Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells

Abstract

Hematopoietic stem cells (HSCs) maintain blood homeostasis and are the functional units of bone marrow transplantation. To improve the molecular understanding of HSCs and their proximal progenitors, we performed transcriptome analysis within the context of the ImmGen Consortium data set. Gene sets that define steady-state and mobilized HSCs, as well as hematopoietic stem and progenitor cells (HSPCs), were determined. Genes involved in transcriptional regulation, including a group of putative transcriptional repressors, were identified in multipotent progenitors and HSCs. Proximal promoter analyses combined with ImmGen module analysis identified candidate regulators of HSCs. Enforced expression of one predicted regulator, Hlf, in diverse HSPC subsets led to extensive self-renewal activity ex vivo. These analyses reveal unique insights into the mechanisms that control the core properties of HSPCs.

Figure 1

Population Distances Define HSPCs in Transcriptional Space (A) Population-distance analysis of microarray data presented in three principal components (PCs 1–3). Each point represents a single array. Cell types are color-coded. B, B cells; DC, dendritic cells; GN, granulocytes; MF, macrophages; Mo, monocytes; NK, NK cells; NKT, NKT cells; preT, T cell precursors; proB, B cell precursors; T, T cells; Tgd, γδ T cells. (B) Population-distance analysis of HSPC subsets including HSCs, MPPs (MPP1 and MPP2), and oligopotent progenitors (CLP, CMP, MEP, and GMP). See also Figure S1.

Figure 2

HSPCs Are Enriched for Gene Sets that Enable Transit Amplification (A) Reduced representation of hematopoiesis showing normalized and averaged values of 1,605 HSPC-enriched genes. (B) DAVID analysis showing enriched categories, with adjusted p value (Benjamini). (C) Normalized and averaged values for the indicated categories across the ImmGen data set. Cell types were grouped as indicated. (D) Normalized and averaged values for the indicated categories in ImmGen data sets. (E) Heatmap of positive and negative regulators of cell cycle in the indicated cell types. See also Figure S2.

Figure 3

Hematopoietic Multipotent Stem and Progenitor Cells Express a Family of KRAB Domain-Containing Zinc-Finger Transcriptional Repressors (A) Reduced representation of hematopoiesis showing normalized and averaged values of 433 MPP-enriched genes. (B) DAVID analysis showing enriched categories, with adjusted p value (Benjamini). (C) Graphs showing the linear values (averaged array replicates ± SEM) of the indicated genes along differentiation trajectories from HSC to MEP (green), GMP (red), PreB (purple), and PreT (blue). Biological replicates: n = 2 (MPP1, MPP2, and MEP), n = 3 (HSC, CMP, GMP, PreB, and PreT), and n = 4 (CLP). See also Figure S3.

Figure 4

Identification of HSC-Specific Transcriptional Regulators (A) Reduced representation of hematopoiesis showing normalized and averaged values of 322 HSC-enriched genes. (B) Heatmap of all HSC-enriched genes across hematopoiesis. Functional classification as determined by DAVID. (C) Expression of transcriptional regulators enriched (>4-fold) in murine HSCs presented as a ratio of mean expression in HSCs over the mean expression in all other ImmGen cell types. (D) Expression of the orthologs in (C) in human HSCs (Novershtern et al., 2011). (E) Connectivity map based on correlated expression showing the 51 identified HSC-enriched transcriptional regulators, with known regulators of HSCs highlighted in orange. TF1 = 2810021G02Rik, TF2 = 2610008E11Rik, TF3 = A630033E08Rik, and TF4 = 10305D13Rik. (F) Significantly enriched sequence motifs ± 1,000 bp of TSS in HSC-enriched genes, showing enrichment values (E values) and predicted binding factors.

Figure 5

ImmGen Module Analysis Identifies Putative Regulators of HSCs (A) Graph showing modules (identifier numbers) significantly enriched with HSC-specific genes. Number of common genes and hypergeometric p values are indicated. (B) Heatmap showing the averaged normalized expression of HSC genes in module #40. (C) Absolute expression of HSC regulators predicted by ImmGen module analysis. Log₂ values are shown. See also Figure S4.

Figure 6

MoHSPCs Express a Defined Gene Signature (A) Schematic of the Cy/G treatment used to mobilize HSPCs. Mice were injected with a single dose of cyclophosphamide (Cy; 4 mg/mouse, i.p.), followed by two daily G-CSF (G; 5 μg/mouse) injections (D2 Cy/G treatment). HSC^Slam and MPP^Slam were sorted from untreated and D2 Cy/G-treated mice for RNA extraction and microarray hybridization. (B) Multiplot analysis to identify differentially expressed genes between each comparison (Hochberg test; FDR < 10%, fold change > 1.5). (C) Heatmap of differentially expressed genes in moHSPC versus steady-state HSPC (FDR < 10%). (D) Statistically significant transcription factor binding motifs (TFBs; in the upstream regulatory region and TSS [±1,000 bp]) of differentially expressed genes. The putative TF family binding motif and the p value before the null model correction are noted. (E) Table of the known upstream regulators of genes in the data set identified by the Ingenuity knowledge base (p < 0.05, right-tailed Fisher’s exact test). See also Figures S5 and S6.

Figure 7

HLF Is a Positive Regulator of Multipotency and Self-Renewal In Vitro (A) Representative flow-cytometry plots showing CD11b and CD150 staining (left) and the time course (right) of the indicated HSPC subsets transduced with control (ZsGreen) or HLF lentiviruses. Plots (left) were generated 2 weeks posttransduction in liquid culture. Cells were pregated on lineage markers (CD3, B220, Ter119, and Gr1). Representative experiment with three biological replicates (±SEM). ^∗p < 0.05. (B) Cytospin showing representative cell types generated by HSCs transduced with control or HLF-expressing lentiviruses and maintained in liquid culture for 30 days. (C) Colony number and composition from HSCs transduced with control, HoxB4, or HLF-expressing lentiviruses and cultured for 45 days prior to plating. Three biological replicates per sample (±SEM). (D) Colony number and composition upon serial plating in methylcellulose of the indicated stem and progenitor cells transduced with control or HLF-expressing lentiviruses. Three biological replicates per sample (±SEM). See also Figure S7.