A functional screen to identify novel effectors of hematopoietic stem cell activity

Abstract

Despite tremendous progress made toward the identification of the molecular circuitry that governs cell fate in embryonic stem cells, genes controlling this process in the adult hematopoietic stem cell have proven to be more difficult to unmask. We now report the results of a novel gain-of-function screening approach, which identified a series of 18 nuclear factors that affect hematopoietic stem cell activity. Overexpression of ten of these factors resulted in an increased repopulating activity compared to unmanipulated cells. Interestingly, at least four of the 18 factors, Fos, Tcfec, Hmgb1, and Sfpi1, show non-cell-autonomous functions. The utilization of this screening method together with the creation of a database enriched for potential determinants of hematopoietic stem cell self-renewal will serve as a resource to uncover regulatory networks in these cells.

Figure 1. Experimental Design of Nuclear Factors Screening Strategy

(A) A list of candidate genes (see Table S1 for the complete list) was generated as described in the Results. The 689 nuclear factors were subsequently ranked on the basis of an algorithm that stratifies them according to properties predictive of self-renewal regulation. The highest scoring candidates (n = 139) were further selected for functional assessment with a retroviral overexpression approach. Of these, 104 were tested (see “*” in Table S1), and the remaining 35 genes were excluded for technical reasons. (B) The coding sequence of each tested candidate was subcloned into one out of three modified MSCV vectors, each containing a different reading frame (pKOF-1, -2 and -3). Respective retroviral producers were seeded in a single well of a 96-well plate and cocultured for 5 days with 1500 CD150⁺CD48⁻Lin⁻ freshly sorted bone marrow CD45.1⁺ cells. Immediately upon infection (day 0), one-eighth of each well was transplanted into two congenic recipient mice along with 2 × 10⁵ total BM cells (CD45.2⁺). A similar assay, this time with three recipient mice, was performed after an additional week of ex vivo culture (day 7), on which the screen was performed. (C) Expression of candidate proteins in retroviral-producing cells was tested by western immunoblotting and revealed with an anti-FLAG antibody. A list of predicted and observed molecular weights for most proteins tested in this screen is available in Table S2. NS, nonspecific signal; *, example of a protein that could not be detected by western blot analysis (see also Table S2). (D) Range of retroviral gene transfer efficiencies of sampled candidate genes on the basis of EGFP expression assessed at day 4 of HSC culture (only eight representatives shown; dashed line represents average on all 104 genes).

Figure 2. Identification of Positive Candidates with Hoxb4-like Activity

(A) Estimation of HSC activity during viral transduction and culture. Lines show estimation of HSC activity in recipients of day −5, day 0, or day 7 bone marrow (BM) cells transduced with Hoxb4 (red) or control vector (black). Two independent experiments were performed with purified and whole bone marrow cells for Hoxb4, and three with purified BM cells for controls. Extrapolation of HSC numbers in recipients (y axis) was based on relative reconstitution levels observed in the CRU assay performed with our starting HSC subpopulation in Figures S2B–S2C. In all experiments, each mouse received eight equivalent day ~5 HSCs (representing 100% HSC activity and evaluated by CRU assay) and 20 equivalent fresh competitor HSCs (see legend of Figure S2 for details). Cutoff for identification of Hoxb4-like candidates used in the primary screen/ validation experiments (shaded area) is set on the basis of the standard deviation/error of the mean reconstitution level observed in multiple recipients of Hoxb4-transduced HSCs. Cutoff for other less potent candidates (area between dotted lines) is used only in validation experiments and is based on statistical difference between candidates and vector control. (B) Graft-derived hematopoiesis was evaluated at 4 week intervals in recipients of cultured HSCs during the primary screen. As a set of reference values, the left panel indicates peripheral blood reconstitution levels from mice transplanted with cells from cultures initiated with a positive regulator of self-renewal (Hoxb4) in relation to values observed with control vectors (mean of pKOF-1, -2 and -3), all after 7 days of culture. Mean reconstitution level values for each of the 104 tested candidates (at day 7) are compiled and presented in the middle panel, with the established cutoff level for a gain-of-function readout. Candidates clustering above the cutoff level for identification of Hoxb4-like genes (shaded area in Figure 2A), corresponding to 30% CD45.1⁺ donor-derived cells in the primary screen, were selected for the validation experiments (upper-right panel), while those below were disregarded (lower-right panel). One candidate (Hes1) was eliminated on the basis of the marked reduction in repopulation noted between early and late time points (upper line in lower-right panel). Values are presented as mean ±SEM of independent experiments (n) for the left panel (n = 2 for Hoxb4 and n = 3 for control vector; mean of three mice per experiment) and as mean ±SD for the middle and right panels (n = 3 mice for each candidate cDNA). Note that several mice were eliminated at 12 or 16 weeks after transplantation because they did not meet our criteria for hit selection (see also Table S3, ninth and tenth columns). (C) Validation experiments confirming ten Hoxb4-like genes and eight other less potent candidates. p values were established at the 16 weeks after transplantation time point. Values are shown as mean ±SEM. The number of independent experiments (n) per candidate gene equals four, except for control vectors (n = 8); Sox4, Zfp472, Xbp1, and Hnrpdl (n = 5); and Hoxb4, Cnbp, Ski, and Prdm16 (n = 3). For each experiment, a mean of three mice per gene was evaluated. cand., candidates.

Figure 3. HSC Activity Is Enhanced by Overexpression of the Newly Identified Hoxb4-like Genes

(A) Percentages of donor-derived blood cells at 16 weeks after transplantation in primary mice recipients of day 7 culture cells (experiments in Figure 2C) for the ten identified hits. Bars at the far left show values for freshly purified CD150⁺CD48⁻Lin⁻ cells, day 0 control cells (empty vector), and day 7 control and Hoxb4-transduced cells, as references. The shaded area represents mean reconstitution levels observed in mice transplanted with day 0 control-transduced HSCs, ±1 SEM. Reconstitution values falling within this range are considered to reflect HSC activity derived from an injected dose of HSCs equivalent to culture input numbers, i.e., 8 competitive repopulation units (CRUs) (see Figure S2C). d-5, day −5; d0, day 0; d7, day 7. Note that two different cDNA were tested for Trim27 (see Figure S5). (B) The mean activity of stem cells (MAS) was calculated from the data obtained in (A). As previously established, the MAS is equivalent to repopulation units (RUs) divided by CRUs (Ema and Nakauchi, 2000), where RU represents the donor-derived reconstitution level divided by the competitor-derived reconstitution level. MAS index was normalized to 1 for freshly sorted cells and excluded the gene transfer efficiency in its estimation for the candidate genes. In cases where gene transfer is low, this could lead to underestimated values. Grafts overexpressing genes shown in red and marked by an asterisk give rise to a MAS significantly higher than day 0 control grafts (p ≤0.05). Note that values are presented as the MAS relative to that of fresh cells (d −5), which was set at a value of 1. d-5, day −5; d0, day 0; d7, day 7. (C) p values derived from MAS values presented in (B) comparing data obtained from control vectors (day 0 or 7) and validated genes. Day 0 p values framed in red (penultimate column) mirror the order and color code of candidate genes presented in (B) and are ≤0.05. In comparison, day 7 p values are listed in the adjacent column.; n, number of independent experiments; d0, day 0; d7, day 7.

Figure 4. In Vitro Differentiation, Survival, and Proliferation Profiles of Cultured Cells

(A) Morphological analysis of cytological preparations of the starting HSC fraction overexpressing most of identified primary hits at day 7 of culture. Proportions of immature (blasts: black arrow in middle-left insert) versus terminally differentiated cells (neutrophils, monocytes and masts cells: black arrows in upper-left insert) for respective cultures are depicted in the right panel. A field comprising 100 cells was examined per independent experiment (n), and values are presented as mean; n = 3, except for vector (n = 6) and Hoxb4, Ski, Tcfec, Sfpi1, and Hmgb1 (n = 1). The shaded area represents the mean of vector plus two standard deviations. Note that a vast majority of the less significant hits described in Figure 2C are included in this study (i.e., Tcfec, Hmgb1, Cnbp, Xbp1, Hnrpdl, and Hdac1). BM, bone marrow. (B) Annexin V and PI stains were used to determine the fraction of cell death in cultures initiated with our validated hits and the less potent gene candidates (Tcfec and Hmgb1) as well as empty vector, Hoxb4, or NA10HD, serving as controls. Assessment was performed at the day 4 time point of culture. Values are presented as mean ±SD of two independent experiments (n), where n represents the analysis of 30,000 cells. * p ≤ 0.05. (C) Cell proliferation was assessed by flow cytometry-based cell counts (y axis) at day 4 of cultures. Analyses were performed for the same gene candidates as in (B). Values are presented as mean ±SD of two independent experiments. * p ≤ 0.05.

Figure 5. In Vivo Differentiation Potential of HSCs Overexpressing Validated Hits

(A) In vivo differentiation potential along the lymphomyeloid lineages was assessed in long-term recipients (20 weeks after transplantation) of HSCs transduced with Trim27, used as an example. Immunophenotypic analysis by flow cytometry was performed with specific antibodies against B, T, and myeloid cell surface markers (B220, CD3, and CD11b, respectively) on the CD45.1⁺ population of cells derived from the peripheral blood, bone marrow (BM), and thymus of these mice (and on CD45.1⁺/GFP⁺ cells in Figure S3A). (B) Compilation of B-/T-lymphoid and myeloid cell percentages within the CD45.1⁺ population (left panels) and of CD45.1⁺ cell proportions in the B-lymphoid, T-lymphoid, or myeloid populations (right panels) of blood, thymus, and BM tissues, as gathered in (A), for most of the primary hits. Values are presented as mean ±SD. Mouse identification numbers are presented between brackets. Dashed lines indicate values obtained with control mice (vector) for the different hematopoietic tissues. Note that multilineage reconstitution was observed in all of mice analyzed except for those transplanted with cells transduced with Ski, which showed a block in B-lymphoid differentiation. The proportion of CD45.1⁺ cells within the B-lymphoid or myeloid populations in the thymus was not calculated in the right panels because these populations represent less than 5% of total cells in this tissue. Since weak donor-derived reconstitution levels were observed in mice transplanted with control vector cells at day 7 of culture (i.e., 4% in Figure 3A), we used mice transplanted with control vector cells at day 0 of culture in this case. Values pertaining to less statistically significant hits are also presented (Tcfec, Zfp472, Hmgb1, Cnbp, Xbp1, Hnrpdl, and Hdac1). (C) Proviral integration pattern studies by Southern blot analysis performed on genomic DNA extracted from bone marrow (left panel) and thymus (right panel) of three long-term recipients of Trim27-overexpressing HSCs. Each lane represents a specific mouse (ID number below). For a given animal, identical integrations are found in both tissues, indicating a common precursor cell origin. Identical clones are also observed in two distinct recipients, retrospective molecular evidence for a self-renewal division in vitro. Multipotentiality (BM and thymus) analyses in reconstituted tissues harvested from primary recipients of culture cells overexpressing the various validated hits are shown in Figure S3B. (D) Quantitative RT-PCR analysis of mRNA expression levels of nine of the ten newly identified Hoxb4-like gene transcripts. For technical reasons, Prdm16 was excluded from the analysis. RNA was extracted from distinct bone marrow cell fractions isolated from long-term, highly reconstituted recipients of day 7 culture cells (S, CD150⁺CD48⁻Lin⁻; P, CD150⁺CD48⁺Lin⁻; B, B220⁺; M, Mac⁺). Average ΔCt values (representative of expression levels) were determined with β-actin serving as an endogenous control to normalize levels of target gene expression. Relative fold differences were determined using control cells as a reference calibrator for each candidate gene. Reactions were done in triplicate; black bars represent mean endogenous expression levels ±SEM of three independent wild-type mice (Ctrl); red bars represent mean overexpression levels ±SEM of two transplanted mice (Trx) from two independent experiments. The identification numbers of mice used in this assay are presented between brackets. Note that control black bars on each panel are set at a relative fold difference value of 1.

Figure 6. Clonal Analysis to Track HSC Self-Renewal Divisions

Southern blot analyses of genomic DNA extracted from the bone marrow (BM) of selected long-term recipients (20 weeks after transplantation) of day 7 culture cells. Each blot was hybridized with a GFP-specific probe and systematically exposed for the same period of time. Each well was equally loaded, taking into consideration donor-derived peripheral blood reconstitution level of recipients as measured 16 weeks after transplantation (i.e., 17%–83% CD45.1⁺ cells). Top and bottom panels show gene sets for which proviral DNA was either detected or absent in the majority of recipients analyzed, respectively. For most bottom panels, the brightness and contrast was enhanced using Photoshop to further verify the absence of integrated proviral DNA, and a β-actin probe was also used to confirm the presence of genomic DNA. Clones that self-renewed during the 7 day culture, prior to transplantation, are labeled “a” to “i” and identified in more than one recipient. “X” indicates that GFP expression was not detectable for these constructs/clones. Note that panel 5, representing the Trim27 gene, is also included in Figure 5C (left panel).