Functional evidence implicating chromosome 7q22 haploinsufficiency in myelodysplastic syndrome pathogenesis

Chromosome 7 deletions are highly prevalent in myelodysplastic syndrome (MDS) and likely contribute to aberrant growth through haploinsufficiency. We generated mice with a heterozygous germ line deletion of a 2-Mb interval of chromosome band 5A3 syntenic to a commonly deleted segment of human 7q22 and show that mutant hematopoietic cells exhibit cardinal features of MDS. Specifically, the long-term hematopoietic stem cell (HSC) compartment is expanded in 5A3+/del mice, and the distribution of myeloid progenitors is altered. 5A3+/del HSCs are defective for lymphoid repopulating potential and show a myeloid lineage output bias. These cell autonomous abnormalities are exacerbated by physiologic aging and upon serial transplantation. The 5A3 deletion partially rescues defective repopulation in Gata2 mutant mice. 5A3+/del hematopoietic cells exhibit decreased expression of oxidative phosphorylation genes, increased levels of reactive oxygen species, and perturbed oxygen consumption. These studies provide the first functional data linking 7q22 deletions to MDS pathogenesis. DOI: http://dx.doi.org/10.7554/eLife.07839.001


Introduction
The myelodysplastic syndromes (MDSs) are clonal stem cell disorders characterized by ineffective hematopoiesis, morphologic dysplasia, and a variable risk of progression to acute myeloid leukemia (AML) (Elias et al., 2014). Monosomy 7 (−7) and deletions affecting the long arm of chromosome 7 [del(7q)] are highly prevalent acquired cytogenetic abnormalities in de novo and in therapy-related MDS and AML (t-MDS/t-AML) (Smith et al., 2003). The proportion of −7/del(7q) cells is markedly increased in the hematopoietic stem cell (HSC) and progenitor compartments of MDS patients relative to T and B lymphocytes (Kere et al., 1987b;Abrahamson et al., 1991;Bernell et al., 1996;Will et al., 2012;Elias et al., 2014). Recent studies demonstrating quantitative changes in the frequencies of phenotypic primitive long-term HSCs, common myeloid progenitors (CMPs), and granulocyte-monocyte progenitors (GMPs) in MDS patients with −7/del(7q) further support diverse effects on hematopoiesis Pang et al., 2013).

Results and discussion
Abnormal differentiation and repopulation of 5A3 +/del stem and progenitor cells We generated mice carrying a 2 Mb germ line 5A3 deletion that removes 13 genes syntenic to a human 7q22 CDS ( Figure 1A) (Wong et al., 2010). 5A3 +/del mice are smaller than wild-type (WT) littermates, and homozygous deletion of the 5A3 region causes embryonic lethality before 10.5 dpc (data not shown). Total nucleated bone marrow (BM) cell counts as well as spleen and thymus weights are reduced in mutant animals ( Figure 1B-D), which maintain normal peripheral blood cell counts. eLife digest Stem cells in the bone marrow are essential for creating new blood cells.
Myelodysplastic syndrome (MDS) is a common type of blood cancer in the elderly that occurs when blood cells fail to develop normally. Depending on which types of blood cells are affected, individuals with MDS may bleed more easily, feel weak and tired, or be unable to effectively fight off infections.
Animals and plants store their genetic information in the form of chromosomes. Humans have 23 pairs of chromosomes, with one copy inherited from the mother, and the other from the father. The bone marrow cells of many people with MDS delete a section from one of their copies of chromosome 7. As this section contains many different genes, it is difficult to fully understand which specific genes contribute to the development of MDS when one copy is lost.
Wong et al. have now genetically engineered mice to lack a section of one of their copies of chromosome 7 that is often missing in patients with MDS. Bone marrow cells from these mice exhibit many of the same abnormalities found in human MDS. For example, most of the immature blood stem cells expand, but these stem cells do not correctly specialize into mature blood cells-in particular, not enough immune cells are produced. The developing blood cells also have problems expressing several genes, including one that helps to protect the cells from damaging molecules called reactive oxygen species. These problems worsen as the mice age.
These mice provide the first evidence directly linking the missing section of chromosome 7 to abnormalities found in MDS patients. Future studies using the mice will advance our understanding of how the loss of this section of chromosome 7 interacts with other genes involved in MDS to alter the course of this disease and how it responds to treatment. Figure 1. A heterozygous 5A3 deletion corresponding to human 7q22 perturbs steady-state hematopoiesis. (A) Top, candidate 7q myeloid tumor suppressor genes described previously (Asou et al., 2009;Ernst et al., 2010;Nikoloski et al., 2010;Zhou et al., 2011;McNerney et al., 2013;Chen et al., 2014;Hosono et al., 2014;Poetsch et al., 2014) appear above the diagram of chromosome 7q while commonly deleted segments (CDSs) within 7q22, 7q34, and 7q35-36 identified by different research groups (Kere et al., 1987a;Le Beau et al., 1996;Fischer et al., 1997;Liang et al., 1998;Tosi et al., 1999;Jerez et al., 2012;McNerney et al., 2013;Hosono et al., 2014) are Figure 1. continued on next page Differential expression of CD150 distinguishes HSC populations with different self-renewal, differentiation, and repopulating potentials. Specifically, HSCs, with a surface c-kit + , lineage − , Sca-1 + (KLS), and CD150 hi (CD150 hi HSC) immunophenotype possess potent self-renewal capacity, are predisposed to myeloid differentiation and expand upon aging (Kiel et al., 2005;Beerman et al., 2010a;Hock, 2010). Strikingly, the proportion of CD150 hi HSCs is increased in 5A3 +/del BM with a corresponding decrease in the percentage of CD150 negative multi-potent progenitors (CD150 neg MPP) ( Figure 1E, Figure 1-figure supplement 1A). This results in a normal frequency of CD150 hi HSCs in 5A3 +/del mice, despite an overall reduction in the size of the stem/progenitor compartment ( Figure 1F). The proportion of CMPs is elevated in 5A3 +/del mice and the frequency of GMPs is decreased ( Figure 1G,H, Figure 1-figure supplement 1B), which is consistent with changes in these populations in MDS patients Pang et al., 2013). Thus, the 5A3 deletion perturbs HSC and myeloid progenitor populations. By contrast, the proportions and frequencies of common lymphoid progenitors are similar in WT and 5A3 +/del mice (Figure 1-figure supplement 1C-E).
We mixed donor 5A3 +/del or WT BM cells with WT BM at ratios of 1:1 and 1:2 and transplanted them into irradiated recipients. Whereas 5A3 mutant BM had markedly reduced lymphoid repopulating capacity, these cells efficiently contributed to the c-kit + lin − Sca-1 + (KLS) compartment (Figure 2A,B). To investigate if the altered repopulating potential of 5A3 +/del BM is intrinsic to CD150 hi HSC, we injected 15 of these cells into lethally irradiated recipients with WT BM competitors. Similar to whole BM, CD150 hi HSC from 5A3 +/del mice exhibited reduced overall repopulation potential due to defective lymphoid reconstitution ( Figure 2C-F). Importantly, however, 5A3 +/del HSC efficiently reconstituted KLS and myeloid compartments in both primary and secondary recipients ( Figure 2E,F). 5A3 +/del CD150 hi HSC exhibited markedly reduced lymphoid repopulating potential in WT and 5A3 +/del recipients, whereas WT cells restored lymphoid repopulation in 5A3 +/del hosts almost as well as in WT recipients, demonstrating that the repopulation defects in 5A3 +/del CD150 hi HSCs are cell intrinsic ( Figure 2C-F).
WT and 5A3 +/del HSCs generated similar numbers of myeloid colonies in methylcellulose cultures supplemented with cytokines; however, colonies grown from 5A3 +/del CD150 hi HSC contained significantly fewer cells ( Figure 2G,H). By contrast, 5A3 +/del CD150 neg MPP showed a 1.4-fold increase in colony forming activity but a similar number of cells per colony as WT MPP ( Figure 2G,I). In vivo labeling experiments revealed similar rates of BrdU incorporation, cell division, and apoptosis in WT and 5A3 +/del K + L − S + and myeloid progenitor (MP) cells ( Figure 2-figure supplement 1A,B and data not shown) (Nygren and Bryder, 2008).
Effects of aging on 5A3 +/del HSC and interaction with Gata2 haploinsufficiency Physiologic aging is characterized by impaired HSC repopulating potential, diminished lymphoid differentiation, the dominance of CD150 hi HSCs that are skewed toward myeloid differentiation and a markedly increased risk of MDS (Beerman et al., 2010a;Beerman et al., 2010b). depicted by brackets immediately below it. Middle, dotted lines demarcate the segments of mouse chromosome 5A3 corresponding to the human 7q22 CDS targeted in this study. Bottom, expressing Cre recombinase in embryonic stem (ES) cells doubly targeted with LoxP sequences within the Fbxl13 and Srpk2 genes excised a 2-Mb interval. Gene order is based on the Ensembl database and is not drawn to scale. (B) Total numbers of bone marrow (BM) cells from 2 femurs and 2 tibiae in 5A3 +/del mice and wild-type (WT) littermates at 8-12 weeks of age. (C, D) Spleen (C) and thymus (D) weights in 5A3 +/del mice and WT littermates at 8-12 weeks of age. (E, F) Percent contributions (E) and frequencies (F) of cells with high (CD150 hi HSC), low (CD150 lo HSC), and absent CD150 expression (CD150 neg MPP) within the K + L − S + CD41 − CD48 − compartment of WT and 5A3 +/del mice at 8-12 weeks of age (n = 6 of each genotype). (G) Percent contribution of common myeloid progenitor (CMP), granulocyte-monocyte progenitor (GMP), and megakaryocyte erythroid progenitors (MEP) within the Lin − Sca1 + c-kit + compartment of 5A3 +/del mice and WT littermates. (H) Frequencies of CMP, GMP, and MEP in WT and 5A3 +/del BM. The error bars indicate S.E.M. with significant differences between WT and 5A3 +/del mice designated by asterisks as follows: *p < 0.05, **p < 0.01. DOI: 10.7554/eLife.07839.003 The following figure supplement is available for figure 1:  . Defective repopulating potential of 5A3 +/del BM and CD150 hi HSC. (A, B) BM cells from WT or 5A3 +/del mice (n = 9 per genotype) were mixed at ratios of 1:1 and 1:2 with WT competitor cells and transplanted into 2-3 irradiated WT recipients. Percent contribution to the K + L − S + (KLS), K + L − S − (MP), myeloid, B and T cell lineages in the BM of recipient mice 6 months after primary (A) and secondary (B) transplants are shown. (C) Leukocyte chimerism after competitive transplantation of 15 5A3 +/del or WT CD150 hi HSC into WT or mutant recipients (n = 12 for WT hematopoietic stem cell (HSC) in WT recipients; n = 12 for 5A3 +/del HSC in WT recipients; n = 8 for WT HSC in 5A3 +/del recipients; n = 9 for 5A3 +/del HSC in 5A3 +/del recipients).  Similarly, the abnormal distribution of HSCs is exacerbated in 24-to 30-month-old 5A3 +/del mice ( Figure 3A,B). Consistent with data from younger mice (Figure 2A-F), aged 5A3 mutant BM displayed markedly reduced lymphoid repopulating potential, but efficiently contributed to myeloid reconstitution ( Figure 3C,D). Old 5A3 +/del BM cells also repopulated the KLS compartment significantly better than WT BM in recipients analyzed 4 months after transplantation, and 5A3 +/del cells exhibited a twofold increase in contribution to the KLS and MP populations upon serial transplantation ( Figure 3C,D). Despite these HSC abnormalities, 5A3 +/del mice have a normal lifespan, and the underlying causes of death are similar to WT littermates (data not shown).
Changes in gene expression and metabolic activities in 5A3 +/del hematopoietic cells Transcriptome (RNA-Seq) and TaqMan quantitative real-time PCR analyses revealed a ∼50% reduction in the expression of multiple genes and of the long intergenic non-coding RNA 503142E22Rik within the 5A3 interval in mutant HSC and MPP ( Figure 4A,B). Gene Set Enrichment Analysis (GSEA) of the RNA-Seq data from 5A3 +/del HSCs further demonstrated reduced expression of multiple gene sets related to oxidative phosphorylation (OXPHOS) that are similarly down-regulated in the early stages of human therapy-induced MDS and AML ( Figure 4C) (Mootha et al., 2003;Li et al., 2011). OXPHOS is the metabolic pathway used by cells to generate adenosine triphosphate (ATP). OXPHOS is regulated by mitochondrial membrane potential, and defects in this metabolic pathway can increase levels of reactive oxygen species (ROS). However, sorted WT and 5A3 +/del HSC and MPP showed similar ATP levels ( Figure 4D). Membrane potential and intracellular ROS levels were also similar in HSC and MPP from young mice, but ROS levels were increased by ∼50% in the HSC and MPP of aged 5A3 +/del mice ( Figure 4E,F). Elevated ROS levels in HSCs correlate with reduced self-renewal capacity, impaired multi-lineage repopulating ability, and myeloid-biased differentiation (Jang and Sharkis, 2007). ROS levels are also increased in t-MDS/AML BM (Reinecke et al., 2009;Li et al., 2011).
Down-regulation of OXPHOS genes is expected to reduce mitochondrial respiration in HSC (Warr and Passegue, 2013). We attempted to directly measure oxygen consumption rates (OCRs) in CD150 hi and CD150 lo HSC but could not obtain reproducible results due to limiting cell numbers. We therefore compared the OCRs of KLS, MP, B, and T cells isolated from 1-year-old WT and 5A3 +/del mice. 5A3 +/del KLS cells showed a similar basal OCR as their WT counterparts, but a slightly lower maximal respiratory capacity that did not reach statistical significance (p = 0.2562) ( Figure 4G). 5A3 +/del MPs surprisingly showed a significantly higher basal respiration and maximal (G-I) 100 CD150 hi HSC, CD150 lo HSC, and CD150 neg MPP from 8-to 12-week-old 5A3 +/del mice and their WT littermates were plated into methylcellulose medium supplemented with cytokines (n = 6 for each genotype). The total number of colonies (G) and the average number of cells per colony (H, I) were assessed after 7 days. Dots represent individual mice, and the horizontal lines indicate median values. Data shown are mean values ±SEM of results from three independent experiments with significant differences between WT and 5A3 +/del mice designated by asterisks as follows: *p < 0.05, **p < 0.01, ***p < 0.001. DOI: 10.7554/eLife.07839.005 The following figure supplement is available for figure 2:   Figure 4H). Meanwhile, mature 5A3 +/del B and T cells have similar mitochondrial stress profiles as WT cells. We conclude that global changes in OXPHOS gene expression exert a modest impact on cellular metabolism in aged 5A3 mutant HSC and progenitors. Interestingly, treatment with N-acetyl-L-cysteine (NAC) did not reverse the hematopoietic abnormalities in young 5A3 +/del mice (data not shown), suggesting that they are a direct consequence of the 5A3 deletion and are not secondary to ROS production.
Segmental deletions are among the most frequent genetic alterations in human cancer, and simultaneous loss of multiple haploinsufficient TSGs that individually have minimal phenotypic consequences appears to underlie the growth advantage conferred by most of these chromosomal losses (Solimini et al., 2012). We show that a haploinsufficient deletion in mice that models loss of a human 7q22 CDS causes hematopoietic abnormalities that include a myeloid lineage output bias, impaired lymphoid repopulating potential, and a pronounced age-associated expansion of HSC and MPs. These functional abnormalities support a role of 7q22 deletions in MDS pathogenesis. The seven genes within the deleted 5A3 segment that are expressed in HSC encode proteins that regulate diverse cellular processes including transcription (Mll5 and Dnajc2), mitochondrial quality control (Pmpcb, Armc10), protein degradation (Psmc2), biosynthesis of N-acylethanolamines (Napepld), and DNA replication (Orc5) (Luciano et al., 1997;Quintana et al., 1998;Fujiki et al., 2009;Sebastian et al., 2009;Richly et al., 2010;Nijhawan et al., 2012;Tsuboi et al., 2013;Zhou et al., 2013;Serrat et al., 2014). Given this, it is likely that the haploinsufficiency for multiple interacting genes leads to altered hematopoietic differentiation and function in 5A3 +/del mice. Similar to the 5A3 +/del mice described here, other mutations found in MDS patients perturb hematopoiesis, but do not consistently induce hematologic disease in the absence of cooperating mutations (Beurlet et al., 2013). This is not unexpected given the advanced age of most MDS patients and the presence of multiple genetic lesions in diseased BM. The 5A3 +/del mice reported here thus provide a novel resource for addressing how this common deletion cooperates with other mutations to drive myeloid transformation, progression to AML, and drug resistance.

Mice
We expressed Cre recombinase in embryonic stem cells containing LoxP sites and hypoxanthine phosphoribosyl transferase (HPRT) sequences flanking the Fbxl13 and Srpk2 genes (Wong et al., 2010) and analyzed clones that grew in hypoxanthine-aminopterin-thymidine (HAT) medium to identify the desired 2 Mb deletion. 5A3 del/+ mice were generated by standard blastocyst injection followed by mating coat color chimeras and were backcrossed for at least 10 generations onto a C57BL/6J background. Gata2 +/− mice were a generous gift from Dr Stuart Orkin (Harvard Medical School) (Tsai et al., 1994). Study mice were housed in a specific pathogen-free facility at the University of California San Francisco, and all animal experiments were conducted under protocols approved by the Institutional Animal Care and Use Committee. Genotyping and disease monitoring were performed as previously described (Wong et al., 2010). littermates at 8-12 weeks of age. (F) Spleen weights in 5A3 +/del mice, Gata2 +/− mice, compound Gata2 +/− ; 5A3 +/del mice, and WT littermates at 8-12 weeks of age. (G) Percent contributions of cells with high (CD150 hi HSC), low (CD150 lo HSC), and absent CD150 expression (CD150 neg MPP) within the K + L − S + CD41 − CD48 − compartment of WT, 5A3 +/del , Gata2 +/− , and compound Gata2 +/− ; 5A3 +/del mice at 8-12 weeks of age (n = 5 of each genotype). (H) BM cells from WT, 5A3 +/del , Gata2 +/− or compound Gata2 +/− ; 5A3 +/del mice (n = 5 of each genotype) were each mixed at ratios of 1:1 with WT competitor cells and transplanted into two irradiated WT recipients. Percent contribution to the K + L − S + (KLS), K + L − S − (MP), myeloid, B and T cell lineages in the BM of recipient mice 6 months after primary transplants. Data shown are mean values ±SEM from five independent experiments with significant differences designed by asterisks as follows: *p < 0.05, **p < 0.01, ***p < 0.001. The enhanced repopulating ability of compound Gata2 +/− ; 5A3 +/del vs Gata2 singly mutant HSC achieved borderline statistical significance in three myeloid populations (KLS (p = 0.09), MP (p = 0.09), and myeloid cells (p = 0.12)). DOI: 10.7554/eLife.07839.007 Figure 4. Changes in gene expression and oxidative phosphorylation in 5A3 +/del HSC and MP. (A) Relative mRNA abundances for genes within the deleted 5A3 interval expressed at detectable levels in sorted HSC populations were determined by TaqMan reverse transcriptase PCR (n = 3 per genotype). (B) Expression levels of genes located within and flanking the deleted interval measured by RNA-Seq in sorted CD150 hi HSC and CD150 lo HSC from 5 mice of each genotype. Each column presents data from an individual mouse, and genes within the 5A3 deleted region are delimited with a black box. Three non-coding RNAs (6030443J06Rik, AC112688.1 and 5031425E22Rik) are located within the 5A3 deletion. Two of these (6030443J06Rik and AC112688.1) are expressed at extremely low levels in HSC, and the other (5031425E22Rik) showed ∼50% lower expression in 5A3 +/del HSC. 5031425E22Rik is homologous to the human KMT2E (a.k.a. MLL5) antisense RNA1. Expression levels of the flanking Fbxl13 and Srpk2 Figure 4. continued on next page Flow cytometry BM cells flushed from tibias and femurs were subjected to ammonium-chloride potassium red cell lysis before staining with antibodies. For experiments requiring cell sorting, the spinal cord, flat bone of the pelvis, humerus, and sternum of the mice were also crushed and lysed. Low-density mononuclear cells were separated using a HISTOPAQUE-1119 gradient (Sigma-Aldrich, St. Louis, MO, United States). For identification and sorting of CD150 hi -HSC, CD150 lo -HSC, and CD150 neg -MPP, cells were pre-incubated with purified CD16/32 (2.4G2), followed by staining with a lineage cocktail of PEconjugated antibodies including B220 (RA3-6B2), CD8 (53-6.7), Gr-1 (RB6-8C5), CD3 (17A2), Ter119 (TER-119), CD41 (MWReg30), and CD48 (HM48-1), as well as PE-Cy7 c-kit (2B8), PacBlue Sca-1 (E13-161.7), and APC CD150 (TC15-12F12.2) from BioLegend (San Diego, CA, United States). For experiments requiring cell sorting, cells expressing c-kit were enriched by magnetic cell sorting by staining with mouse CD117 microbeads and positively selected on the MS columns (Miltenyi Biotec, Germany) according to manufacturer's protocol before antibody staining. Cells were classified as CD150 hi -HSC, CD150 lo -HSC, or CD150 neg -MPP based in levels of CD150 expression.

Competitive repopulation
BM cells from WT, 5A3 +/del , Gata2 +/− , Gata2 +/− 5A3 +/del mice on a C57BL/6J background (CD45.2) were used as donor cells. Competitor cells were isolated from 8-to 12-week-old BoyJ mice (CD45.1). Recipient F1 hybrid mice from a cross between C57BL/6J and BoyJ mice (CD45.1 + CD45.2) were at least 8 weeks old at the time of lethal irradiation (9.5 Gy from a cesium source delivered in split dose 3 hr apart). After irradiation, the cells were injected via the tail vein of recipient mice. For evaluation of the competitiveness of whole BM, we injected 10 6 whole BM cells at a 1:1 or 1:2 donor to competitor ratio. To evaluate the repopulating potential of purified CD150 hi -HSC, we injected 15 CD150 hi -HSC sorted from 8-to 12-week-old WT and 5A3 +/del mice together with 2.5 × 10 5 BM competitor cells into lethally irradiated recipients.
Blood was obtained from recipient mice every 30 days beginning 1 month after transplant, and cells were stained with Alexa Fluor 700 CD45.2 (104), PE-Cy7 CD45.1 (A20), PacBlue B220 (RA3-6B2), Figure 4. Continued genes are modestly up-regulated in 5A3 +/del HSC, which is consistent with the targeting strategy used to generate the segmental deletion. (C) Gene Set Enrichment Analysis of 5A3 +/del CD150 hi HSCs revealed negative enrichment for genes associated with oxidative phosphorylation (OXPHOS). False discovery rate (FDR) q-val, nominal p-value (NOM p-value), and normalized enrichment scores (NESs) are indicated. (D) ATP levels in HSC and MPP from 8-to 12-week-old WT (n = 6) and 5A3 +/del (n = 5) mice. Data shown are mean values ±SEM of results from two independent experiments. (E) Fold change in the mean MitoTracker Orange fluorescence levels in 5A3 +/del cells normalized to values in WT cells analyzed in the same experiment. (F) Fold change in the mean fluorescence level (MFI) of 5A3 +/del cells that are CellROX Orange positive normalized to values in WT cells analyzed in the same experiment. For the MitoTracker and CellROX experiments, n = 13 for WT and n = 12 for 5A3 +/del young mice, three independent experiments; n = 5 for WT and n = 6 for 5A3 +/del aged mice, two independent experiments. Data shown are mean values ±SEM of results from independent experiments. (G and H) Oxygen consumption rate (OCR) was assessed basally and in response to the mitochondrial inhibitors oligomycin (oligo), carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP), and antimycin A and rotenone (A/R) for (G) KLS and (H) MP cells. Data are shown as mean ±SEM of n = 5 mice of each genotype from two independent experiments. DOI: 10.7554/eLife.07839.008 FITC CD4 (GK1.5), FITC CD8 (53-6.7), PE Mac-1 (M1/70), and PE Gr-1 (RB6-8C5) to determine the percent donor cell contribution to myeloid and B and T lymphoid lineages. Primary recipient mice were euthanized 6 months after transplantation, BM were isolated from the tibiae and femur, and 2 × 10 6 BM cells were injected into secondary recipients to test serial repopulation potential.
Methylcellulose colony assays CD150 hi -HSC, CD150 lo -HSC, and CD150 neg -MPP were isolated as described above, and 100 cells were seeded into methylcellulose medium as described (Mohrin et al., 2010). Colonies were counted on day 7, and the entire contents of a methylcellulose culture from an individual plate were then flushed out using phosphate-buffered saline and counted in a hemocytometer. Cells were also spun in a Cytospin 3 Cytocentrifuge (Shandon/Thermo Fisher Scientific, Waltham, MA, United States) at 400 rpm for 8 min, and differential cell counting and morphological analysis performed after Wright-Giemsa staining. For TaqMan analysis, reverse transcription was carried out using the High Capacity RNA-to-cDNA Master Mix (Life Technologies). Relative quantification of gene expression was determined by performing quantitative real-time PCR using the following TaqMan Gene Expression Assays (Applied Biosystems):

RNA isolation and expression
, and Gapdh (Mm99999915_g1) with the TaqMan Gene Expression Master Mix (ABI). PCR reactions were performed on an ABI 7900HT Real-Time PCR System (Applied Biosystems, Foster City, CA, United States) with the Taqman Gene Expression Master Mix (Applied Biosystems) according to manufacturer's instructions. PCR cycling conditions were 2 min at 50˚C and 10 min at 95˚C, followed by 40 cycles of 15 s at 95˚C and 1 min at 60˚C. All reactions were carried out in triplicate, and target quantities were determined using a relative standard curve. The amounts of target were normalized to the endogenous control gene Gapdh and compared with the corresponding WT BM (calibrator sample) to determine relative fold differences.
For RNA-Seq analysis, total RNA (10 ng) was converted into double-stranded cDNA using the Ovation RNA Amplification System V2 (NuGen, San Carlo, CA, United States) per manufacturer's recommendations. The amplified cDNA products were then used to generate RNA-seq libraries using the TruSeq RNA Sample Preparation Kit v2 reagents (Illumina, San Diego, CA, United States) per manufacturer's instructions, with 10 PCR amplification cycles. Library quality and quantity were assessed by the Agilent DNA1000 Chip (Agilent, Santa Clara, CA, United States) and qPCR (Kappa Biosystems Inc, Woburn, MA, United States). 10 pM of each library was sequenced using Illumina SBS chemistry at 2 × 100 bp reads on the HiSeq2000 (Illumina, San Diego, CA, United States).
The RNA-Seq paired-end reads were mapped to the mouse mm9 genome using an in-house mapping and quality assessment pipeline (Zhang et al., 2012). The expression of each gene was estimated by the mean coverage of the highest covered coding exon. Genes with low-expression level (<10) across all samples were filtered out, followed by quantile normalization. Differential expression analysis was performed using limma (Smyth, 2004) with estimation of false discovery rate (Benjamini and Hochberg, 1995). GSEA (Subramanian et al., 2005(Subramanian et al., , 2007 was used to assess pathway enrichment.

ATP quantification
HSC and MPP were sorted into phosphate buffered saline (PBS), and 600 CD150 hi -HSC, 1000 CD150 lo -HSC, and 1000 CD150 neg -MPP were aliquoted into a well of a 96-well plate in triplicate. ATP was quantified using the CellTiter-Glo Luminescent Cell Viability Assay (Promega, Madison, WI, United States) following manufacturer's recommendations. Illumination was quantified with a Synergy 2 (Biotek, Winooski, VT, United States).
The OCR was analyzed in an XF96 extracellular flux analyzer following manufacturer's protocol (Seahorse Biosciences, Billerica, MA, United States). Freshly isolated K + L − S + cells and K + L − S − cells were cultured in StemSpan serum-free medium (STEMCELL Technologies, Vancouver, Canada) supplemented with SCF (100 ng/ml) and Tpo (100 ng/ml), while freshly isolated thymic cells and B-220 + splenic cells were cultured in RPMI medium 1640 supplemented with 10% fetal calf serum and incubated at 37˚in a humidified atmosphere containing 8% CO 2 for 12-15 hr. Cells were then washed three times with Mito Stress Media (XF base media supplemented with glucose [3 mg/ml], sodium pyruvate [1 mM], and Glutamax [2 mM] adjusted to a pH = 7.4) and seeded in XF96 microplates coated with poly-L-lysine (Sigma). 60000 K + L − S + cells, 100000 K + L − S − cells, 200000 thymic cells, and 200000 B220 + splenic cells were plated per well, respectively. K + L − S + and K + L − S − cells were stimulated with SCF (100 ng/ml) and Tpo (100 ng/ml), while thymic cells were stimulated with interleukin (IL)-2 (20 ng/ml) and IL-7 (10 ng/ml) and B-220 + splenic cells were stimulated with IL-7 (10 ng/ml) and maintained in a non-CO 2 incubator for 1 hr before the assay. Five baseline recordings were made, followed by sequential injection of Oligomycin (Sigma), Carbonyl Cyanide 4-(trifluoromethoxy)phenylhydrazone (Sigma), and a combination of Antimycin A (Sigma) and Rotenone (Sigma) to determine the mitochondrial respiration rate under various conditions.

Statistical analysis
Data are presented as mean values ±SEM unless stated otherwise. Statistical significance was determined by performing two-tailed Student's t-tests.