁻CD24⁻AA4.1⁺CD43^mid; percentage of total BM cells. (G) Increased numbers of pre-pro-B cells in 2- to 3-week-old Flt3^ITD/ITD mice (mean [SEM] values for 2- to 3-week-old mice, n = 8–10 of each genotype). (H) Reduced numbers of pro-B cells (Lin⁻B220⁺CD43⁺CD19⁺CD24^intAA4.1⁺) in Flt3^ITD/ITD mice. (I) Mean (SEM) expression of lymphoid-affiliated genes in pre-pro-B cells from 2- to 3-week-old mice (n = 2 mice per genotype, 3 separately sorted replicates per mouse). (J) Mean (SEM) expression of myeloid-affiliated genes in pre-pro-B cells from Flt3^ITD/ITD mice. (K) In vitro B cell potential (B220⁺CD19⁺ cells) of pre-pro-B cells from 2- to 3-week-old mice (n = 10 cells/well, 2 mice per genotype, 10 replicate wells per mouse). Error bars represent SEM. See also Figure S3.

Figure 4

Involvement of PU1 Upregulation in the Myeloid Bias of Flt3^ITD/ITD Mice (A–C) Representative FACS analysis of PU1-YFP expression in lineage-negative (A), LSKCD48⁺150⁻ MPPs (B), and Lin⁻CD19⁻CD24⁻AA4.1⁺CD43^midB220⁺ pre-pro-B (C) cells in BM of 2- to 3-month-old Flt3^+/+ and Flt3^ITD/ITD mice. Also shown is the mean fold difference in PU1-YFP expression for each population from six mice of each genotype. (D) GSEA demonstrating upregulation of Pu1 target genes in LSKCD48⁺150⁻ MPPs from Flt3^ITD/ITD versus Flt3^+/+ mice (n = 4 of each genotype). (E) Percentage of B220⁺CD19⁺ in the BM of 6- to 8-week-old Flt3^+/+Pu1^+/+, Flt3^+/+Pu1^+/−, Flt3^ITD/ITDPu1^+/+, and Flt3^ITD/ITDPu1^+/− mice (n = 8–11 mice of each genotype; fold difference and p value are for the difference between Flt3^ITD/ITDPu1^+/+ and Flt3^ITD/ITDPu1^+/− mice). (F) Percentage of pre-pro-B cells in the BM of 6- to 8-week-old Flt3^+/+Pu1^+/+, Flt3^+/+Pu1^+/−, Flt3^ITD/ITDPu1^+/+ and Flt3^ITD/ITDPu1^+/− mice (n = 3 mice of each genotype). (G) Percentage of pro-B cells in the BM of 6- to 8-week-old Flt3^+/+Pu1^+/+, Flt3^+/+Pu1^+/−, Flt3^ITD/ITDPu1^+/+ and Flt3^ITD/ITDPu1^+/− mice (n = 3 mice of each genotype). (H) Percentage of LSKCD48⁺150⁻ MPPs in the BM of 6- to 8-week-old Flt3^+/+Pu1^+/+, Flt3^+/+Pu1^+/−, Flt3^ITD/ITDPu1^+/+ and Flt3^ITD/ITDPu1^+/− mice (n = 7–9 mice of each genotype). (I) Percentage of Mac1^lowcKit^low myeloid precursor cells in the BM of 6- to 8-week-old Flt3^+/+Pu1^+/+, Flt3^+/+Pu1^+/−, Flt3^ITD/ITDPu1^+/+ and Flt3^ITD/ITDPu1^+/− mice (n = 7–9 mice of each genotype). (J) GSEA demonstrating upregulation of STAT3 target genes in Flt3^ITD/ITD versus Flt3^+/+ LSKCD48⁺150⁻ MPPs (n = 4 mice of each genotype). (K and L) Expression of Stat3 target genes in Flt3^+/+ and Flt3^ITD/ITD LSKCD48⁺150⁻ MPPs (K) and pre-pro-B cells (L) (n = 2–4 mice of each genotype, 2–3 replicates per mouse). ND, not detected. Error bars represent SEM. See also Figure S4.

Figure S1

Mutation of Runx1 in Flt3^ITD/ITD Mice Results in High-Penetrance Aggressive Myeloid Leukemia, Related to Figure 1 (A–C) Hematologic indices in Flt3^ITD/ITDRunx1^fl/flMx1Cre⁺ leukemic mice demonstrating a marked increase in white blood cell count (WBC) (A), anemia (B), and thrombocytopenia (C) compared with Flt3^ITD/ITDRunx1^fl/flMx1Cre⁻ controls. Mean (SEM) values from 6-14 mice from 5-11 independent experiments. Hematologic indices were measured using a Sysmex^® automated analyzer. (D) Representative FACS analysis of infiltrated livers and spleens from Flt3^ITD/ITDRunx1^fl/flMx1Cre⁺ leukemic mice showing lineage surface markers typical of myeloid leukemic cells (results representative of 3 [liver] and 11 [spleen] further analyzed cases). (E) Recombination at the Runx1 locus without poly I:C induction in Flt3^ITD/ITDRunx1^fl/flMx1Cre⁺ leukemic BM. Representative PCR analysis of Runx1^fl/fl recombination in paired BM and earclip (EC) DNA from Flt3^ITD/ITDRunx1^fl/flMx1Cre⁺ leukemic and Flt3^ITD/ITDRunx1^fl/flMx1Cre⁻ and Flt3^+/+Runx1^fl/flMx1Cre⁺ controls, all without polyI:C induction. The upper band represents non-deleted Runx1 allele and the lower band indicates deleted Runx1 alleles. Results are representative of 3 further analyzed leukemic samples. Error bars represent SEM.

Figure S2

Flt3-ITDs Expand Myeloid-Biased LMPPs, Related to Figure 2 (A) Lack of cell surface Flt3 expression in Flt3^ITD/ITD mice; representative FACS analysis of surface Flt3 expression in LSK cells from Flt3^+/+ and Flt3^ITD/ITD mice. Percentages in the graph represent mean frequency of Flt3-positive cells in the LSK compartment of Flt3^+/+ (n = 27) and Flt3^ITD/ITD (n = 23) mice. (B) Flt3^ITD/+ mice show an intermediate expansion of LSK cells relative to Flt3^+/+ and Flt3^ITD/ITD mice (Flt3^+/+ n = 27; Flt3^ITD/+ n = 13; and Flt3^ITD/ITD n = 23). (C) Flt3^ITD/+ mice show an expansion of LSKCD48⁺CD150⁻ MPPs intermediate between Flt3^+/+ and Flt3^ITD/ITD mice (Flt3^+/+ n = 27; Flt3^ITD/+ n = 13; and Flt3^ITD/ITD n = 23). (D) LMPPs reside in the LSKCD150⁻48⁺ compartment; representative FACS analysis of CD48 and CD150 expression in relation to high-level Flt3 expressing LMPPs within the LSK compartment. High-level Flt3 expression was defined as the highest 20% of Flt3 staining cells in Flt3^+/+ LSK cells. Percentages in the graph represent mean frequency of indicated cells relative to parental gate from Flt3^+/+ (n = 17) mice. (E) HSC associated gene expression is not upregulated in the LSKCD150⁻48⁺ compartment in Flt3^ITD/ITD mice. Mean (SEM) HSC affiliated gene expression in indicated cell populations from Flt3^+/+ and Flt3^ITD/ITD mice. P-values are shown if < 0.05 (not reached for any comparison of Flt3^+/+ and Flt3^ITD/ITD MPPs); ND indicates not detected. (F) Expression of lymphoid affiliated genes in E15 FL LSKCD150⁺CD48⁻ HSCs and LSKCD150⁻CD48⁺ MPPs from Flt3^+/+ and Flt3^ITD/ITD mice (n = 9 replicates from 3 mice per genotype). P values less than 0.05 are shown for comparison of Flt3^+/+ and Flt3^ITD/ITD MPPs. (G) LSKCD150⁻48⁺ MPPs are not expanded in the fetal liver (FL) of Flt3^ITD/ITD mice; representative FACS analysis from E15 FL from Flt3^+/+ and Flt3^ITD/ITD mice. Numbers in the graph represent mean frequencies of total FL cells from 7-9 mice of each genotype from 3 independent experiments. There were no significant differences in the frequency of MPPs between Flt3^+/+ and Flt3^ITD/ITD mice. (H) Percentage of B220⁺CD19⁺ cells in E15 Flt3^+/+ and Flt3^ITD/ITD FL (8-9 FL of each genotype). (I) Percentage of Mac1^lowcKit^low cells in E15 Flt3^+/+ and Flt3^ITD/ITD FL (8-9 FL of each genotype). NS indicates not significant. (J) Expression of lymphoid affiliated genes in LSKFlt3⁺CD48⁺150⁻ MPPs from Runx1^fl/flVavCre⁻ and Runx1^flflVavCre⁺ mice (n = 4 mice 4-6 weeks of age per genotype). Error bars represent SEM.

Figure S3

Early T and B Cell Progenitors Are Suppressed and Myeloid Biased in Flt3^ITD/ITD Mice, Related to Figure 3 (A and B) Progressive loss of DN2Kit⁺ (A) and DN3 (B) thymocyte progenitors in Flt3^ITD/ITD thymus (mean (SEM) values from 7-8 mice of each genotype at indicated ages in 3 independent experiments). (C) Representative FACS profile demonstrating loss of Ccr9 expression on the cell surface of LSKCD150⁻ cells in Flt3^ITD/ITD mice. (D) Quantification of Ccr9 positive LSKCD150⁻CD48⁺ cells in Flt3^+/+ and Flt3^ITD/ITD BM (mean (SEM) values from 5-6 mice of each genotype analyzed at 6-8 weeks of age). (E) Lineage-affiliated gene expression analysis of DN1 thymocytes from Flt3^+/+ and Flt3^ITD/ITD mice (mean (SEM) expression, 2 mice per genotype; 3 separately sorted replicates per mouse). (F) Representative FACS analysis showing gating strategy for identification of pro-B (Lin⁻B220⁺CD19⁺CD24^midAA4.1⁺) cells in Flt3^+/+ and Flt3^ITD/ITD mice (percentages are relative to total bone marrow cells). Error bars represent SEM.

Figure S4

Involvement of Pu1 Upregulation in the Myeloid Bias of Flt3^ITD/ITD Progenitors, Related to Figure 4 (A) Gene set enrichment analysis demonstrating upregulation of Pu1 target genes in Lin⁻CD34⁺CD38⁻CD90⁻CD45RA⁺ cells from FLT3-ITD mutated human AML (n = 8) relative to FLT3-WT counterparts (n = 18). (B) Representative FACS analysis of Pu1-YFP expression levels during early B cell commitment demonstrating marked downregulation of Pu1 expression at the pre-pro-B to pro-B transition. Representative of 2 experiments. (C) Western blot showing increased pStat3 activation in the BM of Flt3^ITD/ITD mice in comparison with Flt3^+/+ BM. The blot shown is representative of two independent experiments.