scholarly journals Revisiting the erythroid-myeloid lineage decision – a data-driven dynamical model analysis

2017 ◽  
Author(s):  
Jose Teles ◽  
Victor Olariu ◽  
Carsten Peterson

AbstractIt is widely conjectured that the mutually antagonizing pair of transcription factors GATA1 and PU.1, deter-mines the choice between the erythroid and myeloid lineages in hematopoiesis. In theoretical approaches, this appears natural with a bistable switch driving the decision. Recent extensive binding and gene expression experiments with some focus on the triad GATA1, GATA2 and PU.1 indicate that GATA2 may be more involved in this lineage decision than previously anticipated. Here, we analyze these experimental data by modeling regulatory sub-networks with deterministic rate equations. Using network dynamical parameters determined by the data, we deduce from increasing the self-interaction bindings in silico among the triad genes that GATA2 and PU.1 exhibit non-linear behavior with one unstable and one stable state. This is in contrast to GATA1, which shows smoother behavior. We extend the network to include the downstream regulators FOG1 and CEBPA, and extract the nature of the corresponding regulatory interactions, excitatory or suppressing, between this pair and the triad by fitting to experimental gene expression time series. Based on this extended network, we simulate and explore different knockout scenarios, providing insight into the role of these regulators in the process of lineage specification, as well as predictions for future experimental validation. We address the mechanism of GATA switching as a mechanism of lineage differentiation by investigating the dynamics of FOG1 regulation by GATA2 and GATA1. Overall, this analysis strongly suggests that within this network, GATA2 is the key driver of erythroid lineage specification through its repression of PU.1, whereas GATA1 appears to be more relevant for the downstream differentiation events.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4219-4219
Author(s):  
Tariq Enver ◽  
Sui Huang

Abstract Adopting a lineage from amongst two or more options is a fundamental developmental decision in multicellular organisms. Transcription factors and their binding sites have been studied as candidate instigators of lineage. However, how the logic of gene regulatory networks translates into, for example, a binary lineage decision remains unanswered. We use mathematical modeling to understand a simple lineage decision between two hypothetical lineages A and B governed by a gene circuit containing positive auto-regulation and cross-inhibition between two regulatory factors, a and b (Fig. 1a). Experimental evidence for such a circuit is provided by the regulatory interactions of GATA-1 and PU.1 in erythroid vs. myelomonocytic lineage specification. A set of non linear ordinary differential equations describing this circuit predicts a robust generic dynamics represented in a ‘potential landscape’ (Fig. 1b, and as schematic cross section, Fig. 1c). Strikingly, the model generates three stable states or ‘attractors’ which we infer to correspond to the committed A or B lineage cells and the uncommitted bipotent A/B progenitors, which are characterized by low-level co-expression of both a and b lineage-affiliated regulators. Thus, this bipotent cell fate attractor provides, for the first time, a mathematical rationale for experimental observations of co-expression of lineage-specific regulators in uncommitted cells, a phenomenon termed ‘multi-lineage priming’. The model predicts a particular trajectory in the a/b space for bipotent cells undergoing differentiation. Specifically, lineage determination involves moving towards a region in a/b space that becomes unstable (Fig. 1c bottom) so that the two lineage-committed territories in the a/b-space directly meet (asterisk, Fig. 1b). The precipitous nature of this boundary region is predicted to afford the initiation and consolidation of a lineage decision in response to relatively modest changes in cell intrinsic or extrinsic cues. We tested these predictions through examination of global gene expression profiles of uncommitted FDCP-mix cells undergoing differentiation to erythroid (E) versus myelomonocytic (M) cell fates. Consistent with the model, differentiation down these two paths follows almost identical high-dimensional ‘trajectories’ in gene expression state space during the first 24–48h towards a characteristic, destabilized state, and only hereafter do the trajectories diverge into the attractors that represent the committed cell fates. Specifically, differentiation into myelomonocytic cells was associated with the counterintuitive transient suppression of myeloid specific PU.1, precisely as predicted by the model (Fig. 1b). In conclusion, although the mathematical model describes a small network module rather than the genome-wide gene regulatory, it captures many of the essential features of a multilineage cell differentiation hierarchy and successfully predicts the genome-scale behaviour of cells undergoing differentiation and lineage specification. Figure Figure


Blood ◽  
2012 ◽  
Vol 119 (17) ◽  
pp. 4034-4046 ◽  
Author(s):  
Giuseppe Zardo ◽  
Alberto Ciolfi ◽  
Laura Vian ◽  
Linda M. Starnes ◽  
Monia Billi ◽  
...  

Abstract Epigenetic modifications regulate developmental genes involved in stem cell identity and lineage choice. NFI-A is a posttranscriptional microRNA-223 (miR-223) target directing human hematopoietic progenitor lineage decision: NFI-A induction or silencing boosts erythropoiesis or granulopoiesis, respectively. Here we show that NFI-A promoter silencing, which allows granulopoiesis, is guaranteed by epigenetic events, including the resolution of opposing chromatin “bivalent domains,” hypermethylation, recruitment of polycomb (PcG)–RNAi complexes, and miR-223 promoter targeting activity. During granulopoiesis, miR-223 localizes inside the nucleus and targets the NFI-A promoter region containing PcGs binding sites and miR-223 complementary DNA sequences, evolutionarily conserved in mammalians. Remarkably, both the integrity of the PcGs-RNAi complex and DNA sequences matching the seed region of miR-223 are required to induce NFI-A transcriptional silencing. Moreover, ectopic miR-223 expression in human myeloid progenitors causes heterochromatic repression of NFI-A gene and channels granulopoiesis, whereas its stable knockdown produces the opposite effects. Our findings indicate that, besides the regulation of translation of mRNA targets, endogenous miRs can affect gene expression at the transcriptional level, functioning in a critical interface between chromatin remodeling complexes and the genome to direct fate lineage determination of hematopoietic progenitors.


2021 ◽  
Author(s):  
Jing Nie ◽  
Yoshitomo Ueda ◽  
Alexander Solivais ◽  
Eri Hashino

Abstract Mutations in the chromatin remodeling enzyme CHD7 cause CHARGE syndrome, which affects multiple organs including the inner ear. We investigated how CHD7 mutations affect otic development in human inner ear organoids. We found loss of CHD7 or its chromatin remodeling activity leads to complete absence of hair cells and supporting cells, which can be explained by dysregulation of key otic development-associated genes in mutant otic progenitors. Further analysis of the mutant otic progenitors suggested that CHD7 can regulate otic genes through a chromatin remodeling-independent mechanism. Results from transcriptome profiling of hair cells revealed disruption of deafness gene expression as a potential underlying mechanism of CHARGE-associated sensorineural hearing loss. Notably, co-differentiating CHD7 knockout and wild-type cells in chimeric organoids partially rescued mutant phenotypes by restoring otherwise severely dysregulated otic genes. Taken together, our results suggest that CHD7 plays a critical role in regulating human otic lineage differentiation and deafness gene expression.


Blood ◽  
1992 ◽  
Vol 79 (10) ◽  
pp. 2733-2740 ◽  
Author(s):  
K Yoshimura ◽  
RG Crystal

Abstract Human neutrophil elastase (NE), a 29-Kd potent serine protease stored in azurophilic granules of mature neutrophils, is coded for by the NE gene, a single copy gene with 5 exons spanning a 6-kb segment of chromosome 11 at q14. With the knowledge that the NE gene expression is limited to early myeloid cell differentiation, mechanisms modulating expression of the NE gene were evaluated in the HL-60 promyelocytic leukemia cell line, a model of early bone marrow precursor cells. Consistent with the presence of NE messenger RNA (mRNA) transcripts in undifferentiated HL-60 cells, nuclear transcription run-on analyses showed that HL-60 cells actively transcribed the NE gene. However, the transcription rate of the NE gene was relatively low, only 40% of the myeloperoxidase gene, a gene expressed in parallel with NE. When induced toward the mononuclear phagocytic lineage with phorbol 12- myristate 13-acetate (PMA), HL-60 cells exhibited marked suppression of NE gene transcription, declining to 17% of the resting rate within 2 days. Induction toward mononuclear phagocytic lineage differentiation caused no change in NE mRNA transcript half-life (T1/2), but mRNA levels decreased markedly over time, with levels undetectable 1.5 days after PMA stimulation. In contrast, when induced toward the myelocytic lineage with dimethyl sulfoxide, the rate of NE gene transcription increased 1.9-fold within 5 days. Interestingly, the mRNA transcript levels increased 2.5-fold by 5 days despite the fact that induction toward myelocytic lineage differentiation was accompanied by a marked reduction of NE mRNA transcript T1/2. Together, these observations suggest that the NE gene expression during bone marrow differentiation is modulated mainly at the transcriptional level, with some posttranscriptional modulation contributing, particularly during myelocytic lineage differentiation.


2019 ◽  
Vol 5 (12) ◽  
pp. eaax8898 ◽  
Author(s):  
Roshane Francis ◽  
Haiyang Guo ◽  
Catherine Streutker ◽  
Musaddeque Ahmed ◽  
Theodora Yung ◽  
...  

Transcription factors (TFs) are spatially and temporally regulated during gut organ specification. Although accumulating evidence shows aberrant reactivation of developmental programs in cancer, little is known about how TFs drive lineage specification in development and cancer. We first defined gastrointestinal tissue–specific chromatin accessibility and gene expression during development, identifying the dynamic epigenetic regulation of SOX family of TFs. We revealed that Sox2 is not only essential for gastric specification, by maintaining chromatin accessibility at forestomach lineage loci, but also sufficient to promote forestomach/esophageal transformation upon Cdx2 deletion. By comparing our gastrointestinal lineage-specific transcriptome to human gastrointestinal cancer data, we found that stomach and intestinal lineage-specific programs are reactivated in Sox2high/Sox9high and Cdx2high cancers, respectively. By analyzing mice deleted for both Sox2 and Sox9, we revealed their potentially redundant roles in both gastric development and cancer, highlighting the importance of developmental lineage programs reactivated by gastrointestinal TFs in cancer.


2001 ◽  
Vol 276 (27) ◽  
pp. 25279-25286 ◽  
Author(s):  
Haiyan Wang ◽  
Pierre Maechler ◽  
Beate Ritz-Laser ◽  
Kerstin A. Hagenfeldt ◽  
Hisamitsu Ishihara ◽  
...  

2017 ◽  
Vol 97 (1) ◽  
pp. 5-17 ◽  
Author(s):  
Qingqing Wei ◽  
Liang Zhong ◽  
Shaopeng Zhang ◽  
Haiyuan Mu ◽  
Jinzhu Xiang ◽  
...  

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4408-4408
Author(s):  
Hirokazu Hidaka ◽  
Hiroshi Yagasaki ◽  
Yoshiyuki Takahashi ◽  
Keizo Horibe ◽  
Kenji Kadomatsu ◽  
...  

Abstract Midkine (MK) is a heparin-binding growth factor and overexpressed in a number of solid tumors, contributing to their growth. Its expression in acute leukemia, however, has not been clarified. We examined relative levels of MK gene expression defined in K562 cells as 1.00 using real-time quantitative polymerase chain reaction (PCR) in 94 children with acute leukemia and compared with those in normal bone marrow (BM; n=18) and peripheral blood (PB; n=10). Median age was 6 years (range, 0–15 years). Diagnosis included B-precursor ALL (n=41), T-ALL (n=14), B-ALL (n=4), Ph1-ALL (n=6), infant ALL (n=5) and AML (n=24). 8 normal BM samples were separated into CD34+ and CD34− fractions. MK gene expression was detected in normal control samples. Median MK gene expression level was significantly lower in normal PB (2.9×10e-3) than in normal BM (8.0×10e-3) (p<0.01). Expression of MK gene was higher in normal CD34+ BM cells (0.78×10e-3) than in normal unfractionated BM cells (p<0.001). Overexpression of MK was difined as expression at least twice as high as the maximal MK gene expression in normal PB and BM. In 30 of the 41 patients with B-precursor ALL (73.2%), MK gene is overexpressed. We classified B-cell lineage ALL into 3 stage: DR+,CD19+,CD10+,CD20−,slg−, DR+,CD19+,CD10+,CD20+,slg−, DR+,CD19+,CD20+,slg+. MK gene expression decreased with B-cell lineage differentiation of leulkemic blast. It was also overexpressed in more than half of the patients with FAB M1 and M2 types of AML. In contrast, overexpression of MK gene was observed only in one of the 13 patients with T-ALL and none of the 6 patients with AML-M5. Supporting the possible involvement of MK in carcinogenesis, overexpression of MK may be not only merely assoziated with total development but also related to leukemic transformation of hematopoietic progenitors. Quantification of MK gene by real-time PCR is relatively simple and widely applicable in patients with acute leukemia. This technique offers particular promise as a prognostic marker and a marker for minimal residual disease in children with B-precursor ALL.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4597-4597
Author(s):  
Elena Marinelli Busilacchi ◽  
Jacopo Olivieri ◽  
Nadia Viola ◽  
Antonella Poloni ◽  
Giorgia Mancini ◽  
...  

Abstract INTRODUCTION Dermal fibrosis and sclerosis are pathologic features shared by Scleroderma-like chronic graft-versus-host disease (Scl-cGVHD) and Systemic Scleroderma (SSc). Moreover, in both diseases stimulating anti-PDGF-R antibodies were found, leading to abnormal collagen production by fibroblasts, eventually contributing to organ damage. Targeted therapy with tyrosine kinase inhibitors (TKI) like Imatinib and Nilotinib demonstrated clinical efficacy in Scl-cGVHD; however, the molecular basis underpinning the clinical effects are not fully elucidated. We investigated here a potential terapeutical target of the dermal cGVHD pathophysiology: the cellular and molecular features of pathological skin fibroblasts (GVHD-Fbs) and the efficacy of Nilotinib on fibrosis modulation. MATERIALS AND METHODS Fibroblast cultures (GVHD-Fbs) were obtained from skin biopsies of affected skin from 6 patients with active cGVHD, control fibroblasts are Human Dermal Fibroblasts adult (n-FBS). Fibroblasts were characterized by flow cytometry (FACS CANTO II) for the detection of molecules: CD10, CD14, CD29, CD34, CD44, CD45, CD73, CD90, CD105, CD106, CD117, CD146. In order to evaluate the adipogenic, osteogenic or chondrogenic differentiation cGVHD-Fbs and n-Fbs (n = 3) were cultured in differentiation medium (respectively NH AdipoDiff, NH OsteoDiff, NH ChondroDiff) after four passages. Intracellular lipid droplets indicated adipogenic lineage differentiation. The differentiation potential in the osteogenic lineage was evaluated by calcium accumulation, as assessed by Alizarin Red. The pellet obtained from chondrogenic lineage differentiation was embedded in paraffin, cut in the microtome and the sections placed on a glass slide were stained with Alcian Blue [Junker JP, Cells Tissues Organs, 2010]. For incubation with Nilotinib (Santa Cruz Biotechnology) the 10 mM stock solution was diluted to the final concentration in DMEM supplemented with 0,2% FBS (starvation), added to cell cultures at a concentration of 1 μM or 2 μM for 48h, which covered the mean plasma levels in cGVHD patients after standard doses. In subsets of experiments, after starvation, fibroblasts were stimulated with recombinant TGFβ at 10 ng/ml (GIBCO, Invitrogen). After incubation, total RNA was isolated and reverse transcribed. Gene expression was quantified by real-time PCR using the Sybr Green Mix for qPCR. Specific primer pairs for COL1α1 and COL1α2 were designed with the Primer 3 software. The transcript levels were normalized for the expression of GAPDH constitutive gene. Differences were calculated with the threshold cycle (Ct) and the comparative Ct method for relative quantification. RESULTS GVHD-Fbs are morphologically and phenotypically similar to normal fibroblasts (n-FBS). GVHD-FBS did not show a different immunophenotype from n-Fbs, both in early and late culture passages. Also, no differences were noted between GVHD-Fbs and n-FBS in terms of multilineage differentiation capacity towards the adipogenic, osteogenic and chondrogenic lineage. Gene expression of COL1α1 and COL1α2 in GVHD-Fbs was respectively 4 and 1,6 times higher compared to n-FBS (p = 0.02). However, the increased collagen expression was exclusive of early-passage GVHD-Fbs; in late-passage (>4) GVHD-Fbs, collagen mRNA levels were similar to n-FBS (p=0.6 for COL1α1; p=0.4 for COL1α2). As expected, TGFβ boosted collagen expression in n-FBS, but it did not increase COL1α1 and COL1α2 mRNA levels in GVHD-Fbs. Therapeutic doses of Nilotinib (1μM) were able to reduce expression of COL1α1 and COL1α2 mRNA by 86,5% and 49%, respectively (p <0.01). CONCLUSIONS Early-passage GVHD-Fbs are a valuable cellular model to study the molecular mechanisms of cGVHD fibrosis in vitro, as they show increased collagen production, which is a strong hallmark of fibrosis. The failure to increase collagen expression in GVHD-Fbs upon TGFβ stimulation indirectly supports a TGFβ-dependent mechanism underpinning the fibrogenesis. Finally Nilotinib inhibits in vitro collagen expression in GVHD-Fbs confirming that the activity of TKI in Scl-cGVHD is mediated, at least in part, by direct antifibrotic effects on the fibroblasts. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.


Development ◽  
2015 ◽  
Vol 142 (15) ◽  
pp. 2586-2597 ◽  
Author(s):  
Aoife O'Shaughnessy-Kirwan ◽  
Jason Signolet ◽  
Ita Costello ◽  
Sarah Gharbi ◽  
Brian Hendrich

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