Microarray Analyses of SREBP-1 Target Genes

Abstract Background Adult T-cell leukemia/lymphoma (ATL) is a mature T-cell neoplasm originating from human T-cell leukemia virus type-1 (HTLV-1) infected cells. Its clinical behavior differs among patients and is sub-classified into 4 sub-types: smoldering and chronic as indolent subtypes, and acute and lymphoma as aggressive subtypes. Prognosis for patients with the aggressive subtypes is very poor with standard chemotherapy, thus a new therapeutic approach is urgently needed. Previously, we reported that EZH2, a part of the PRC2 complex, not only methylates histone, but also serves as a recruitment platform for DNA methyltransferases that methylate the promoter regions of target genes (tumor suppressor gene and miRNAs) and is overexpressed in ATL cells. We found that ATL cell lines were sensitive to DZNep (3-deazaneplanosin A), which has been shown to deplete EZH2 expression, and their proliferation was attenuated. In the present study, we clarified which target genes and miRNAs are involved in DZNep-induced ATL cell death. Results We performed microarray analyses using the ATL cell lines KK1, SO4, LMY1, and KOB to compare their gene expression profiles between cells treated and untreated with DZNep. The results showed that BCL2 transcripts in ATL cell lines were commonly suppressed by DZNep. In accordance with those findings, quantitative PCR analysis revealed that BCL2 transcripts were suppressed in DZNep-treated as compared to untreated ATL cell lines. We also confirmed that EZH2 and BCL2 protein expressions were clearly suppressed in the ATL cell lines by DZNep. These findings indicated that DZNep suppresses BCL2 expression at the transcriptional level in ATL cells. In addition, we performed another set of microarray analyses for miRNA expression profiles using primary ATL cells obtained from ATL patients and CD4 positive T-cells from healthy volunteers. The ATL cells showed decreased expression levels of several miRNAs, such as miR-101, miR-126, and miR-181a. Importantly, miR-181a has been shown to be regulated by EZH2, while miR-181a is a candidate negative regulator of BCL2 expression. Quantification of miR-181a transcripts to determine whether miR-181a is induced by DZNep showed that miR-181a was up-regulated in ATL cells by DZNep. These results strongly support the notion that miR-181a is suppressed by EZH2 and that BCL2 expression is regulated by miR-181a in ATL cells. Together, our findings indicate a unique apoptotic pathway of BCL2 suppression via miR181a and that the EZH2 inhibitor DZNep may become a novel therapeutic agent for ATL. Disclosures: No relevant conflicts of interest to declare.

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Deacetylase Activity Is Required for Recruitment of the Basal Transcription Machinery and Transactivation by STAT5

Molecular and Cellular Biology ◽

10.1128/mcb.23.12.4162-4173.2003 ◽

2003 ◽

Vol 23 (12) ◽

pp. 4162-4173 ◽

Cited By ~ 103

Author(s):

Anne Rascle ◽

James A. Johnston ◽

Bruno Amati

Keyword(s):

Chromatin Remodeling ◽

Chromatin Immunoprecipitation ◽

Transcription Initiation ◽

Cellular Response ◽

Target Genes ◽

Trichostatin A ◽

Basal Transcription ◽

Basal Transcription Machinery ◽

Transcription Machinery ◽

Microarray Analyses

ABSTRACT The signal transducer and activator of transcription STAT5 plays a major role in the cellular response to cytokines, but the mechanism by which it activates transcription remains poorly understood. We show here that deacetylase inhibitors (trichostatin A, suberoylanilide hydroxamic acid, and sodium butyrate) prevent induction of endogenous STAT5 target genes, implying that a deacetylase activity is required for that process. Microarray analyses revealed that this requirement is common to all STAT5 target genes. Using chromatin immunoprecipitation, we show that, following STAT5 DNA binding, deacetylase inhibitors block transcription initiation by preventing recruitment of the basal transcription machinery. This inhibition is not due to effects on histone H3 and H4 acetylation or chromatin remodeling within the promoter region. This novel mechanism of transactivation by STAT5 provides a rationale for the use of deacetylase inhibitors for therapeutic intervention in STAT5-associated cancers.

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The transcriptome of the leukemogenic homeoprotein HOXA9 in human hematopoietic cells

Blood ◽

10.1182/blood-2003-07-2202 ◽

2004 ◽

Vol 103 (5) ◽

pp. 1676-1684 ◽

Cited By ~ 60

Author(s):

Sheri Tinnell Dorsam ◽

Christina M. Ferrell ◽

Glenn P. Dorsam ◽

Mika Kakefuda Derynck ◽

Ulka Vijapurkar ◽

...

Keyword(s):

Target Genes ◽

Expression Patterns ◽

Gene Families ◽

Lymphoid Cells ◽

Biologic Effects ◽

Human Acute Myeloid Leukemia ◽

Transient Overexpression ◽

High Level ◽

Microarray Analyses ◽

Hematopoietic Cell Lines

AbstractHematopoietic defects in HOXA9–/– mice demonstrate a key role for this homeoprotein in blood cell development. Conversely, enforced HOXA9 expression is leukemogenic in mice, and HOXA9 is frequently activated in human acute myeloid leukemia (AML). Although HOXA9 is thought to function as a transcription factor, few downstream targets have been identified. We searched for early HOXA9 target genes by using a transient overexpression strategy in 3 hematopoietic cell lines (2 myeloid, 1 lymphoid). cDNA microarray analyses identified 220 genes whose expression was modulated at least 2-fold. Expression signatures in myeloid and lymphoid cells demonstrated that HOXA9 functions as both an activator and repressor of a variety of genes in cell-specific patterns suggesting that the transcriptional effects of HOXA9 are largely dependent on the cell context. Transient transcription assays and target gene expression patterns in HOXA9–/– marrow cells imply that we have identified direct physiologic targets. Many target genes are expressed in CD34+ stem cells or are members of gene families involved in proliferation or myeloid differentiation. Expression of 14 HOXA9 target genes correlated with high-level HOXA9 expression in primary AML. These data suggest that many genes identified in this survey may mediate the biologic effects of HOXA9 in normal and leukemic hematopoiesis.

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Coordinative control of G2/M phase of the cell cycle by non-coding RNAs in hepatocellular carcinoma

PeerJ ◽

10.7717/peerj.5787 ◽

2018 ◽

Vol 6 ◽

pp. e5787 ◽

Cited By ~ 2

Author(s):

Jun Shi ◽

Guangqiang Ye ◽

Guoliang Zhao ◽

Xuedong Wang ◽

Chunhui Ye ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Cell Cycle ◽

Target Genes ◽

Expression Profiles ◽

M Phase ◽

Non Coding Rnas ◽

Regulatory Model ◽

Microarray Analyses ◽

The Relationship

Objective To investigate the interaction of non-coding RNAs (ncRNAs) in hepatocellular carcinoma. Methods We compared the ncRNAs and mRNAs expression profiles of hepatocellular carcinoma and adjacent tissue by microarray and RT-PCR. The relationship between different ncRNAs and mRNA was analyzed using bioinformatics tools. A regulatory model of ncRNAs in hepatocellular carcinoma cells was developed. Results A total of 1,704 differentially expressed lncRNAs, 57 miRNAs, and 2,093 mRNAs were identified by microarray analyses. There is a co-expression relationship between two ncRNAs (miRNA-125b-2-3p and lncRNA P26302). Bioinformatics analysis demonstrated cyclin-dependent kinases 1 and CyclinA2 as potential targets of miR-125b-2-3p and Polo-like kinase 1 as potential target of lncRNAP26302. All three gene are important components in the G2/M phase of cell cycle. Subsequently real-time polymerase chain reaction (PCR) studies confirmed these microarray results. Conclusion MiR-125b-2-3p and lncRNAP26302 may affect the G2/M phase of the cell cycle through the regulation of their respective target genes. This study shows a role of ncRNAs in pathogenesis of hepatocellular carcinoma at molecular level, providing a basis for the future investigation aiming at early diagnosis and novel treatment of hepatocellular carcinoma.

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Correction: Microarray Analyses of Glucocorticoid and Vitamin D3 Target Genes in Differentiating Cultured Human Podocytes

PLoS ONE ◽

10.1371/annotation/ce9027f6-dbf9-4fc9-af40-9e244edf6a6e ◽

2013 ◽

Vol 8 (6) ◽

Cited By ~ 2

Author(s):

Xiwen Cheng ◽

Xuan Zhao ◽

Simran Khurana ◽

Leslie A. Bruggeman ◽

Hung-Ying Kao

Keyword(s):

Vitamin D3 ◽

Target Genes ◽

Microarray Analyses

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Expression profiling of lipopolysaccharide target genes in RAW264.7 cells by oligonucleotide microarray analyses

Archives of Pharmacal Research ◽

10.1007/bf02973911 ◽

2006 ◽

Vol 29 (10) ◽

pp. 890-897 ◽

Cited By ~ 13

Author(s):

Hao Huang ◽

Cheol Kyu Park ◽

Ji Yoon Ryu ◽

Eun-Ju Chang ◽

Youngkyun Lee ◽

...

Keyword(s):

Expression Profiling ◽

Target Genes ◽

Oligonucleotide Microarray ◽

Raw264.7 Cells ◽

Microarray Analyses

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Multiple Defects in Erythroid Gene Expression in Erythroid Krupple-Like Factor (EKLF) Target Genes in EKLF-Deficient Mice.

Blood ◽

10.1182/blood.v104.11.1602.1602 ◽

2004 ◽

Vol 104 (11) ◽

pp. 1602-1602

Author(s):

Patrick G. Gallagher ◽

Andre M. Pilon ◽

Murat O. Arcasoy ◽

David M. Bodine

Keyword(s):

Gene Expression ◽

Pyruvate Kinase ◽

Target Genes ◽

Fetal Liver ◽

Globin Gene ◽

Subtractive Hybridization ◽

Liver Cells ◽

Fetal Liver Cells ◽

Microarray Analyses ◽

Deficient Mice

Abstract EKLF is the founding member of the KLF family of transcription factors. EKLF-deficient (−/−) mice die at d14-15 of gestation of severe anemia, attributed to decreased expression of the β-globin gene. Morphology of fetal-liver derived circulating erythroid cells in EKLF −/− mice does not mimic that seen in thalassemia, and mice expressing high levels of γ-globin bred onto an EKLF −/− background do not correct the anemia or rescue the −/− mice. These data suggest additional red cell defects are present in EKLF −/− mice contributing to the anemia. To address this hypothesis, we performed subtractive hybridization and microarray analyses with RNA isolated from d13.5 fetal livers of wild type (WT,+/+) and EKLF-deficient mice. In subtractive hybridization, WT (1X) was the tester population and EKLF −/− (30X) was the driver. >200 differentially expressed clones were sequenced. 122 clones were β-globin; 21 alpha hemoglobin stabilizing protein (AHSP); and the remainder were RBC membrane proteins including band 3 and β-spectrin. Microarray analyses were performed with Affymetrix GeneChip Mouse Genome 430 2.0 arrays; 3 independent EKLF +/+ and −/− RNA samples were analyzed. AHSP had the most significantly decreased expression in −/− samples, reduced to 5% of WT (p<0.0001). Other significantly down regulated genes, in addition to those identified by subtractive hybridization, included pyruvate kinase and ankyrin. Reduced expression in EKLF −/− RNA was confirmed using ribonuclease protection assay and/or real-time RT-PCR. AHSP mRNA was decreased by 75–90%; band 3 and β-spectrin were decreased by ~40%; ankyrin by 45%, and pyruvate kinase 15%. Flow cytometry of +/+ and −/ − fetal liver cells using TER119 revealed a TER119Hi population of cells absent in −/ − fetal liver cells, suggesting a block in differentiation to more mature erythroid progenitors. To ensure that the potential EKLF target genes were expressed in the TER119Lo population and were not identified because they were present only in the TER119Hi, the expression of each selected gene was analyzed in TER119Lo and TER119Hi cells by real time PCR. Target gene/α-globin ratios indicated the selected genes were expressed at levels >2 fold higher in TER119Lo than TER119Hi cells. Studies of the AHSP locus identified a strong DNaseI hypersensitive site (HS) in WT fetal liver nuclei between 5′ of the AHSP promoter, that was absent in −/ − chromatin. Chromatin immunoprecipitation analysis of WT fetal liver chromatin spanning 3.5kb of the AHSP locus using 13 primer pairs (~300bp intervals from >1kb 5′ and 3′) demonstrated 2 regions of hyperacetylation of histones H3 and H4. The 5′ region corresponded to the DNaseI HS, and the other region maps 3′ of the AHSP polyA signal. Histones H3 and H4 were also acetylated in the interval between these hyperacetylated regions, while the chromatin upstream and downstream of these regions were hypoacetylated. In chromatin from −/ − fetal liver cells, all sites were hypoacetylated, correlating with the severe reduction in AHSP gene expression. These results support the hypothesis that the anemia in EKLF −/ − mice is due to both decreased expression of the β-globin gene and other erythroid genes including those involved in membrane integrity, stabilization of α-globin protein, and glycolysis leading to defects in erythrocyte structure, function, and metabolism. They also suggest that EKLF may act as a transcription factor and a chromatin modulator for genes other than β-globin.

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Characterization of Oncogene Dysregulation in Multiple Myeloma by Combined FISH and DNA Microarray Analyses.

Blood ◽

10.1182/blood.v104.11.4844.4844 ◽

2004 ◽

Vol 104 (11) ◽

pp. 4844-4844

Author(s):

Antonino Neri ◽

Sonia Fabris ◽

Luca Agnelli ◽

Michela Mattioli ◽

Luca Baldini ◽

...

Keyword(s):

Gene Expression ◽

Multiple Myeloma ◽

Dna Microarray ◽

Plasma Cell ◽

Target Genes ◽

Expression Profiles ◽

Molecular Cytogenetic ◽

Igh Locus ◽

Microarray Analyses

Abstract Chromosomal translocations involving the immunoglobulin heavy chain (IGH@) locus and variuos partner loci are frequently associated with multiple myeloma (MM). We investigated the expression profiles of FGFR3/MMSET, CCND1, CCND3, MAF and MAFB genes, respectively involved in t(4;14)(p16.3;q32), t(11;14)(q13;q32), t(6;14)(p21;q32), t(14;16)(q32;q23) and t(14;20)(q32;q12), in purified plasma cell populations from 39 MMs and six plasma cell leukemias (PCL) using DNA microarray analysis, and compared the results with the presence of translocations as assessed by dual-color FISH or RT-PCR. The t(4;14) was found in six MMs, t(11;14) in 9 MMs and 1 PCL, t(6;14) in one MM, t(14;16) in 2 MMs and 1 PCL, and t(14;20) in one PCL. The translocations were associated with the spiked expression of target genes in all cases. Furthermore, gene expression profiling allowed the identification of putative translocations dysregulating CCND1 (1 MM and 1 PCL) and MAFB (1 MM and 1 PCL) without any apparent involvement of immunoglobulin loci. Notably, all of the translocations were mutually exclusive. Markedly increased levels of MMSET expression were found in one MM showing associated FGFR3 and MMSET signals on an unidentified chromosome. Our data suggest the importance of using combined molecular cytogenetic and gene expression approaches to detect genetic aberrations in MM.

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