The Transcriptional Program of Terminal Granulocytic Differentiation in Man.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1469-1469
Author(s):  
Niels Borregaard ◽  
Lars C. Jacobsen ◽  
Rehanah Borup ◽  
Thomas Rasmussen ◽  
Malene D. Bjerregaard ◽  
...  
Keyword(s):  
Host Defense ◽  
Target Genes ◽  
Major Gene ◽  
Expression Patterns ◽  
Correlation Coefficients ◽  
Quantitative Measure ◽  
Effector Proteins ◽  
Transcriptional Program ◽  
Granulocytic Differentiation

Abstract To characterize the transcriptional program that governs terminal granulocytic differentiation in vivo, we performed comprehensive microarray analyses of human bone marrow (BM) populations highly enriched in promyelocytes (PMs), myelocytes/metamyelocytes (MYs), and neutrophils (bm-PMNs). These analyses identified 11,310 genes involved in differentiation, of which 6,700 were differentially regulated including granule proteins and surface receptors previously not identified in neutrophils. Functional clustering demonstrated that differentially expressed genes were assigened to all of the major gene categories including apoptosis, cell cycle, chaperones, enzymes, immunity proteins, kinases, motor proteins, signal transducers, structural proteins, and transcription factors. In an attempt to define the developmental distance between PM, MY, and bm-PMN populations, we assessed the Pearsons correlation coefficient (γ) by correlating the transcriptomes (=all 44.760 probe sets, Affymetrix) of BM populations. The correlation coefficients among replicates of BM populations were in the range of 0.97–0.99. On the other hand the correlation coefficients between BM populations were 0.81 (γPM - MY), 0.79 (γMY - bm-PMN), and 0.52 (γPM - bm-PMN), and thus, provided a useful quantitative measure reflecting the hierarchical relationship between the three BM populations. Additional correlation of bm-PMN and peripheral blood-PMN transcriptomes revealed a high similarity of both populations (γbm-PMN - pb-PMN=0.95) indicating a termination of granulocytic differentiation in the BM microenvironment during steady state hematopoesis. Differentiation of PMs towards MYs was accompanied by a marked decline of proliferative and general cellular activity as defined by downregulation of E2F target genes, cyclin dependent kinases 2/4/6, and various metabolic, proteasomal, and mitochondrial genes. Expression patterns of apoptosis genes indicated death control by the p53-pathway in PMs and by death receptor pathways in bm-PMNs. Effector proteins critical for host defense were expressed successively throughout granulocytic differentiation, whereas receptors and receptor ligands essential for the activation of the host defense program were terminally upregulated in bm-PMNs. The upregulation of ligand-receptor pairs, which are defined inducers as well as target genes of NF-kB, suggests a constitutive activation of NF-kB in bm-PMNs by autocrine loops. Overall, these results define a granulocytic differentiation model governed by a highly coordinated fail-safe program, which promotes completion of differentiation before cells gain responsiveness towards activating stimuli that accompany infections.

The transcriptional program of terminal granulocytic differentiation

Blood ◽  
2005 ◽  
Vol 105 (4) ◽  
pp. 1785-1796 ◽  
Author(s):  
Kim Theilgaard-Mönch ◽  
Lars Christian Jacobsen ◽  
Rehannah Borup ◽  
Thomas Rasmussen ◽  
Malene Digmann Bjerregaard ◽  
...  
Keyword(s):  
Host Defense ◽  
Target Genes ◽  
Expression Patterns ◽  
Death Receptor ◽  
Nuclear Factor Κb ◽  
Effector Proteins ◽  
Transcriptional Program ◽  
Granulocytic Differentiation ◽  
Surface Receptors

AbstractTo characterize the transcriptional program that governs terminal granulocytic differentiation in vivo, we performed comprehensive microarray analyses of human bone marrow populations highly enriched in promyelocytes (PMs), myelocytes/metamyelocytes (MYs), and neutrophils (bm-PMNs). These analyses identified 11 310 genes involved in differentiation, of which 6700 were differentially regulated, including previously unidentified effector proteins and surface receptors of neutrophils. Differentiation of PMs toward MYs was accompanied by a marked decline of proliferative and general cellular activity as defined by down-regulation of E2 promoter binding factor (E2F) target genes; cyclin dependent kinases 2, 4, and 6; and various metabolic, proteasomal, and mitochondrial genes. Expression patterns of apoptosis genes indicated death control by the p53 pathway in PMs and by death receptor pathways in bm-PMNs. Effector proteins critical for host defense were expressed successively throughout granulocytic differentiation, whereas receptors and receptor ligands essential for the activation of the host defense program were terminally up-regulated in bm-PMNs. The up-regulation of ligand-receptor pairs, which are defined inducers as well as target genes of nuclear factor-κB (NF-κB), suggests a constitutive activation of NF-κB in bm-PMNs by autocrine loops. Overall, these results define a granulocytic differentiation model governed by a highly coordinated fail-safe program, which promotes completion of differentiation before cells gain responsiveness toward activating stimuli that accompany infections. (Blood. 2005; 105:1785-1796)

scholarly journals Circular RNA circSDHC serves as a sponge for miR-127-3p to promote the proliferation and metastasis of renal cell carcinoma via the CDKN3/E2F1 axis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Junjie Cen ◽  
Yanping Liang ◽  
Yong Huang ◽  
Yihui Pan ◽  
Guannan Shu ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Target Genes ◽  
Expression Patterns ◽  
Luciferase Reporter ◽  
Circular Rnas ◽  
Proliferation And Metastasis

Abstract Background There is increasing evidence that circular RNAs (circRNAs) have significant regulatory roles in cancer development and progression; however, the expression patterns and biological functions of circRNAs in renal cell carcinoma (RCC) remain largely elusive. Method Bioinformatics methods were applied to screen for circRNAs differentially expressed in RCC. Analysis of online circRNAs microarray datasets and our own patient cohort indicated that circSDHC (hsa_circ_0015004) had a potential oncogenic role in RCC. Subsequently, circSDHC expression was measured in RCC tissues and cell lines by qPCR assay, and the prognostic value of circSDHC evaluated. Further, a series of functional in vitro and in vivo experiments were conducted to assess the effects of circSDHC on RCC proliferation and metastasis. RNA pull-down assay, luciferase reporter and fluorescent in situ hybridization assays were used to confirm the interactions between circSDHC, miR-127-3p and its target genes. Results Clinically, high circSDHC expression was correlated with advanced TNM stage and poor survival in patients with RCC. Further, circSDHC promoted tumor cell proliferation and invasion, both in vivo and in vitro. Analysis of the mechanism underlying the effects of circSDHC in RCC demonstrated that it binds competitively to miR-127-3p and prevents its suppression of a downstream gene, CDKN3, and the E2F1 pathway, thereby leading to RCC malignant progression. Furthermore, knockdown of circSDHC caused decreased CDKN3 expression and E2F1 pathway inhibition, which could be rescued by treatment with an miR-127-3p inhibitor. Conclusion Our data indicates, for the first time, an essential role for the circSDHC/miR-127-3p/CDKN3/E2F1 axis in RCC progression. Thus, circSDHC has potential to be a new therapeutic target in patients with RCC.

Engineering of clinical glioma treatment: Prediction of pro-invasive molecular events in treated gliomas

2008 ◽  
Vol 222 (7) ◽  
pp. 1149-1160 ◽  
Author(s):  
D Trog ◽  
K Yeghiazaryan ◽  
H H Schild ◽  
O Golubnitschaja
Keyword(s):  
Malignant Glioma ◽  
Target Genes ◽  
Expression Patterns ◽  
Malignant Gliomas ◽  
Treatment Algorithm ◽  
Poor Response ◽  
Response To Therapy ◽  
Molecular Events ◽  
Therapeutic Algorithms

The diffusely infiltrative nature of malignant gliomas is the main obstacle to successful treatment approaches. Advanced simulation models of the in vivo response to therapy conditions are expected to improve malignant glioma treatment substantially. In parallel experiments, human malignant glioma cells underwent either radiation or chemotherapy treatment (chemotreatment) with temozolomide alone, or combined chemoradiation. Cells were treated according to diverse, clinically relevant, therapeutic algorithms. Quantitative ‘real-time’ polymerase chain reaction (PCR) measurements were performed for target genes, namely vascular endothelial growth factor, p53, and cyclooxygenase-2, which allow a comparative evaluation of pro-invasive molecular events in treated gliomas. The proof-of-principle study simulated variable intratumoural regional conditions. Pro-invasive molecular patterns were strongly dependent on the treatment algorithm, cellular density, and drug delivery. The highest pro-invasive potential was demonstrated for simulated peripheral regions under continued chemoradiation. This result strongly supports the clinical observations of increased aggressiveness and relatively poor response to second-line therapies in post-operatively chemoradiation-treated malignant gliomas at the time of relapse. Individualized and potentially the most effective treatment algorithms can be designed using established gene expression patterns applied on primary cell cultures obtained from individual patients. Individual drug toxicity and response to anti-cancer therapy can be predicted.

scholarly journals MiRNA expression profiling and zeatin dynamic changes in a new model system of in vivo indirect regeneration of tomato

2020 ◽  
Author(s):  
Huiying Cao ◽  
Xinyue Zhang ◽  
Yanye Ruan ◽  
Lijun Zhang ◽  
Zhenhai Cui ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Target Genes ◽  
Higher Plants ◽  
Callus Formation ◽  
Expression Patterns ◽  
Adventitious Shoot ◽  
Model System ◽  
Indirect Regeneration ◽  
Mirna Expression Profiling

AbstractCallus formation and adventitious shoot differentiation could be observed on the cut surface of completely decapitated tomato plants. We propose that this process can be used as a model system to investigate the mechanisms that regulate indirect regeneration of higher plants without the addition of exogenous hormones. This study analyzed the patterns of trans-zeatin and miRNA expression during in vivo regeneration of tomato. Analysis of trans-zeatin revealed that the hormone cytokinin played an important role in in vivo regeneration of tomato. Among 183 miRNAs and 1168 predicted target genes sequences identified, 93 miRNAs and 505 potential targets were selected based on differential expression levels for further characterization. Expression patterns of six miRNAs, including sly-miR166, sly-miR167, sly-miR396, sly-miR397, novel 156, and novel 128, were further validated by qRT-PCR. We speculate that sly-miR156, sly-miR160, sly-miR166, and sly-miR397 play major roles in callus formation of tomato during in vivo regeneration by regulating cytokinin, IAA, and laccase levels. Overall, our microRNA sequence and target analyses of callus formation during in vivo regeneration of tomato provide novel insights into the regulation of regeneration in higher plants.

scholarly journals P11.54 Identification of PDGFRA and MYC(N) as somatic driver genes in Glioblastoma

2019 ◽  
Vol 21 (Supplement_3) ◽  
pp. iii55-iii56
Author(s):  
A D Berezovsky ◽  
A Transou ◽  
S Irtenkauf ◽  
L Poisson ◽  
K Hank Wu ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Cell Lines ◽  
Gene Amplification ◽  
Median Survival ◽  
Tyrosine Kinases ◽  
Target Genes ◽  
Expression Patterns ◽  
Mycn Amplification ◽  
Driver Genes

Abstract BACKGROUND Somatic oncogene amplification happens frequently in glioblastoma (GBM). The second most frequently amplified gene encoding receptor tyrosine kinases in GBMs is platelet derived growth factor alpha (PDGFRA) (15%). In contrast, MYC and MYCN amplification occurs in 1.6% and 2.9%, respectively. Our goal was to characterize the role of PDGFRɑ and Myc in GBM. MATERIAL AND METHODS Neurosphere cultures were implanted in cohorts of 10–15 nude mice. 5 PDX lines, presenting median survival of 29–59 days were classified as short survivors, and 5 lines with median survival between 104–134 days classified as long survivors. Total RNA was extracted from PDX terminal tumors (3 biological replicates) and sequenced in a paired-end read format. Mouse reads were filtered out using Xenome. MYC and PDGFRA expression patterns were analyzed in tissue microarrays representing duplicated samples from 40 glioma neurosphere-derived PDX lines by IHC (1 anaplastic oligodendroglioma, 8 recurrent GBM with 2 newly diagnosed/recurrent pairs). Normalized staining intensity (MI) and area (A) were quantified using Fiji/ImageJ. RESULTS PDGFRA, MYC, MYCN gene amplifications were represented in a molecularly diverse panel of GBM patient-derived cancer stem-like cells (CSC) and orthotopic mouse xenografts (PDX). Transforming to a normal distribution (log10), 4/13 of cell lines had a PDGFRA mRNA expression (RPKM) higher than 1.5. Similarly, one PDX line had a staining index of greater than 10, 11 (27.5%) had an index between 5–10. The range of intra-tumoral variance, represented by standard deviation, was 0.09–24.25 highlighting the heterogeneity of PDGFRɑ expression. PDGFRɑ phosphorylation (Y754) did not differ between 8 cell lines cultured in NMGF, but deviated in alternate medias without growth factors, supplemented with FBS. In comparison, MYC(N) mRNA expression is only elevated in the context of a known amplification. Furthermore, a a MYC activity signature consisting of 18 target genes was only evident in the 5 amplified CSC lines. Taking advantage of genomic heterogeneity, we have isolated subclones lacking PDGFRA amplification from a PDGFRA amplified GBM CSC. The absence of PDGFRA amplification reduced the self-renewal potential to 37% of the PDGFRA amplified cell population (p=0.001) in clone 1 and 57% in clone 2 (p=0.013). Pertaining to determinants of in vivo survival, MYC was altered in 80% of short survivors (2/5 MYC, 2/5 MYCN amplification) and in 0% of long survivors. Myc signature was highly correlated with in vivo survival (Pearsons’ corr. = -0.77) and MYC gene expression was correlated with in vivo TMZ resistance (corr. = 0.7). CONCLUSION These results suggest that PDGFRɑ expression and activity can occur in the absence of gene amplification, while Myc activity is dependent on gene amplification. Both oncogenes drive oncogenic pathways that should be explored as therapeutic targets.

scholarly journals Modulation by Steroid Receptor Coactivator-1 of Target-Tissue Responsiveness in Resistance to Thyroid Hormone

Endocrinology ◽  
2003 ◽  
Vol 144 (9) ◽  
pp. 4144-4153 ◽  
Author(s):  
Yuji Kamiya ◽  
Xiao-Yong Zhang ◽  
Hao Ying ◽  
Yusuhito Kato ◽  
Mark C. Willingham ◽  
...  
Keyword(s):  
Thyroid Hormone ◽  
Target Genes ◽  
Thyroid Hormone Receptor ◽  
Expression Patterns ◽  
Steroid Receptor ◽  
Target Tissue ◽  
Dependent Manner ◽  
Resistance To Thyroid Hormone ◽  
Steroid Receptor Coactivator

Abstract Mutations in the thyroid hormone receptor-β gene (TRβ) cause resistance to thyroid hormone. How the action of mutant thyroid hormone nuclear receptors (TRs) is regulated in vivo is not clear. We examined the effect of a TR coactivator, steroid receptor coactivator-1 (SRC-1), on target-tissue responsiveness by using a mouse model of resistance to thyroid hormone, TRβPV knockin mice, in the SRC-1 null background. Lack of SRC-1 intensified the dysfunction of the pituitary-thyroid axis and impaired growth in TRβPV/+ mice but not in TRβPV/PV mice. In TRβPV/PV mice, however, lack of SRC-1 intensified the pathological progression of thyroid follicular cells to papillary hyperplasia, reminiscent of papillary neoplasia. In contrast, lack of SRC-1 did not affect responsiveness in the liver in regulating serum cholesterol in either TRβPV/+ or TRβPV/PV mice. Lack of SRC-1 led to changes in the abnormal expression patterns of several T3 target genes in the pituitary and liver. Thus, the present studies show that a coactivator such as SRC-1 could modulate the in vivo action of TRβ mutants in a tissue-dependent manner.

scholarly journals p53 drives a transcriptional program that elicits a non-cell-autonomous response and alters cell state in vivo

2020 ◽  
Vol 117 (38) ◽  
pp. 23663-23673 ◽  
Author(s):  
Sydney M. Moyer ◽  
Amanda R. Wasylishen ◽  
Yuan Qi ◽  
Natalie Fowlkes ◽  
Xiaoping Su ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Cellular Response ◽  
Target Genes ◽  
Transcriptional Program ◽  
Sequencing Data ◽  
Tissue Specific ◽  
Chip Sequencing ◽  
Cell State ◽  
P53 Activation

Cell stress and DNA damage activate the tumor suppressor p53, triggering transcriptional activation of a myriad of target genes. The molecular, morphological, and physiological consequences of this activation remain poorly understood in vivo. We activated a p53 transcriptional program in mice by deletion ofMdm2, a gene that encodes the major p53 inhibitor. By overlaying tissue-specific RNA-sequencing data from pancreas, small intestine, ovary, kidney, and heart with existing p53 chromatin immunoprecipitation (ChIP) sequencing, we identified a large repertoire of tissue-specific p53 genes and a common p53 transcriptional signature of seven genes, which includedMdm2but notp21. Global p53 activation caused a metaplastic phenotype in the pancreas that was missing in mice with acinar-specific p53 activation, suggesting non-cell-autonomous effects. The p53 cellular response at single-cell resolution in the intestine altered transcriptional cell state, leading to a proximal enterocyte population enriched for genes within oxidative phosphorylation pathways. In addition, a population of active CD8+ T cells was recruited. Combined, this study provides a comprehensive profile of the p53 transcriptional response in vivo, revealing both tissue-specific transcriptomes and a unique signature, which were integrated to induce both cell-autonomous and non-cell-autonomous responses and transcriptional plasticity.

Dissecting the Molecular Mechanisms of Mutant C/EBPalpha (p30) in Normal and Malignant Human Hematopoiesis.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2995-2995
Author(s):  
Jorg Cammenga ◽  
Birte Niebuhr ◽  
Stefan Horn ◽  
Ruud Delwel ◽  
Carol Stocking
Keyword(s):  
Leucine Zipper ◽  
Target Genes ◽  
Expression Patterns ◽  
Dominant Negative ◽  
Myelogenous Leukemia ◽  
Granulocytic Differentiation ◽  
Translational Initiation ◽  
Human Cd34 ◽  
Negative Function ◽  
Cd34 Cells

Abstract Acute myelogenous leukemia (AML) is often associated with mutations in transcription factors that are essential for normal hematopoietic development and differentiation. The basic leucine zipper (bZIP) protein C/EBPalpha is mutated in 7–10% of AML. Two different classes of C/EBPalpha mutations are found in AML: 1) mutations that introduce a stop codon between the primary translational initiation site and a downstream ATG, resulting in translation of an N-terminally truncated protein (p30) 2) mutations that disrupt the basic region of the bZIP domain in the C-terminus, abolishing DNA binding. Of note, biallellic mutations are often but not always observed. It has been proposed that p30 is dominant-negative over wt C/EBPalpha (p42), blocking its transcriptional activity. We have previously shown that p30 blocks erythrocytic commitment and inhibits terminal granulocytic differentiation when expressed in human but not murine primary hematopoietic cells. To identify the molecular mechanism by which the p30 inhibits differentiation and to evaluate the role of homo- and heterodimerization between p30 and p42 in leukemogenesis, we created a p30 that carries point mutations in bZIP (p30-L12V) that disrupt dimerization. Expression of p30-L12V had no effect on the differentiation of human CD34+ cells, arguing for the requirement of dimerization. To inhibit potential heterodimerization between p30 and p42 but permit p30 homodimerization, we generated a p30-GZ, in which the leucine zipper was replaced by an artificial dimerization domain. Expression of p30-GZ induced a similar differentiation block as the normal p30, arguing against a dominant-negative function of p30 over p42 mediated by dimerization. In a second approach to understand the mechanism by which p30 inhibits differentiation, we wanted to identify gene targets of p30. For this purpose, p30 was fused to the modified ligand-binding domain of the estrogen receptor (p30-ERtm). Expression of p30-ERtm in CD34+ cells in the presence of tamoxifen showed a phenotype very similar to the one observed after the expression of p30, while in the absence of tamoxifen no effect was observed. We used this system of inducible p30 expression in human CD34+ cells to evaluate gene expression patterns. If p30 is dominant-negative and interferes with the transcriptional activation of p42, reciprocal expression patterns of target genes should be observed for wt C/EBPalpha and p30. Our data show that homodimerization of p30 is necessary and sufficient to block erythrocytic commitment and terminal granulocytic differentiation of human CD34+ cells and to induce known C/EBPalpha target genes. These data argue that the formation of p30/p42 heterodimers is not required for the effect of C/EBPalpha p30, questioning the proposed dominant-negative function.

2008 Distinguished Scientist Lecture—MicroRNA Control of Heart Disease: From New Biology to New Therapeutics

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Eric N. Olson
Keyword(s):  
Heart Disease ◽  
Complex Disease ◽  
Target Genes ◽  
Expression Patterns ◽  
Loss Of Function ◽  
Systemic Delivery ◽  
Pathological Cardiac Hypertrophy ◽  
New Biology ◽  
Entire Gene

MicroRNAs act as negative regulators of gene expression by inhibiting the translation or promoting the degradation of target mRNAs. Because individual microRNAs often regulate the expression of multiple target genes with related functions, modulating the expression of a single microRNA can, in principle, influence an entire gene network and thereby modify complex disease phenotypes. We have identified signature expression patterns of microRNAs associated with pathological cardiac hypertrophy, heart failure, and myocardial infarction in humans and mouse models of heart disease. Gain- and loss-of-function studies in mice have revealed profound and unexpected functions for these microRNAs in numerous facets of cardiac biology, including the control of myocyte growth, contractility, energy metabolism, fibrosis, and angiogenesis, providing glimpses of new regulatory mechanisms and potential therapeutic targets for heart disease. Especially intriguing is the discovery of a network of muscle-specific microRNAs embedded within myosin heavy chain genes, which control myosin expression and the response of the heart to stress and thyroid hormone signaling. Recent studies have demonstrated that disease-inducing cardiac microRNAs can be persistently silenced in vivo through systemic delivery of anti-miRs, allowing for the direct therapeutic modulation of disease mechanisms. The myriad roles of microRNAs in the control of cardiac function and dysfunction and therapeutic opportunities for manipulating microRNA biology in the setting of heart disease will be discussed.

Switching the in vivo specificity of a minimal Hox-responsive element

Development ◽  
1997 ◽  
Vol 124 (10) ◽  
pp. 2007-2014 ◽  
Author(s):  
S.K. Chan ◽  
H.D. Ryoo ◽  
A. Gould ◽  
R. Krumlauf ◽  
R.S. Mann
Keyword(s):  
Binding Sites ◽  
Target Genes ◽  
Expression Patterns ◽  
High Specificity ◽  
Mouse Embryos ◽  
Homeodomain Protein ◽  
Homeodomain Proteins ◽  
Responsive Element

The homeodomain proteins encoded by the Hox complex genes do not bind DNA with high specificity. In vitro, Hox specificity can be increased by binding to DNA cooperatively with the homeodomain protein extradenticle or its vertebrate homologs, the pbx proteins (together, the PBC family). Here we show that a two basepair change in a Hox-PBC binding site switches the Hox-dependent expression pattern generated in vivo, from labial to Deformed. The change in vivo correlates with an altered Hox binding specificity in vitro. Further, we identify similar Deformed-PBC binding sites in the Deformed and Hoxb-4 genes and show that they generate Deformed or Hoxb-4 expression patterns in Drosophila and mouse embryos, respectively. These results suggest a model in which Hox-PBC binding sites play an instructive role in Hox specificity by promoting the formation of different Hox-PBC heterodimers in vivo. Thus, the choice of Hox partner, and therefore Hox target genes, depends on subtle differences between Hox-PBC binding sites.

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