Variable SATB1 Levels Regulate Hematopoietic Stem ... - Cell Press

Article

Variable SATB1 Levels Regulate Hematopoietic Stem Cell Heterogeneity with Distinct Lineage Fate Graphical Abstract

Authors Yukiko Doi, Takafumi Yokota, Yusuke Satoh, ..., Junji Takeda, Kenji Oritani, Yuzuru Kanakura

Correspondence [email protected]

In Brief Doi et al. show that hematopoietic stem cells (HSCs) with robust lymphopoietic and long-term reconstituting capability express special AT-rich sequencebinding protein 1 (SATB1). SATB1expressing and non-expressing HSCs are interconvertible. Moreover, they provide insights into the heterogeneity of HSCs, which are correlated with changes in SATB1 expression levels.

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SATB1 is indispensable for both self-renewal and lymphopoiesis of adult HSCs SATB1+ HSCs have higher reconstituting and lymphopoietic potential than SATB1 HSCs SATB1 and SATB1+ HSCs have distinct lineage potential but are interconvertible Difference in SATB1 expression levels contributes to HSC heterogeneity

Doi et al., 2018, Cell Reports 23, 3223–3235 June 12, 2018 ª 2018 The Authors. https://doi.org/10.1016/j.celrep.2018.05.042

Data and Software Availability GSE94630

Cell Reports

Article Variable SATB1 Levels Regulate Hematopoietic Stem Cell Heterogeneity with Distinct Lineage Fate Yukiko Doi,1 Takafumi Yokota,1,8,* Yusuke Satoh,1,2 Daisuke Okuzaki,3 Masahiro Tokunaga,1 Tomohiko Ishibashi,1,4 Takao Sudo,1,5 Tomoaki Ueda,1 Yasuhiro Shingai,1 Michiko Ichii,1 Akira Tanimura,1 Sachiko Ezoe,1 Hirohiko Shibayama,1 Terumi Kohwi-Shigematsu,6 Junji Takeda,7 Kenji Oritani,1 and Yuzuru Kanakura1 1Department

of Hematology and Oncology, Osaka University Graduate School of Medicine, Suita, Japan of Lifestyle Studies, Kobe Shoin Women’s University, Kobe, Japan 3DNA-chip Development Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Japan 4Department of Vascular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan 5Department of Immunology and Cell Biology, Osaka University Graduate School of Medicine, Suita, Japan 6Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA 7Department of Genome Biology Graduate School of Medicine, Osaka University Graduate School of Medicine, Suita, Japan 8Lead Contact *Correspondence: [email protected] https://doi.org/10.1016/j.celrep.2018.05.042 2Department

SUMMARY

Hematopoietic stem cells (HSCs) comprise a heterogeneous population exhibiting self-renewal and differentiation capabilities; however, the mechanisms involved in maintaining this heterogeneity remain unclear. Here, we show that SATB1 is involved in regulating HSC heterogeneity. Results in conditional Satb1-knockout mice revealed that SATB1 was important for the self-renewal and lymphopoiesis of adult HSCs. Additionally, HSCs from Satb1/Tomatoknockin reporter mice were classified based on SATB1/Tomato intensity, with transplantation experiments revealing stronger differentiation toward the lymphocytic lineage along with high SATB1 levels, whereas SATB1 HSCs followed the myeloid lineage in agreement with genome-wide transcription and cell culture studies. Importantly, SATB1 and SATB1+ HSC populations were interconvertible upon transplantation, with SATB1+ HSCs showing higher reconstituting and lymphopoietic potentials in primary recipients relative to SATB1 HSCs, whereas both HSCs exhibited equally efficient reconstituted lympho-hematopoiesis in secondary recipients. These results suggest that SATB1 levels regulate the maintenance of HSC multipotency, with variations contributing to HSC heterogeneity. INTRODUCTION Hematopoiesis is maintained by cell differentiation, during which signaling pathways and transcription factors coordinately induce stepwise maturation of hematopoietic stem cells (HSCs) toward effector cells. During this process, HSCs lose pluripotency and acquire lineage-related functions. HSCs have been rigorously studied as the most purified among tissue stem cells in humans and mice by using a combination of various surface markers;

however, even highly enriched stem cells are functionally heterogeneous at a clonal level (Copley et al., 2012). Indeed, recent clonal assays of HSCs in serial transplantation revealed that the HSC fraction consists of diverse long-term reconstituting cells whose differentiation potential, particularly toward the lymphoid lineage, varies substantially (Benz et al., 2012; Challen et al., 2010; Morita et al., 2010; Yamamoto et al., 2013). Slow and occasional interconversion between lymphoid-potential-positive and negative HSCs has also been reported, although lineage potential can be inherited from parental HSCs (Benz et al., 2012; Shimazu et al., 2012). Elucidation of molecular mechanisms that regulate the differentiation potential of HSCs is necessary to exploit the capabilities of HSCs for various applications. Self-renewal proliferation and multilineage differentiation, which are seemingly contradictory features of HSCs, are regulated by the changing demand for blood cells in vivo. Accordingly, interactions among lineage-related genes are required to mediate the differentiation potential of HSCs (Sexton and Cavalli, 2015). We previously identified a special AT-rich-sequencebinding protein 1 (SATB1), a global chromatin organizer, as a lymphoid-lineage-inducing gene in HSCs (Satoh et al., 2013). We demonstrated that exogenous induction of SATB1 in murine HSCs strongly enhanced both their T and B lymphopoietic potentials, whereas SATB1 deficiency caused malfunctions in the lymphopoietic activity of HSCs. Furthermore, another report showed that HSCs derived from the fetal livers of conventional SATB1-deficient mice were less capable of reconstituting long-term hematopoiesis in adult wild-type (WT) recipients and that SATB1-deficient HSCs differentiated preferentially into myeloid-erythroid lineages (Will et al., 2013). These results suggested that SATB1 was involved in both the lymphopoietic potential and stability of HSCs. However, it remains unclear whether SATB1 plays versatile roles in homeostatic HSCs in adult bone marrow (BM) and what molecular mechanisms might contribute to these effects. In this study, we generated hematological lineage-restricted Satb1-conditional-knockout (cKO) mice to examine whether SATB1 was involved in the two fundamental but contradictory functions of HSCs (i.e., self-renewal and differentiation) in adult BM. Furthermore, we developed a reporter mouse model in

Cell Reports 23, 3223–3235, June 12, 2018 ª 2018 The Authors. 3223 This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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Figure 1. Functional Significance of SATB1 in HSC Self-Renewal and Differentiation

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which Satb1 expression was monitored during HSC differentiation in vivo. This model allowed us to identify authentic lymphoid-biased self-renewing HSCs in homeostatic adult BM. Furthermore, our data suggested that at least some lymphoidbiased HSCs fluctuate in a dynamic trajectory for self-renewal and lineage commitment. RESULTS SATB1 Is Indispensable for the Self-Renewal and Differentiation of Adult HSCs Conventional SATB1-null mice have been used to study the roles of SATB1 in hematopoiesis and lymphopoiesis (Alvarez et al., 2000; Satoh et al., 2013; Will et al., 2013). However, the function of SATB1 in physiological adult hematopoiesis is difficult to 3224 Cell Reports 23, 3223–3235, June 12, 2018

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(A) The number of LSK CD150+ Flt3 cells/femur in Tie2-Cre+ Satb1+/+ or Satb1flox/flox mice (n = 4; mean ± SE). (B) Long-term reconstituting capacity of HSCs obtained from Tie2-Cre+ Satb1+/+ or Satb1f/f mice. The chimerism of CD45.2+ MNCs in recipient BM is shown (n = 7–8). (C–E) Transplantation results using Mx1-Cre Satb1cKO mice. (C) Long-term reconstituting capacity of HSCs obtained from CD45.2+ Mx1-Cre+ Satb1+/+ or Satb1flox/flox mice in WT recipients (n = 3 or 7, respectively; left). HSCs obtained from CD45.1+ WT mice were inversely transplanted into Mx1-Cre+ Satb1+/flox or Satb1flox/flox mice (n = 10 or 13, respectively; right). The chimerisms of donor-type MNCs in recipient PB are shown. (D and E) Reconstituted lineage proportion in primary recipients with (D) Mx1-Cre+ Satb1-cKO HSCs or (E) in primary recipients in inverse transplantation. Percentages of Mac1+ and/or Gr1+ myeloid cells and Mac1 Gr1 B220+ or CD3ε+ lymphoid cells in CD45.2+ MNCs are shown. (F) Differentiation capacity of HSCs from Tie2-Cre+ Satb1+/+ or Satb1flox/flox mice. Results of co-cultures with MS5 stromal cells are shown. Co-cultures were started with 100 LSK CD150+ Flt3 cells/well on day 0, and analyses were performed on day 10. B-lymphocyte formation rates in CD45+ Mac1 Gr1 cells are shown as contour plots. The bar graph shows the absolute number of B lymphocytes/well grown from Tie2-Cre+ Satb1+/+ or Satb1flox/flox HSCs (n = 4). (G and H) Growth capacity of Mx1-Cre+ Satb1+/+ or Satb1flox/flox HSCs in co-cultures with OP9 or OP9-DL1 cells. On day 0, cultures were started with 100 cells/well. (G) The absolute number of B lymphocytes/well was counted on days 4, 7, and 10 (n = 4). The absolute number of CD45+ CD4 CD8 double-negative (DN) T lymphocytes/well were counted on day 14 (n = 4). (H) The number of DN CD44+ CD25 (DN1) cells and DN CD44+ CD25+ (DN2) cells are shown (n = 4). *p < 0.05 (see also Figure S1). *p < 0.05; **p < 0.01.

discern because of neonatal mortality in these mice. To determine whether SATB1 is essential for normal hematopoiesis in adult BM, we prepared Satb1-cKO mice by crossing Satb1-floxed mice (Skowronska-Krawczyk et al., 2014) with Cre-recombinase-expressing mice under control of Tie2 promoter. Analysis of the BM of these mice showed that there was a 25% decrease in the number of HSCs bearing lineage marker (Lin ) Sca-1+ c-KitHi (LSK) CD150+ Flt3 in Tie2-Cre+ Satb1flox/flox mice as compared with those in their Tie2-Cre+ Satb1+/+ littermates (Figure 1A). Analyses with the Vav1-Cre-expressing model also showed similar reductions in HSCs (Figure S1A). Furthermore, cell cycle analyses of Satb1-cKO HSCs indicated that they were more likely to enter the DNA-synthesis stage than control HSCs (Figure S1B). Next, we conducted in vivo transplantation experiments to examine whether SATB1 deficiency affected the long-term

reconstituting capability of HSCs. We collected HSCs from Tie2Cre+ Satb1+/+ or Tie2-Cre+ Satb1flox/flox CD45.2+ mice by flow cytometry and transplanted these CD45.2+ HSCs into lethally irradiated CD45.1+ congenic WT mice (Figure S1C). At 4 months post-transplantation, chimerism in donor cells was significantly lower in recipients of Satb1-cKO HSCs than in those of control HSCs (Figure 1B). Transplantation with HSCs obtained from Mx1-Cre Satb1-cKO mice also provided similar results, whereas WT HSCs reconstituted long-term hematopoiesis normally in Mx1-Cre Satb1-cKO recipients (Figures 1C, S1C, and S1D). Additionally, the lineage composition of BM and peripheral blood (PB) following Satb1-cKO HSC transplantation was skewed toward the myeloid lineage (Figures 1D, 1E, S1E, and S1F). We previously reported that SATB1 plays critical roles in the early differentiation of fetal and neonatal HSCs to lymphocytes (Satoh et al., 2013). To determine whether SATB1 is also important for the lymphoid lineage differentiation of adult HSCs, we cultured Tie2-Cre Satb1-cKO and control HSCs. Although both HSCs effectively produced myeloid-erythroid colonies in methylcellulose medium (Figure S1G), their growth in co-cultures with stromal cells revealed that B lymphocyte production from Satb1-cKO HSCs was reduced to 50% that of WT HSCs (Figure 1F). Using Mx1-Cre Satb1-cKO mice, we also confirmed that Satb1-cKO HSCs are compromised in lymphopoietic activity for T and B lineages (Figures 1G and 1H). In OP9-DL1 co-cultures, SATB1 deficiency specifically damaged the transition from DN1 to DN2 (Figure 1H). Taken together, these results supported previous observations and highlighted the versatile roles of SATB1 in adult HSCs (i.e., maintenance of HSCs in the BM, reconstitution of long-term hematopoiesis, and generation of lymphoid-lineage cells). In Vivo Monitoring of Satb1-Expression-Mediated Subdivision of the Adult HSC Fraction We previously found that Satb1 expression was altered dramatically during HSC differentiation or aging (Satoh et al., 2013). To visualize the intensity of Satb1 expression under physiological conditions, we generated genetically modified mice in which Tomato, the gene encoding a red fluorescent protein, was stably expressed under control of the endogenous Satb1 promoter. Tomato was knocked in at the coding region of the genomic allele of Satb1 in embryonic stem cells by homogeneous recombination, replacing one Satb1 allele with Tomato (Figure 2A). Flow cytometric analysis of mononuclear cells (MNCs) from the BM of these reporter mice showed a distinct cell fraction in the FL2 channel as compared with that in their WT littermates (Figure S2A). A previous study reported that homogeneous Satb1-null mice died shortly after birth, whereas heterozygous mice grew normally without apparent abnormalities of the immune system (Alvarez et al., 2000). Similarly, our heterozygote Satb1-reporter mice were characterized by normal body size, fertility, and lympho-hematopoiesis (Figure S2B). Using these new reporter mice, we evaluated Satb1 expression in vivo at the single-cell level. We could distinguish clusters of hematopoietic stem and/or progenitor cells based on a combination of SATB1/Tomato-, c-Kit-, and Flt3-expression intensities (Figure 2B). One prevalent model for lymphopoiesis posits

that effector lymphocytes differentiate from HSCs to common lymphoid progenitors (CLPs) via lymphocyte-primed multipotent progenitors (LMPPs) (Adolfsson et al., 2005; Kondo et al., 1997). In the present study, SATB1 levels increased gradually as lymphoid-lineage differentiation proceeded from HSCs but remained low in granulocyte and/or macrophage-lineagerestricted progenitors (GMPs) and megakaryocyte and/or erythrocyte-lineage-restricted progenitors (MEPs) (Figure 2B). We previously found that Satb1 expression increased as HSCs differentiated into LMPPs and CLPs (Satoh et al., 2013). To confirm whether SATB1/Tomato could be a sensitive indicator of endogenous Satb1 mRNA levels, we precisely evaluated the intensity of SATB1/Tomato in HSCs and progeny cells. Notably, the fluorescence intensity of Tomato in lymphoid-lineage progenitors increased in a stepwise manner during differentiation of the lymphoid lineage, which corresponded with the changes in mRNA levels (Figures 2C and S2C). By contrast, the intensity of SATB1/Tomato decreased as cells differentiated into GMPs and MEPs (Figures 2C and S2C). To further investigate whether Satb1 expression is useful for analysis of early differentiation into the lymphoid lineage, we crossed SATB1/Tomato-reporter mice with recombination activating 1 (RAG1)-reporter mice. We previously found that Rag1 acts as an early lymphoid lineage-related gene and developed a method to separate early lymphoid progenitors (ELPs) from HSCs by monitoring RAG1/GFP expression in vivo (Igarashi et al., 2002; Yokota et al., 2003). Indeed, RAG1+ ELPs overlap with LMPPs and BM precursors in early thymus-immigrating cells and are depleted by pregnancy or sex steroid treatment (Lai and Kondo, 2007; Yokota et al., 2008). When we examined the double reporter mice carrying alleles of SATB1/Tomato and RAG1/GFP, the LSK fraction contained several cells with both SATB1/Tomato and RAG1/GFP expression (data not shown). However, when we added the CD150+ Flt3 criterion to purify HSCs without LMPP contamination, a substantial number of SATB1/Tomato+ cells still existed in the highly enriched HSC fraction, whereas RAG1/GFP-expressing cells were completely absent (Figure S2D). This result indicated that the SATB1/Tomato-reporter model permitted evaluation of early lymphoid differentiation of HSCs. Murine HSCs are categorized as the LSK fraction with other HSC-related markers, including CD150, CD48, Flt3, CD34, endothelial cell-selective adhesion molecule (ESAM), CD86, and CD41 (Gekas and Graf, 2013; Kiel et al., 2005; Wilson et al., 2008; Yamamoto et al., 2013; Yokota et al., 2009). Here, we utilized the SATB1/Tomato-reporter mice to subfractionate LSK CD150+ Flt3 HSCs into SATB1/Tomato and SATB1/Tomato+ groups and compared their expression with those of other HSC-related markers. The result showed that SATB1/Tomato HSCs had higher average levels of CD150 and ESAM and lower average levels of CD48 and CD34 than SATB1/Tomato+ HSCs (Figure 2D), suggesting that SATB1/Tomato HSCs were likely to contain more undifferentiated cells than SATB1/Tomato+ HSCs. Additionally, the fluorescence intensity of CD86, a reported lymphoid-lineage-related marker (Shimazu et al., 2012), was higher in SATB1/Tomato+ HSCs than in SATB1/Tomato HSCs (Figure S2E). These results indicated that the highly enriched HSC fraction was still Cell Reports 23, 3223–3235, June 12, 2018 3225

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Figure 2. Establishment of SATB1-Reporter Mice (A) Knockin strategy and construct of a targeting vector for SATB1-reporter mice. Margins for recombination are represented with dotted lines. (B) Observation of BM MNCs in SATB1/Tomato-reporter mice. Each axis shows SATB1, c-Kit, and Flt3 levels. Gating strategies for each fraction in BM MNCs are shown: HSCs, LSK CD150+ CD48 Flt3 ; LMPPs, LSK Flt3+ interleukin-7Ra (IL-7Ra) ; CLPs, Lin c-Kitlow Sca-1 /low Flt3+ IL-7Ra+; GMPs, Lin CD4 CD8 IgM IL-7Ra Sca-1 c-Kit+ FCgRHi CD34Hi; and MEPs, Lin CD4 CD8 IgM IL-7Ra Sca-1 c-Kit+ FCgRLo CD34Lo. (C) SATB1/Tomato expression in HSCs and progenitors. Red histograms show the fluorescent intensity of cells obtained from SATB1-reporter mice. Gray shadows indicate autofluorescence of the same fraction of WT littermates. Each panel represents HSCs, lymphoid-lineage progenitors (upper panels), and progenitors for myeloid and megakaryoid and/or erythroid lineages (lower panels). (D) Expression levels of HSC-related antigens in SATB1 and SATB1+ CD150+ Flt3 LSK cells. Mean fluorescence intensity (MFI) was calculated and is shown as bar graphs (n = 4). *p < 0.05; **p < 0.01 (see also Figure S2).

heterogeneous and could be sorted into different categories according to SATB1/Tomato-expression levels. SATB1 and SATB1+ HSCs Differed in Lineage Potential In Vitro We then conducted in vitro experiments to evaluate the functional characteristics of SATB1/Tomato and SATB1/Tomato+ HSCs. We sorted both fractions and confirmed high-purity sorting (Figures 3A and 3B) and also confirmed that the fluorescence intensities of Tomato reflected Satb1-transcript levels (Figure 3C). We cultured the sorted HSCs in methylcellulose medium and evaluated the growth of myeloid and erythroid colonies. The SATB1+ HSCs showed a significantly lower capability to produce all types of colonies, including colonyforming unit (CFU)-Mix, CFU-granulocyte-monocyte (GM)/ G/M, and erythroid burst-forming unit (BFU-E), than SATB1 HSCs (Figure 3D). To evaluate simultaneous differentiation into lymphoid and myeloid lineages in each fraction of HSCs, we performed co-cultures with MS5 stromal cells capable of supporting both lymphoid and myeloid growth. Under these conditions, SATB1+ HSCs gave rise to a robust population of hematopoietic cells, including myeloid cells (Figure 3E). Additionally, we observed marked differences in lymphopoietic potential between the two HSCs. After 1 week of culture, SATB1+ HSCs generated a large number of B-lymphocytes, which continued to expand, whereas SATB1 HSCs did not efficiently produce lymphocytes (Figure 3E). Given the heterogeneity of LSK CD150+ Flt3 cells, the discrepancy in myeloid-lineage growth between the two culture conditions might reflect that the CFU assays measure the clonal growth of rather committed hematopoietic progenitors, whereas MS5 co-cultures support more immature progenitors. These results demonstrated that SATB1 and SATB1+ HSCs substantially differed in the growth and differentiation potential, particularly in the lymphoid lineage. SATB1 and SATB1+ HSCs Differ in Gene-Expression Patterns To obtain comprehensive information about gene expression in SATB1 and SATB1+ HSCs, we performed next-generation

3226 Cell Reports 23, 3223–3235, June 12, 2018

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RNA sequencing (RNA-seq) analyses. The results revealed that 509 genes, including 316 upregulated and 193 downregulated genes, were significantly altered (p < 0.05) in SATB1/Tomato+ HSCs (Figure 4A), indicating that SATB1+ HSCs were transcriptionally more active than SATB1 HSCs. Among the top 10 genes that were down- or upregulated (p < 0.05), we found that the expression of several lymphoid-lineage-related genes was significantly induced in SATB1+ HSCs (Figure 4B). Biological pathway analyses using Ingenuity Pathway Analysis (IPA) software revealed that the ‘‘hematological system development and function’’ and ‘‘hematopoiesis’’ pathways were upregulated in SATB1+ HSCs (Figure S3A). Among subcategories of hematopoiesis, 18 pathways were predicted to increase, including differentiation of lymphocytes (p = 1.09E 24; Figure 4C) and development of hematopoietic progenitor cells (p = 9.08E 14; Figure 4C). Additionally, nine of 18 increased pathways were involved in lymphoid-lineage cell generation (Figure 4C). Evaluation of the total pathways among subcategories of hematological system development and function showed that lymphocyte-differentiation-related pathways were markedly increased (Figure S3B). We also tested the expression of genes related to hematopoietic lineage-fate decision in SATB1 and SATB1+ HSCs by realtime PCR. We observed that lymphoid-lineage-related genes

Figure 3. Functional Assessment SATB1 and SATB1+ HSCs In Vitro

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(A) A sorting strategy for SATB1 and SATB1+ cells from the LSK CD150+ Flt3 HSC-enriched fraction. (B) Evaluation of the intensities of SATB1/Tomato in sorted HSCs. (C) Determination of Satb1 mRNA levels in sorted SATB1 and SATB1+ HSCs (n = 6). (D) Colony formation in methylcellulose colony assays. Sorted SATB1 and SATB1+ LSK CD150+ Flt3 cells (n = 100) were seeded on day 0, and the number of each type of colony (CFU-Mix, CFU-GM/M/G, and BFU-E) were counted on day 10 (n = 3). (E) Growth capacity of SATB1 and SATB1+ HSCs in co-cultures with MS5 cells. On day 0, cultures were started with 100 cells/well. The absolute numbers of CD45+ hematopoietic cells (bar graphs, left upper panel), myeloid cells (bar graphs, left lower panel), and B lymphocytes (line graph, right) per well were counted on days 4 and 10 (n = 4). *p < 0.05; **p < 0.01; ***p < 0.005.

were generally upregulated (Figure 4D), whereas myeloid-lineage-related genes and erythroid-lineage-related genes were downregulated in SATB1+ HSCs (Figure 4E). The expression of genes required for preservation of HSC stemness was not significantly altered (Figure 4F). Notably, the expression of nuclear factor of activated T cells, reportedly involved in maintaining the lymphoid-lineage-differentiating capacity in HSCs (Luchsinger et al., 2016), was lower in SATB1+ HSCs. Furthermore, expression of the nuclear receptor subfamily 4 group A member 1, a marker of myeloid-biased HSCs (Land et al., 2015), was significantly decreased in SATB1+ HSCs (Figure 4F). SATB1 and SATB1+ HSCs Differ Functionally but Were Mutually Interconvertible In Vivo We performed transplantation assays to evaluate the differentiation potential of SATB1 and SATB1+ HSCs in vivo. HSCs are defined functionally by their ability to serially engraft in lethally irradiated recipients and regenerate their hematopoietic and immune systems. SATB1/Tomato and SATB1/Tomato+ HSCs were sorted from adult BM of CD45.2+ SATB1/Tomato-reporter mice, and 1,000 cells from each HSC fraction were independently transplanted into lethally irradiated CD45.1+ congenic WT mice along with 2 3 105 rescue BM cells (Figure S4A). After 4 months, we sacrificed the recipients and examined their PB and BM. We found that, although both SATB1 and SATB1+ HSCs engrafted in the BM, the latter contributed to recipient hematopoiesis with higher chimerism than the former (Figure 5A). This result was unexpected, because SATB1+ HSCs exhibited a more differentiated phenotype on average in terms of cell-surface antigens (Figure 2D). Cell Reports 23, 3223–3235, June 12, 2018 3227

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Figure 4. Transcriptome Evaluation of SATB1 and SATB1+ HSCs (A–C) Results of RNA-seq analysis of total RNA samples isolated from SATB1 and SATB1+ CD150+ Flt3 LSK cells to evaluate changes in genetic expression between HSC type (see also Figure S3). (A) Volcano plot showing comprehensive changes in gene expression, with changes in individual gene expression compared between HSCs (p < 1; Fisher’s exact test). Red lines divide genes according to increase or decrease in expression level and p < 0.05 (corresponding to 1.3 on the log10 scale). (B) Top 10 downregulated and upregulated genes and their fold changes (FCs). Lymphoid-lineage-related genes are indicated (yellow; genes restricted to p < 0.05). (C) Results of functional annotation analysis (genes restricted to p < 0.05). Several lymphoid-lineage-related pathways are shown in red. (D–F) Expression levels of specific genes were evaluated, and data represent the expression levels in SATB1+ HSCs as compared with those in SATB1 HSCs. *p < 0.05. (D) Lymphoid-lineage-related genes. (E) Myeloid-lineage-related genes (left) and erythroid-lineage-related genes (right). (F) Genes involved in maintaining HSC stemness (left) and lymphoid- or myeloid-biased HSCs (right). *p < 0.05; **p < 0.01.


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Figure 5. Functional Assessment of SATB1 and SATB1+ HSCs In Vivo (A–C) Results of primary BM transplantation. Donor SATB1 and SATB1+ LSK CD150+ Flt3 cells were sorted from CD45.2+ SATB1/Tomato-reporter mice and transplanted into lethally irradiated CD45.1+ WT mice (n = 8–9). (A) Chimerism in primary recipients. Evaluation of percentages of CD45.2+ MNCs in total CD45+ MNCs in the BM of each recipient is shown. (B) Lineage output in the BM of primary recipients (see also Figure S4). Frequencies of CLPs (in CD45.2+ Lin cells) and myeloid progenitors (in CD45.2+ Lin Sca-1 cells) in SATB1 and SATB1+ HSC-transplanted recipients are shown. The gating strategies for each fraction are shown: CLPs, Lin Sca-1 /low c-Kitlow Flt3+ IL-7Ra+ and myeloid progenitors, Lin Sca-1 c-KitHi IL-7Ra . (C) Reconstruction of the HSC fraction in the BM of primary recipients. Each panel is gated on CD45.2+ LSK cells. (D) SATB1 intensity in reconstituted HSCs in primary recipients. Each histogram is gated on CD45.2+ LSK CD150+ Flt3 cells, and the gray shadowed line indicates autofluorescence in WT mice. (E–H) Results of secondary transplantation. Whole-BM MNCs were collected from primary recipients and transplanted into lethally irradiated CD45.1+ WT mice. The gating strategies for each fraction were same as in (A)–(C). (E) Chimerism in recipients of secondary transplantation. Evaluation of percentages of CD45.2+ MNCs in total CD45+ MNCs in the BM of each recipient (n = 4–6). (F) Lineage output in the BM of secondary recipients (see also Figure S4). Frequencies of reconstituted CLPs and myeloid progenitors are shown (n = 5–8). (G) Reconstruction of the original HSC fraction of secondary recipients. (H) SATB1 intensity in reconstituted HSCs of secondary recipients. *p < 0.05; **p < 0.01. See also Figure S4.

Cell Reports 23, 3223–3235, June 12, 2018 3229

In addition to engrafting activity, the pattern of lineage reconstitution varied considerably between the two HSC types. We observed that lymphocyte output was significantly higher, whereas myeloid-cell generation was lower in SATB1+ HSCtransplanted recipients (Figure S4B). To assess whether this imbalance resulted from functional differences in the two types of HSCs in terms of lineage-restricted progenitors, we evaluated the proportions of CLPs and myeloid progenitors among the engrafted donor cells. Notably, significantly more CLPs were produced from SATB1+ HSCs than from SATB1 HSCs, whereas myeloid progenitors were more efficiently generated from the latter HSCs (Figure 5B). Although the two types of HSCs showed obvious differences in their ability to differentiate into either lymphoid or myeloid lineages, both HSCs sufficiently reconstituted the LSK CD150+ Flt3 HSC-enriched fraction, which contained a variety of HSCs in terms of SATB1/Tomato expression (Figures 5C and 5D). Therefore, SATB1 HSCs reconstituted the other HSCs exhibiting positive SATB1/Tomato intensities and vice versa. These results suggested that SATB1 and SATB1+ HSCs are mutually interconvertible and that both SATB1 and SATB1+ fractions contained the definitive characteristics of HSCs. To further examine the long-term repopulating ability of each HSC fraction, we performed serial-transplant assays. BM cells were collected from primary recipients of each group and were transplanted into lethally irradiated secondary CD45.1+ recipients (Figure S4A). After 4 months, we observed high contribution of CD45.2+ cells in both types of recipients; however, the donorcell chimerism in the BM did not differ (Figure 5E). Additionally, both HSCs generated lymphocytes and myeloid cells in the PB, as well as in CLPs, myeloid progenitors, and HSCs, in the BM with equal efficiency (Figures 5F, 5G, and S4C). The intensity of SATB1/Tomato in the reconstituted HSCs was also similar (Figure 5H). These observations suggested that, although SATB1 and SATB1+ HSCs differed in lineage-output potential, they were interconvertible and retained multipotency as authentic HSCs over the long term.

greater engraftment efficiency (Figure 6C). This result showed the significance of SATB1 levels in promoting long-term engraftment of HSCs. Additionally, HSCs that expressed higher Satb1 levels generated the lymphoid lineage, whereas the subfractions for groups 1 and 2 were apparently biased toward the myeloid lineage (Figure 6D). Therefore, our method enabled isolation of lymphoid-lineage-biased HSCs based on Satb1 expression. Furthermore, we concluded that substantial Satb1 expression was vital for HSC retention of both long-term reconstitution and lymphopoietic potential. Satb1 Expression Indicates HSC Heterogeneity Accumulating evidence indicates that even highly enriched HSCs are heterogeneous in their expression of diverse genes at the single-cell level (Copley et al., 2012). Our results showed that HSC heterogeneity was, at least partially, regulated by SATB1 levels, which likely fluctuate over the long term. To confirm SATB1 fluctuation at the clonal level, single HSCs in the five groups were transplanted. We observed that, although the mean and distribution of SATB1 intensities in reconstituted HSCs reflected the original characteristics, individual reconstituted HSCs displayed diverse levels of SATB1 (Figure 6E). To visualize HSC heterogeneity, we plotted the expression of surface markers on HSCs against SATB1 levels in a threedimensional field (Figure 7A). CD86 and CD41 are lineagerelated markers for lymphoid-biased HSCs (Shimazu et al., 2012) and myeloid-biased HSCs (Gekas and Graf, 2013), respectively. The combination of the three parameters demonstrated that HSCs were spread over a spatial expanse without overlapping with each other (Figure 7A). When we focused on two parameters, SATB1 levels in HSCs tended to correlate positively with CD86 levels, but negatively with CD41 levels (Figure 7B). These results suggested that heterogeneity was inherent to HSCs and that the self-renewing and differentiation trajectory of HSCs might be regulated by fluctuating SATB1 levels (Figure 7C). DISCUSSION

Satb1 Expression Indicates HSC Authenticity As described, SATB1+ HSCs engrafted more efficiently than SATB1 HSCs, contrary to our expectations (Figure 5A). Because the transplantations were performed with a bulk fraction containing a diverse cell population, a small population of SATB1+ cells at the threshold level might have contributed to the high engraftment. To address this issue, we segmented the LSK CD150+ Flt3 fraction into five subfractions according to SATB1/Tomato intensity and performed transplantation with only 10 cells of each subfraction in five groups of recipient mice (Figure 6A). CD150 indicates the potential for self-renewal, high reconstitution, and robust myeloid-lineage production of HSCs (Beerman et al., 2010; Morita et al., 2010; Papathanasiou et al., 2009). We found that, although the subfraction for group 1 was virtually negative for Satb1 expression, the mean expression of CD150 was significantly higher than that of other subfractions (Figure 6B). Surprisingly, however, the number of successfully engrafted recipients was lowest in group 1 (Figure 6C). By contrast, higher levels of SATB1 in transplanted cells led to 3230 Cell Reports 23, 3223–3235, June 12, 2018

Although HSC population is atop the hematopoiesis hierarchy, accumulating evidence shows that HSCs comprise diverse cell types exhibiting substantially different self-renewing and differentiation potential (Benz et al., 2012; Challen et al., 2010; Morita et al., 2010; Yamamoto et al., 2013). Specifically, an HSC subtype with robust lymphopoietic activity has attracted attention, because the population initiating lymphoid-lineage differentiation is severely reduced by aging and disease, which is related to immunosenescence (Geiger et al., 2013). Furthermore, the early lymphoid stage proximal to HSCs is negatively regulated during pregnancy (Medina et al., 2001; Yokota et al., 2008) via mechanisms related to vulnerability of the maternal immune system to infections. Therefore, precise information regarding the molecular mechanisms underlying initiation of the lymphoid-differentiation program in HSCs should be essential for repairing a compromised immune system under various circumstances. We previously identified Satb1 as a lymphoid-lineageinducing gene in HSCs (Satoh et al., 2013), with Satb1 overexpression inducing lymphoid differentiation from murine HSCs

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Figure 6. Examination of the Differentiation Potential of HSCs according to SATB1 Levels (A) Transplantation strategy. LSK CD150+ Flt3 cells in SATB1/Tomato-reporter mice were subdivided into five groups according to SATB1/Tomato intensity. The borders of each group are defined by cell-number percentages (histogram). (B) CD150 expression in single HSCs in each subfraction (group 1, 76 cells; group 2, 56 cells; group 3, 64 cells; group 4, 78 cells; and group 5, 79 cells). Medians are shown with bars. (C–E) Ten cells (C and D) or single cells (E) for each fraction were transplanted into lethally irradiated CD45.1+ recipients, and analysis was performed after 4 months. (C) Engraftment rates in recipients of each group. The frequencies of successfully engrafted recipients with at least 2% BM chimerism are shown. Data were summarized from three independent experiments (total analyzed recipients for groups 1, 2, 3, 4, and 5: n = 12, 15, 9, 13, and 13, respectively; successfully engrafted recipients for groups 1, 2, 3, 4, and 5: n = 3, 7, 6, 10, and 10, respectively). (D) Percentages of reconstituted myeloid cells (upper panel) and lymphoid cells (lower panel) in CD45.2+ BM MNCs. The medians are shown with bars.

and aged HSCs, whereas Satb1 deficiency disrupts the HSC lymphopoietic activity. Another report showed that Satb1-deficient HSCs were less quiescent than WT HSCs and differentiated preferentially into myeloid-erythroid lineages in the BM of WT recipients, with hematopoiesis reconstituted by Satb1-deficient or WT HSCs (Will et al., 2013). The results of these two reports partially overlapped regarding the importance of SATB1 in HSC-lineage determination but did not address how a single protein executes contradictory roles by inducing quiescence, self-renewal, and lymphoid-lineage differentiation. To address this question, we used a Satb1-cKO mouse model, because systemic Satb1-KO mice exhibited neonatal lethality, precluding appropriate analysis of homeostatic HSCs in adult BM. BM analysis in these cKO mice revealed decreased HSC number relative to that in their WT littermates. Moreover, certain differences were observed regarding cell cycle status and quiescent cell proportions between Satb1-deficient and WT HSCs. The myeloid-erythroid colony-forming efficiencies of Satb1-deficient and WT HSCs were comparable; however, the lymphopoietic potential of those HSCs was compromised. Furthermore, transplantation experiments demonstrated that Satb1-deficient HSCs were less capable of reconstituting long-term hematopoiesis, which agreed with results of the BM-transplantation assay using 10 HSCs from five subfractions of HSCs isolated based on SATB1/Tomato intensity, which showed that HSCs expressing less Satb1 had lower self-renewal capacity. These results indicated that SATB1 plays important roles in self-renewal and the normal differentiation capability of adult HSCs. Although SATB1 is required to maintain HSC integrity, it also promotes their differentiation toward the lymphoid lineage. Here, we generated SATB1-reporter mice allowing precise monitoring of Satb1 expression in vivo. This model was useful to examine early HSC differentiation toward the lymphoid lineage. The HSC fraction of adult BM comprised a wide range of Satb1-expressing cells, which were generally divided into SATB1 and SATB1+ subfractions. Notably, in methylcellulose colony assays, SATB1+ HSCs were less potent at producing myeloid-erythroid-lineage colonies, whereas the output of lymphocytes from SATB1+ HSCs was more robust than that from SATB1 HSCs in co-cultures with stromal cells. RNA-seq data supported observations from cell-culture experiments, showing that the expression of several lymphocyte-related genes was induced in SATB1+ HSCs as compared with that in SATB1 HSCs. These results strongly indicated that Satb1 expression in HSCs was associated with lymphoid-lineage choice. In agreement with results from in vitro experiments and geneexpression profiles, SATB1+ HSCs generated more lymphocytic cells and fewer myeloid cells in primary transplantation recipients. However, both SATB1 and SATB1+ HSC types

(E) SATB1/Tomato intensity of each single LSK CD150+ Flt3 HSC (plotted as a dot) reconstituted after single-cell HSC transplantation. Vertical axis indicates the distribution of recovered HSCs with respect to SATB1/Tomato intensity. Data from a representative recipient in each group are shown. MFIs are shown with bars. The borders of each group were drawn as dashed lines, which were defined as described in (A). Distribution data are summarized and shown as 100% in the stacked bar chart (in a dashed-line rectangle). *p < 0.05; ***p < 0.005.


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Figure 7. Visualization of HSC Heterogeneity and Fluctuation according to SATB1 Expression (A) Three-dimensional representation of the HSC fraction. SATB1/Tomato, CD86, and CD41 levels were estimated by flow cytometry. Three-dimensional scatterplot and 50% probability ellipsoid for total plots are drawn. Cells with the upper one-third of SATB1 intensity are drawn in red, and others are drawn in blue. (B) Associations between SATB1 and CD86 (left) and between SATB1 and CD41 (right) in each single HSC. The linear approximations for each scatterplot are drawn in red and represented as mathematical formulas. (C) A dynamic view of the cellular states of HSCs and their differentiation. Each axis represents the expression levels of SATB1 and other lineage-related genes. The coil-like trajectory represents time-related fluctuations in each gene-expression level. Lymphoid-biased HSCs are shown as red dots, whereas myeloid-biased HSCs are shown as blue dots.

reconstituted the complete HSC fraction with equal efficiency and successfully reconstituted lympho-hematopoiesis in secondary recipients. These results demonstrated the heterogeneity of HSCs and existence of authentic lymphoid-lineage-biased HSCs, which were isolated based on Satb1 expression. Further analysis showed that HSC populations with minimal Satb1 expression were mostly myeloid biased. Unexpectedly, these SATB1 myeloid-biased HSCs were least capable of reconstituting long-term hematopoiesis, regardless of higher CD150 3232 Cell Reports 23, 3223–3235, June 12, 2018

expression. Instead, SATB1+ HSC fractions exhibited higher reconstituting potential and robust lymphopoietic activity, suggesting that Satb1 expression was a reliable marker of legitimate HSCs. Several previous studies characterized HSCs with lymphopoietic potential. One study applied their side-population (SP) technique combined with conventional HSC markers to distinguish between myeloid- and lymphoid-biased HSCs (Challen et al., 2010). They divided SP HSCs according to Hoechst intensity, reporting that Hoechst-low SP was enriched with myeloidbiased HSCs, whereas Hoechst-high SP was lymphoid biased. However, SATB1/Tomato+ lymphoid-biased HSCs are not identical to Hoechst-high SP cells, because the former are entirely isolated from CD150+ cells, whereas the latter included CD150 cells at a frequency of >60%. Moreover, Hoechst-high SP HSCs are inferior to Hoechst-low SP HSCs, whereas SATB1/Tomato+ HSCs are superior to SATB1/Tomato HSCs in terms of long-term reconstitution potential. Additionally, the previous report showed that some highly lymphoid-biased HSCs exist, even among CD150+ Hoechst-low SP LSK cells (Challen et al., 2010). Our results suggested that SATB1/Tomato expression might facilitate identification of such authentic lymphoid-lineage-biased HSCs. Extensive clonal-transplantation experiments have been conducted using CD45+ endothelial protein C receptor+ CD48 CD150+ cells highly enriched with serially transplantable HSCs (Benz et al., 2012), and it was retrospectively confirmed that the durable HSC fraction comprised two major categories: one producing both myeloid and lymphoid cells and another selectively lacking lymphoid potential. Both categories produced equal numbers of myeloid-erythroid progenitors, but the latter could not produce functional CLPs. Our data showed that SATB1/Tomato+ HSCs successfully reconstituted the lymphoid lineage, including CLPs, whereas SATB1/Tomato HSCs were less potent in lymphoid cell production. Thus, our system enabled isolation of prospective HSCs endowed with robust lymphopoietic potential. Another study identified CD86 as a marker for murine HSCs with lymphoid potential (Shimazu et al., 2012). CD86+ cells in the CD150High CD48 LSK fraction effectively reconstituted a full spectrum of hematopoietic cells, including lymphoid-lineage cells, whereas CD86 cells in the same fraction showed poor lymphopoietic and total hematopoietic potentials, consistent with the high lymphoid-lineage potential of HSCs reported previously (Benz et al., 2012). In the present study, we detected positive correlations between SATB1/Tomato and CD86 levels and previously observed that CD86 expression is strongly induced in HSCs through exogenous induction of Satb1 expression (Satoh et al., 2013). Therefore, these two molecules appear functionally associated with lymphoid lineage. Importantly, occasional interconversion between the two HSC categories was reported (Benz et al., 2012; Shimazu et al., 2012). Although most HSCs retain their original differentiation propensity during primary transplantation, both HSC populations can reconstitute each other in long-term serial-transplant experiments. Consistent with these findings, we observed that SATB1 and SATB1+ HSCs significantly differed in differentiation potential but exhibited both self-perpetuating capacity and reciprocal

reconstitution in serial transplantation. The cell-dividing flow of the two HSC fractions appeared to follow the same trajectory in the primary recipients and demonstrated equal ability for self-renewal and differentiation in secondary recipients. The diversity of SATB1 levels in HSCs recovered after single HSC transplantation also supports this interpretation. Therefore, in addition to successful isolation of authentic lymphoid-lineagebiased HSCs, our results revealed the fluctuating nature of HSCs in terms of SATB1 levels. Recently, a dynamic systems approach was used to study the behavior and nature of stem cells (Furusawa and Kaneko, 2012), suggesting that fluctuating gene expression might be inherent to stem cells, thereby allowing them to execute contradictory specific functions (i.e., self-renewal and differentiation). Because individual cells constituting the stem cell fraction are not completely identical in their expression of diverse genes, all stem cells can be located within a certain area when plotted in a multidimensional field (Figure 7C). Therefore, the ‘‘stem cell fraction’’ intrinsically represents heterogeneity when its fluctuating components are individually analyzed at a certain time point. Several recent reports involving extensive single-cell analyses show that HSCs are essentially heterogeneous in gene expression, epigenetic configuration, and differentiation dynamism (Lummertz da Rocha et al., 2018; Velten et al., 2017; Yu et al., 2016). The flexibility and durability of hematopoiesis according to physiological stress might be attributed to the integrated action of diverse HSCs. Our findings support this notion and shed light on SATB1 in promoting HSC differentiation dynamism. Further studies are necessary to determine whether SATB1 also contributes to the heterogeneity of epigenetic characteristics of HSCs. In summary, we confirmed that SATB1 was functionally involved in maintaining HSC self-renewal and lymphopoietic potential. Additionally, Satb1 expression underlies the fluctuating nature of HSCs with respect to lineage-differentiation potential. These findings suggest that HSCs are not quiescent or inert and do not exist at the top of the hematopoietic hierarchy; they represent active fluctuation in the hematopoietic system. Because SATB1 contributes to the generation of chromatin loops and synchronizes the expression of various genes, it might actively participate in fluctuation of the HSC transcriptome, thereby sustaining the dynamic equilibrium of hematopoiesis. Although determination of whether SATB1 mediates systematic transcriptional fluctuation in a small population, such as HSCs, is challenging, we believe that technical advances will generate reliable analyses for understanding the association of SATB1 and its target genes in HSCs. EXPERIMENTAL PROCEDURES Mice For conditional Cre/loxP-deletion analysis, Tie2-Cre mice, Mx1-Cre mice, and Vav1-Cre mice were purchased from Jackson Laboratories (Bar Harbor, ME, USA). Satb1-floxed mice were kindly provided by Dr. Kondo, Department of Molecular Immunology Toho University School of Medicine (Tokyo, Japan). Mx1-Cre Satb1-floxed mice received three intraperitoneal injections of polyinosinic-polycytidylic acid (250 mg; InvivoGen, San Diego, CA, USA) at 2-day intervals, and they were sacrificed or irradiated after >10 days from the last injection. SATB1/Tomato-knockin mice were generated in our laboratory. The beginning of the cDNA encoding the Tomato fluorescent protein was designed

to match the first adenine-thymine-guanine (ATG) translation initiation codon of the reading frame in the second exon of Satb1. The Tomato gene has the stop and poly-A signal at the end of its reading frame, thereby restricting transcription of the remaining exons of endogenous Satb1. Substitution of one Satb1 allele for Tomato was performed by homologous recombination. All mice used in this study were maintained at the Institute of Experimental Animal Sciences Faculty of Medicine, Osaka University (Osaka, Japan), and all animal experiments were approved by the same institute. Transplantation Assays All donor cells for BM transplantation were isolated from 6- to 12-week-old mice, with recipient mice 8–11 weeks old and backgrounds of either C57BL/6-CD45.2+ or C57BL/SJL-CD45.1+. Recipients for BM transplantation were lethally irradiated and provided with antibiotics 1 week before and 4 weeks after transplantation. Experimental procedures are illustrated in Figures 6A, S1C, S1D, and S4A. Cell Isolation, Analysis, and Sorting BM cells were flushed from tibias, femurs, humeri, and pelvic bones using PBS supplemented with 3% fetal calf serum (FCS) and were gently filtered through a nylon screen (70 mm) to obtain a single-cell suspension. PB was hemolyzed using BD Pharm Lyse lysing buffer (BD Biosciences, Franklin Lakes, NJ, USA) and washed twice with PBS with 3% FCS before antibody staining. For HSC sorting, BM cells were incubated with purified rat antibodies against Lin markers (CD3ε, B220, Mac1, Gr1, and Ter119), followed by depletion of Lin+ cells using goat anti-rat immunoglobulin G (IgG) microbeads and Miltenyi Biotec (MACS) columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The fraction enriched with Lin /low cells underwent further antibody staining, and HSCs were sorted into Falcon tubes or 96-well plates. We used the LSK CD150+ Flt3 phenotype to sort HSCs. Dead cells were excluded by staining with 7-amino-actinomycin D (Merck Millipore, Darmstadt, Germany). Flow cytometric analysis and sorting were performed on FACSCantoII, FACSAria, or FACSAriaIIu cytometers and cell sorters (BD Biosciences). Gates were set using appropriate isotype controls. Fluorescence intensities were calculated using FlowJo software (FlowJo, Ashland, OR, USA). Information concerning antibodies used in this study is provided in the Supplemental Information. Stromal Cell Co-culture and Colony Formation Assays Co-culture and colony formation experiments with murine stromal cell lines MS5, OP9, or OP9-DL1 were performed as described previously (Satoh et al., 2013). RNA-Seq and qPCR Analysis Library preparation was performed using a SMARTer ultra-low RNA kit (Clontech, Mountain View, CA, USA) to prepare amplified cDNA according to manufacturer instructions. Sequencing was performed on an Illumina HiSeq 2500 platform (Illumina, San Diego, CA, USA) in a 101-base single-end mode. Illumina Casava software (v1.8.2; Illumina) was used for base calling. Sequenced reads were mapped to mouse reference genome sequences (mm10) using TopHat (v2.0.13; https://ccb.jhu.edu/software/tophat/index.shtml) in combination with Bowtie2 (v2.2.3; http://bowtie-bio.sourceforge.net/bowtie2/index. shtml) and SAMtools (v0.1.19; http://samtools.sourceforge.net/). The fragments per kilobase of exon per million mapped fragments were calculated using Cufflinks (v2.2.1; http://cole-trapnell-lab.github.io/cufflinks/). For qPCR analysis, total RNA was extracted using TRIzol (Thermo Fisher Scientific, Waltham, MA, USA). Reverse transcription was performed using a high-capacity RNA-tocDNA kit (Applied Biosystems, Foster City, CA, USA). qPCR was performed using THUNDERBIRD SYBR qPCR mix (Toyobo, Osaka, Japan) on a real-time PCR 7900 HT instrument (Applied Biosystems). Data were normalized to the expression of glyceraldehyde 3-phosphate dehydrogenase using the 2 DDCt method. Information concerning the primers used for each gene is provided in the Supplemental Information. DATA AND SOFTWARE AVAILABILITY The accession number for the raw RNA-seq data reported in this paper is GEO: GSE94630.


SUPPLEMENTAL INFORMATION

Geiger, H., de Haan, G., and Florian, M.C. (2013). The ageing haematopoietic stem cell compartment. Nat. Rev. Immunol. 13, 376–389.

Supplemental Information includes Supplemental Experimental Procedures and four figures and can be found with this article online at https://doi.org/ 10.1016/j.celrep.2018.05.042.

Gekas, C., and Graf, T. (2013). CD41 expression marks myeloid-biased adult hematopoietic stem cells and increases with age. Blood 121, 4463–4472.

ACKNOWLEDGMENTS We thank Dr. Kincade (Oklahoma Medical Research Foundation) for critically reading the manuscript and Dr. Ura (Chiba University) and Dr. Furusawa (Osaka University) for valuable discussions. We also thank Ms. Habuchi, Ms. Shih, Ms. Otsuki, and NPO Biotechnology Research and Development for technical assistance and the NGS Core Facility of the Genome Information Research Center at the Research Institute for Microbial Diseases of Osaka University for support in RNA-seq and data analysis. The manuscript was edited by Cactus Communications. This work was supported by grants from FLASH funding from SHIONOGI & Co., Ltd., SENSHIN Medical Research Foundation, and the Japan Society for the Promotion of Science KAKENHI (grant nos. 26461445, 16H05339, and 17K09952). This work was also supported by scholarship donations from Takeda Pharmaceutical Co., Ltd., CHUGAI Co., Ltd., and Bristol-Myers Squibb. AUTHOR CONTRIBUTIONS Y.D. and T.Y. designed experiments and analyzed data, with intellectual input from T.K.-S. Experiments were performed by Y.D., T.K.-S., Y. Satoh, and D.O. with assistance from M.T., T.I., T.S., T.U., Y. Shingai, and J.T. The manuscript was written by Y.D., T.Y., D.O., and Y.K. with assistance from M.I., A.T., S.E., H.S., and K.O. DECLARATION OF INTERESTS The authors declare no competing interests. Received: April 25, 2017 Revised: April 5, 2018 Accepted: May 14, 2018 Published: June 12, 2018 REFERENCES

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