Identification of novel regulators of developmental hematopoiesis using Endoglin regulatory elements as molecular probes

Abstract

Enhancers are the primary determinants of cell identity, and specific promoter/enhancer combinations of Endoglin (ENG) have been shown to target blood and endothelium in the embryo. Here, we generated a series of embryonic stem cell lines, each targeted with reporter constructs driven by specific promoter/enhancer combinations of ENG, to evaluate their discriminative potential and value as molecular probes of the corresponding transcriptome. The Eng promoter (P) in combination with the -8/+7/+9-kb enhancers, targeted cells in FLK1 mesoderm that were enriched for blast colony forming potential, whereas the P/-8-kb enhancer targeted TIE2+/c-KIT+/CD41- endothelial cells that were enriched for hematopoietic potential. These fractions were isolated using reporter expression and their transcriptomes profiled by RNA-seq. There was high concordance between our signatures and those from embryos with defects at corresponding stages of hematopoiesis. Of the 6 genes that were upregulated in both hemogenic mesoderm and hemogenic endothelial fractions targeted by the reporters, LRP2, a multiligand receptor, was the only gene that had not previously been associated with hematopoiesis. We show that LRP2 is indeed involved in definitive hematopoiesis and by doing so validate the use of reporter gene-coupled enhancers as probes to gain insights into transcriptional changes that facilitate cell fate transitions.

Figure 1

Mesoderm to hemangioblast transition is accompanied by increased Eng expression and chromatin accessibility at hematoendothelial regulatory elements. (A) Schematic representation of the ENG locus. The transcription start site is marked with an arrow. The −8-kb, +7-kb, and +9-kb enhancers and the promoter (P) are marked in orange; exons are marked in brown, and the 5′untranslated region is marked in cyan. (B) Schematic representation of Bry-GFP ES cell differentiation. At day 3 of EB differentiation, Bry-GFP+/FLK1− (G+F−) and Bry-GFP+/FLK1+ (G+F+) cells were sorted and analyzed by RT-PCR and ChIP. (C) Bar graph shows Eng mRNA expression levels in sorted FLK1+ve and –ve mesodermal cell populations in day 3 EBs generated from Bry-GFP ES cells. (D) Bar graph shows levels of enrichment of the active chromatin mark, H3K9Ac at Eng −8, P, +7, and +9 hematoendothelial enhancers relative to immunoglobulin G in prehemangioblast mesoderm (G+F−; black) and in hemangioblast mesoderm (G+F+; gray). Eng −4 was included as a negative control region. **P < .01, ***P < .001.

Figure 2

The Eng promoter when combined with the −8, +7, and +9 hematoendothelial enhancers targets FLK1+ mesodermal cells enriched for BL-CFC potential. (A) Schematic representation of the experimental procedure. The Eng −8/P/LacZ, Eng −8/P/LacZ/+7, Eng −8/P/LacZ/+9, Eng −8/P/LacZ/+7/+9, Eng −8/P/LacZ/+7Δ/+9, and Eng −8/P/LacZ/+7Δ/+9Δ reporter constructs were introduced by homologous recombination into the HPRT locus of HM1 ES cells. Recombinant clones were differentiated into day 3 EBs and stained for FLK1 expression and β-galactosidase activity. FLK1+/LacZ− (F+/L−; gray) and FLK1+/LacZ+ (F+/L+; blue) cells were sorted and seeded into BL-CFC assays. Fractions sorted from the Eng −8/P/LacZ/+7/+9 were further analyzed by RNA sequencing. (B) Flow cytometry profiles of Eng −8/P/LacZ/+7/+9 day 3 EBs (left). BL-CFCs from sorted F+/L− (gray) and F+/L+ (blue) fractions. (C) (i) Flow cytometry profile of day 3 EBs derived from ES cells targeted with Eng −8/P/LacZ/+7Δ/+9 (mutated GATA motifs in the +7 enhancer) is shown to the left with corresponding BL-CFCs from sorted F+/L− (gray) and F+/L+ (blue) fractions shown to the right. (ii) Flow cytometry profile of day 3 EBs derived from ES cells targeted with Eng −8/P/LacZ/+7Δ/+9Δ (mutated GATA motifs in the +7 enhancer and mutated ETS motifs in the +9 enhancer) and corresponding BL-CFCs from sorted F+/L− (gray) and F+/L+ (blue) fractions. (D) Flow cytometry profiles of day 3 EBs and BL-CFCs from sorted F+/L− (gray) and F+/L+ (blue) fractions are shown for ES cells targeted with (i) Eng −8/P/LacZ, (ii) Eng −8/P/LacZ/+9, and (iii) Eng −8/P/LacZ/+7. BL-CFC counts are the total number of blast colonies generated from 2 × 10⁴ seeded cells. Statistical analysis was conducted using Student t test, *P < .05, **P < .01.

Figure 3

RNA sequencing of FLK1 mesoderm targeted by Eng −8/P/LacZ/+7/+9 identifies genes associated with hemangioblast activity. (A) RNA-sequencing profiles shows Kdr (Flk1) transcripts (top) and Eng transcripts (bottom) in the F+/L− and F+/L+ fractions. FPKM expression values are shown to the right. (B) (i) Heat map representation of up- and downregulated genes in FLK1+/LacZ− (F+/L−) and FLK1+/LacZ+ (F+/L+) fractions in 3 independent experiments. (ii) Expression (FPKM values) levels of genes that have previously been associated with hemangioblast function. The left panel shows a subset of genes that are differentially expressed between F+/L− and F+/L+ fractions, and the right panel shows a subset of genes that are not. (C) GSEA profiles shows the correspondence of genes that are differentially expressed between F+/L− and F+/L+ fractions and those that are differentially expressed in ETV2^+/− vs ETV2^−/− (top) and LDB wt vs LDB^−/− gene sets. DEG, differentially expressed genes.

Figure 4

The Eng promoter in combination with the −8 endothelial enhancer targets HECs enriched for hematopoietic potential. (A) Schematic diagram outlining the experimental procedure. Recombinant ES cells generated using the Eng reporter constructs were differentiated into day 3 EBs. FLK1+ mesodermal cells were sorted from representative clones for each recombinant ES cell line and cultured in LBM. At 48 hours, CD41−/TIE2+/c-KIT+ (HE) cells were sorted into lacZ+ and lacZ– fractions. The sorted fractions were recultured in LBM for a further 48 hours followed by flow cytometry and CFU-C assays. (B) (i) CD41 and TIE2 expression in sorted c-KIT+ HE LacZ− (white) and LacZ+ (blue) fractions (after 2 days of reculture) derived from Eng −8/P/LacZ ES cells. (ii) Percentage of CD45+ cells generated from LacZ− and LacZ+ HE fractions. (iii) Bar chart shows the number and type of hematopoietic colonies generated by each fraction. (C) (i-iii) Corresponding data to (B) generated from Eng −8/P/LacZ/+7/+9 ES cells. (D) (i-iii) Corresponding data to (B) generated from Eng −8/P/LacZ/+7 ES cells. (E) (i-iii) Corresponding data to (B) generated from Eng −8/P/LacZ/+9 ES cells. Primitive and definitive colonies were scored after 4 and 9 days, respectively. Statistical analysis was conducted using Student t test, *P < .05, **P < .01.

Figure 5

Hematopoietic potential is highest in Eng −8/P/lacZ targeted HE cells that do not express surface ENG. (A) Schematic diagram outlining the experimental procedure. FLK1+ mesodermal cells were sorted from day 3 EBs generated from the Eng −8/P/LacZ recombinant ES cell line and cultured in liquid blast culture media. At 48 hours, CD41−/TIE2+/c-KIT+ (HE) cells were sorted into ENG+/LacZ−, ENG+/LacZ+, and ENG−/LacZ+ fractions. These fractions were either directly seeded into CFU-C assays (B) or recultured in LBM for a further 48 hours and analyzed by flow cytometry and CFU-C assays (C). (B) (i-ii) Flow cytometry shows the frequencies of CD41−/TIE2+/c-KIT+ (HE) cells in ENG+/lacZ+, ENG+/lacZ−, and ENG-lacZ+ fractions. (iii) CFU-C potential of each sorted fractions in (i). (C) (i) Flow cytometry analysis of CD41 and TIE2 expression in sorted HE cell fractions after 2 days of reculture in LBM. (ii) Bar chart shows the percentage of CD45− positive cells in sorted fraction. (iii) Bar chart shows hematopoietic colony numbers from each fraction. Primitive and definitive colonies were scored after 4 and 9 days, respectively. Statistical analysis was conducted using Student t test, **P < .01, and ***P < .001.

Figure 6

Transcriptomic analysis of HE fractions identifies genes associated with HE to hematopoietic transition. (A) RNA-sequencing profiles show Eng transcripts (top) and Runx1 transcripts (bottom) in the E+/L−, E+/L+, and E−/L+ fractions. FPKM expression values are shown to the right. (B) (i) Heat map representation of up- and downregulated genes in ENG+/LacZ− (E+/L−) HE, ENG+/LacZ+ (E+/L+) HE, and ENG−/LacZ+ (E−/L+) HE fractions in 3 independent experiments. (ii) Expression (FPKM values) levels of genes that have previously been associated with HE. The top panel shows a subset of genes that are differentially expressed between E+/L−, E+/L+, and E−/L+ fractions, and the bottom panel shows a subset of genes that are not. (C) GSEA profiles show the correspondence of genes that are differentially expressed between the E+/L−, E+/L+, and E−/L+ fractions and those that are differentially expressed in EC vs HECs (top) and HECs vs HSC gene sets. (D) TFs and CSRs that are up- and downregulated in the Eng −8/P E−/L+ HE fraction. The log fold changes (logFC) and log false discovery rates (logFDR) are listed for each gene.

Figure 7

Lrp2 is required for normal definitive hematopoiesis. (A) Venn diagram shows the overlap of genes that are UP in FLK1 mesoderm enriched for BL-CFCs and/or HE cells enriched for hemogenic potential. (B) Immunohistochemistry of E10.5 Ly6aGFP AGM shows coexpression of GFP and LRP2 in ECs and hematopoietic clusters. The insets show the same sections at low magnification. (C) Homology relationships of zebrafish lrp2a and lrp2b coding sequences with that of Lrp2 in different vertebrate species. (D) ISH for the HSC marker cmyb in zebrafish at 36 hpf. (i) Low (left) and high (right) magnification images of control zebrafish (top row), lrp2 a/b morpholinos (middle row), and lrp2a/b morpholinos coinjected with hLRP2 mRNA (bottom row) zebrafish. (ii) Low (left) and high (right) magnification images of control zebrafish (top row) and lrp2b morpholinos. (E) Confocal images of flk:zsgreen reporter embryos show an intact vasculature in both control (top) and lrp2a/b morphant (bottom) embryos. DA, dorsal aorta; NC, notochord; NT, neural tube.