Role of FOXA and Sp1 in mitochondrial acylcarnitine carrier gene expression in different cell lines

2011 ◽  
Vol 404 (1) ◽  
pp. 376-381 ◽  
Author(s):  
Paolo Convertini ◽  
Vittoria Infantino ◽  
Faustino Bisaccia ◽  
Ferdinando Palmieri ◽  
Vito Iacobazzi
Keyword(s):  
Gene Expression ◽  
Cell Lines

scholarly journals The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Wei Song ◽  
Roded Sharan ◽  
Ivan Ovcharenko
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Target Gene ◽  
Regulatory Elements ◽  
Distal Enhancer ◽  
Human Genes ◽  
Multiple Cell ◽  
A Chain ◽  
Target Promoter

Abstract Background Robustness and evolutionary stability of gene expression in the human genome are established by an array of redundant enhancers. Results Using Hi-C data in multiple cell lines, we report a comprehensive map of promoters and active enhancers connected by chromatin contacts, spanning 9000 enhancer chains in 4 human cell lines associated with 2600 human genes. We find that the first enhancer in a chain that directly contacts the target promoter is commonly located at a greater genomic distance from the promoter than the second enhancer in a chain, 96 kb vs. 45 kb, respectively. The first enhancer also features higher similarity to the promoter in terms of tissue specificity and higher enrichment of loop factors, suggestive of a stable primary contact with the promoter. In contrast, a chain of enhancers which connects to the target promoter through a neutral DNA segment instead of an enhancer is associated with a significant decrease in target gene expression, suggesting an important role of the first enhancer in initiating transcription using the target promoter and bridging the promoter with other regulatory elements in the locus. Conclusions The widespread chained structure of gene enhancers in humans reveals that the primary, critical enhancer is distal, commonly located further away than other enhancers. This first, distal enhancer establishes contacts with multiple regulatory elements and safeguards a complex regulatory program of its target gene.

scholarly journals Foxa3 (HNF-3γ) binds to and activates the rat proglucagon gene promoter but is not essential for proglucagon gene expression

2002 ◽  
Vol 366 (2) ◽  
pp. 633-641 ◽  
Author(s):  
Yuanfang LIU ◽  
Wei SHEN ◽  
Patricia L. BRUBAKER ◽  
Klaus H. KAESTNER ◽  
Daniel J. DRUCKER
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Promoter Activity ◽  
Gene Promoter ◽  
Forkhead Box ◽  
Mild Hypoglycaemia ◽  
Element Binding Protein ◽  
Prolonged Fast

Members of the Forkhead box a (Foxa) transcription factor family are expressed in the liver, pancreatic islets and intestine and both Foxa1 and Foxa2 regulate proglucagon gene transcription. As Foxa proteins exhibit overlapping DNA-binding specificities, we examined the role of Foxa3 [hepatocyte nuclear factor (HNF)-3γ] in control of proglucagon gene expression. Foxa3 was detected by reverse transcriptase PCR in glucagon-producing cell lines and binds to the rat proglucagon gene G2 promoter element in GLUTag enteroendocrine cells. Although Foxa3 increased rat proglucagon promoter activity in BHK fibroblasts, augmentation of Foxa3 expression did not increase proglucagon promoter activity in GLUTag cells. Furthermore, adenoviral Foxa3 expression did not affect endogenous proglucagon gene expression in islet or intestinal endocrine cell lines. Although Foxa3-/- mice exhibit mild hypoglycaemia during a prolonged fast, the levels of proglucagon-derived peptides and proglucagon mRNA transcripts were comparable in tissues from wild-type and Foxa3-/- mice. These findings identify Foxa3 as a member of the proglucagon gene G2 element binding-protein family that, unlike Foxa1, is not essential for control of islet or intestinal proglucagon gene expression in vivo.

scholarly journals Feedback inhibition of immunoglobulin gene rearrangement by membrane mu, but not by secreted mu heavy chains.

1988 ◽  
Vol 168 (4) ◽  
pp. 1363-1381 ◽  
Author(s):  
J Manz ◽  
K Denis ◽  
O Witte ◽  
R Brinster ◽  
U Storb
Keyword(s):  
Gene Expression ◽  
Transgenic Mice ◽  
B Cell ◽  
Cell Lines ◽  
Gene Rearrangement ◽  
Feedback Inhibition ◽  
Allelic Exclusion ◽  
Immunoglobulin Gene ◽  
Heavy Chains

Previous work (6-10) has shown that allelic exclusion of Ig gene expression is controlled by functionally rearranged mu and kappa genes. This report deals with the comparison of membrane mu (micron) and secreted mu (microsecond) in promoting such feedback inhibition. Splenic B cell hybridomas were analyzed from transgenic mice harboring a rearranged kappa gene alone or in combination with either an intact rearranged mu gene or a truncated version of the mu gene. The intact mu gene is capable of producing both membrane and secreted forms of the protein, while the truncated version can only encode the secreted form. The role of the microsecond was also tested in pre-B cell lines. Analysis of the extent of endogenous Ig gene rearrangement revealed that (a) the production of micron together with kappa can terminate Ig gene rearrangement; (b) microsecond with kappa does not have this feedback effect; (c) microsecond may interfere with the effect of micron and kappa; and (d) the feedback shown here probably represents a complete shutoff of the specific recombinase by micron + kappa; the data do not address the question of mu alone affecting the accessibility of H genes for rearrangement.

scholarly journals Dual Role for Transforming Growth Factor β-Dependent Signaling in Trypanosoma cruzi Infection of Mammalian Cells

2000 ◽  
Vol 68 (4) ◽  
pp. 2077-2081 ◽  
Author(s):  
Belinda S. Hall ◽  
Miercio A. Pereira
Keyword(s):  
Gene Expression ◽  
Growth Factor ◽  
Trypanosoma Cruzi ◽  
Host Cell ◽  
Cell Lines ◽  
Mammalian Cells ◽  
Transforming Growth Factor ◽  
Growth Arrest ◽  
Transforming Growth Factor Β

ABSTRACT Expression of functional transforming growth factor β (TGF-β) receptors (TβR) is required for the invasion of mammalian cells by the protozoan parasite Trypanosoma cruzi. However, the precise role of this host cell signaling complex in T. cruzi infection is unknown. To investigate the role of the TGF-β signaling pathway, infection levels were studied in the mink lung epithelial cell lines JD1, JM2, and JM3. These cells express inducible mutant TβR1 proteins that cannot induce growth arrest in response to TGF-β but still transmit the signal for TGF-β-dependent gene expression. In the absence of mutant receptor expression, trypomastigotes invaded the cells at a low level. Induction of the mutant receptors caused an increase in infection in all three cell lines, showing that the requirement for TGF-β signaling at invasion can be divorced from TGF-β-induced growth arrest. TGF-β pretreatment of mink lung cells expressing wild-type TβR1 caused a marked enhancement of infection, but no enhancement was seen in JD1, JM2, and JM3 cells, showing that the ability of TGF-β to stimulate infection is associated with growth arrest. Likewise, expression of SMAD7 or SMAD2SA, inhibitors of TGF-β signaling, did not block infection by T. cruzi but did block the enhancement of infection by TGF-β. Taken together, these results show that there is a dual role for TGF-β signaling in T. cruzi infection. The initial invasion of the host cell is independent of both TGF-β-dependent gene expression and growth arrest, but TGF-β stimulation of infection requires a fully functional TGF-β signaling pathway.

Biological Sequelae of TRAF2 Downregulation in Waldenstrom Macroglobulinemia Cells.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 3526-3526
Author(s):  
Xavier Leleu ◽  
Lian Xu ◽  
Zachary R. Hunter ◽  
Sophia Adamia ◽  
Evdoxia Hatjiharissi ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cells ◽  
Cell Growth ◽  
Cell Lines ◽  
Genomic Alteration ◽  
Rt Pcr ◽  
Growth And Survival ◽  
Healthy Donors ◽  
Cell Growth And Survival

Abstract Background. Several TNF family members (CD40L and BAFF/BLYS) have been implicated in Waldenstrom’s Macroglobulinemia (WM) cell growth and survival. More recently, abnormalities in the APRIL-TACI pathway have been demonstrated by us in WM cells (Hunter, ASH2006, #228). TRAFs (TNFR-associated factor) are a family of adaptor proteins that mediate signal transduction from multiple members of the TNF receptor superfamily. In particular, TRAFs facilitate pro-apoptotic signaling from the TACI receptor, and TRAF2 is of importance among the TRAF adapter proteins since this protein is required for TNF-alpha-mediated activation of SAPK/JNK MAPK known to be involved in drug-induced death of tumor B cells. We therefore examined the role of TRAF2 in WM growth and survival. Method. We investigated TRAF2, 3 and 5 gene expression in WM patient bone marrow (BM) CD19+ cells and cell lines (BCWM.1, WSU-WM) and compared their expression to BM CD19+ cells from healthy donors. Expression of human TRAF transcripts were determined using real time quantitative RT-PCR (qPCR) based on TaqMan fluorescence methodology. To evaluate the role of TRAF2, a knockdown model was prepared in BL2126 B-cells and BCWM.1 WM cells using electroporation, with resulted ≥50% knockdown efficiency using RT-PCR and immunoblotting. Results. We found that TRAF3 and 5 gene expression was higher in WM versus healthy donors, while TRAF2 expression was lower in 8/13 (60%) patients, using qPCR. TRAFs gene expression did not correlate with tumor burden or WM prognostic markers. We next sought to understand the biological sequelae of TRAF2 deficiency in BL2126 and BCWM.1 cells and found that TRAF2 knockdown induced increased survival at 72 hours in both cell lines. We next studied sequence analysis of 20 WM patients CD19+ BM cells to determine whether there was a TRAF2 genomic alteration, and found heterozygous early termination mutation in exon 5 in 1 (5%) patient. Conclusion. Our data demonstrate that TRAF2 is a commonly dysregulated TNF family adapter protein in patients with WM, with important consequences in WM cell growth and survival.

scholarly journals CIRP Promotes the Progression of Non-small Cell Lung Cancer Through Activation of Wnt/β-catenin Signaling via CTNNB1

2021 ◽  
Author(s):  
Yi Liao ◽  
Jianguo Feng ◽  
Weichao Sun ◽  
Chao Wu ◽  
Jingyao Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Cell Cycle ◽  
Small Cell Lung Cancer ◽  
Signaling Pathway ◽  
Cell Lines ◽  
Cell Lung Cancer ◽  
Small Cell ◽  
Small Cell Lung

Abstract Background: Cold-inducible RNA binding protein (CIRP) is a newly discovered proto-oncogene. In this study, we investigated the role of CIRP in the progression of non-small cell lung cancer (NSCLC) using clinic samples, cultured cell lines and animal lung cancer models. Methods: Tissue arrays, IHC and HE staining, immunoblotting, and qRT-PCR were used to detect the indicated gene expression; Plasmid and siRNA transfections as well as viral infection were used to manipulate gene expression; Cell proliferation assay, cell cycle analysis, cell migration and invasion analysis, soft agar colony formation assay, tail intravenous injecting and subcutaneously inoculating of animal models were performed to study the role of CIRP in NSCLC cells; Gene expression microarray was used to select the underlying pathways; RNA immunoprecipitation assay, biotin pull-down assay, immuno-purification assay, mRNA decay analyses and luciferase reporter assay were performed to elucidate the mechanisms. The log-rank (Mantel-Cox) test, independent sample T test, the nonparametric Mann-Whitney test, spearman rank test and two-tailed independent sample T-test were used accordingly in our study. Results: Our data showed that CIRP was highly expressed in NSCLC tissue, and its level was negatively correlated with the prognosis of NSCLC patients. By manipulating CIRP expression in A549, H460, H1299, and H1650 cell lines, we demonstrated that CIRP overexpression promoted the transition of G1/G0 phase to S phase and the formation of enhanced malignant phenotype of NSCLC, reflected by increased proliferation, enhanced invasion/metastasis and greater tumorigenic capabilities both in vitro and in vivo. Transcriptome sequencing further demonstrated that CIRP acted on cell cycle, DNA replication and Wnt signaling pathway to exert its pro-oncogenic action. Mechanistically, CIRP directly bound to the 3’- and 5'-UTR of CTNNB1 mRNA, leading to enhanced stability and translation of CTNNB1 mRNA and promote IRES-mediated protein synthesis, respectively. Eventually, the increased CTNNB1 protein levels mediated excessive activation of the Wnt/β-Catenin signaling pathway and its downstream C-myc, COX-2, CCND1, MMP7, VEGFA and CD44. Conclusion: Our results support CIRP as a candidate oncogene in NSCLC and a potential target for NSCLC therapy.

scholarly journals Arachidonic acid drives adaptive responses to chemotherapy-induced stress in malignant mesothelioma

2021 ◽  
Vol 40 (1) ◽  
Author(s):  
Mario Cioce ◽  
Claudia Canino ◽  
Harvey Pass ◽  
Giovanni Blandino ◽  
Sabrina Strano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arachidonic Acid ◽  
Cell Lines ◽  
Adaptive Response ◽  
Response To Therapy ◽  
Specific Gene ◽  
Induced Stress ◽  
Cell Subpopulations ◽  
Transformed Cell Lines

Abstract Background High resistance to therapy and poor prognosis characterizes malignant pleural mesothelioma (MPM). In fact, the current lines of treatment, based on platinum and pemetrexed, have limited impact on the survival of MPM patients. Adaptive response to therapy-induced stress involves complex rearrangements of the MPM secretome, mediated by the acquisition of a senescence-associated-secretory-phenotype (SASP). This fuels the emergence of chemoresistant cell subpopulations, with specific gene expression traits and protumorigenic features. The SASP-driven rearrangement of MPM secretome takes days to weeks to occur. Thus, we have searched for early mediators of such adaptive process and focused on metabolites differentially released in mesothelioma vs mesothelial cell culture media, after treatment with pemetrexed. Methods Mass spectrometry-based (LC/MS and GC/MS) identification of extracellular metabolites and unbiased statistical analysis were performed on the spent media of mesothelial and mesothelioma cell lines, at steady state and after a pulse with pharmacologically relevant doses of the drug. ELISA based evaluation of arachidonic acid (AA) levels and enzyme inhibition assays were used to explore the role of cPLA2 in AA release and that of LOX/COX-mediated processing of AA. QRT-PCR, flow cytometry analysis of ALDH expressing cells and 3D spheroid growth assays were employed to assess the role of AA at mediating chemoresistance features of MPM. ELISA based detection of p65 and IkBalpha were used to interrogate the NFkB pathway activation in AA-treated cells. Results We first validated what is known or expected from the mechanism of action of the antifolate. Further, we found increased levels of PUFAs and, more specifically, arachidonic acid (AA), in the transformed cell lines treated with pemetrexed. We showed that pharmacologically relevant doses of AA tightly recapitulated the rearrangement of cell subpopulations and the gene expression changes happening in pemetrexed -treated cultures and related to chemoresistance. Further, we showed that release of AA following pemetrexed treatment was due to cPLA2 and that AA signaling impinged on NFkB activation and largely affected anchorage-independent, 3D growth and the resistance of the MPM 3D cultures to the drug. Conclusions AA is an early mediator of the adaptive response to pem in chemoresistant MPM and, possibly, other malignancies.

Azacitidine, as a DNMT Inhibitor Decreases hTERT Gene Expression and Telomerase Activity More Effective Compared with HDAC Inhibitor in Human Head and Neck Squamous Cell Carcinoma Cell Lines

2020 ◽  
Vol 14 (1) ◽  
pp. 60-67
Author(s):  
Sepideh Atri ◽  
Nikoo Nasoohi ◽  
Mahshid Hodjat
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Cell Lines ◽  
Squamous Cell ◽  
Trichostatin A ◽  
Telomerase Activity ◽  
Htert Gene ◽  
Deacetylase Inhibitor

Background: Head and neck squamous cell carcinoma (HNSCC) is one of the most fatal malignancies worldwide and despite using various therapeutic strategies for the treatment of HNSCC, the surveillance rate is low. Telomerase has been remarked as the primary targets in cancer therapy. Considering the key regulatory role of epigenetic mechanisms in controlling genome expression, the present study aimed to investigate the effects of two epigenetic modulators, a DNA methylation inhibitor and a histone deacetylase inhibitor on cell migration, proliferation, hTERT gene expression, and telomerase activity in HNSCC cell lines. Methods: Human HNSCC cell lines were treated with Azacitidine and Trichostatin A to investigate their effects on telomerase gene expression and activity. Cell viability, migration, hTERT gene expression, and telomerase activity were studied using MTT colorimetric assay, scratch wound assay, qRT-PCR, and TRAP assay, respectively. Results: Azacitidine at concentrations of ≤1μM and Trichostatin A at 0.1 to 0.3nM concentrations significantly decreased FaDu and Cal-27 cells migration. The results showed that Azacitidine significantly decreased hTERT gene expression and telomerase activity in FaDu and Cal-27 cell lines. However, there were no significant changes in hTERT gene expression at different concentrations of Trichostatin A in both cell lines. Trichostatin A treatment affected telomerase activity at the high dose of 0.3 nM Trichostatin A. Conclusion: The findings revealed that unlike histone deacetylase inhibitor, Azacitidine as an inhibitor of DNA methylation decreases telomerase expression in HNSCC cells. This might suggest the potential role of DNA methyltransferase inhibitors in telomerase-based therapeutic approaches in squamous cell carcinoma.

Unveiling the Role of MicroRNA155 in Diffuse Large B Cell Lymphoma.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2024-2024
Author(s):  
Deepak Rai ◽  
Shailaja Karanti ◽  
Patricia Dahia ◽  
Ricardo C.T. Aguiar
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
B Cell ◽  
Cell Lines ◽  
Mhc Class Ii ◽  
B Cell Lymphoma ◽  
Tissue Cell ◽  
Transcription Analysis ◽  
Mrna Cleavage

Abstract MicroRNAs (miR) are non-coding RNAs that regulate gene expression by pairing to 3UTRs of target genes inducing translational repression or mRNA cleavage. New evidence suggests that the latter mechanism markedly contributes to miRNA effects. Hence, global gene expression analyses may help elucidate the functional role of miRNA by recognizing pathways modified by their abnormal expression and identifying direct targets. MiR155, the product of the non coding gene BIC, is overexpressed in lymphomas and its role in tumorigenesis is supported by the development of B-cell malignancies in miR155 transgenic mice. However, the functional consequences of miR155 overexpression in tumor development remain unclear. To address this issue, we developed a semi-quantitative RT-PCR assay that specifically amplifies either the nuclear unspliced BIC mRNA (target of the RNase III Drosha) or the spliced BIC mRNA. We found a marked correlation between the expression levels of these two mRNAs, which in turn agreed with the levels of mature miR155 detected in northern blots. Of the 22 DLBCL cell lines studied, only 5 (DHL6, Ly3, Ly10, Farage, RCK-8) expressed significantly high levels of BIC and miR155. To isolate the effects of miR155 in DLBCL we genetically modified its expression and performed global transcription analysis on microarray. In brief, we cloned the BIC transcript in a MSCV-GFP bicistronic retrovirus and confirmed in transduced HeLa cells that the mature miR155 was expressed when this transcript was driven by an LTR promoter. Next, we used two DLBCL cell lines with low levels of miR155 (Ly8 and Ly19) to generate unique populations expressing miR155 or MSCV alone. RNA was isolated from GFP-sorted cells, hybridized to the Affymetrix U133Plus2.0 chip and the data analyzed with dChip. Remarkably, and in agreement with the role of miRNAs, supervised analysis (fold diff >1.7) revealed a vast predominance (>90%) of downregulated genes when comparing miR155 expressing cells to MSCV only. These gene groups included predicted miR155 targets and were significantly enriched for molecules involved in the immune response (p<.001), including MHC class II, chemokine receptors, TDT, NFAT and CD24, a particularly relevant target for miR155 inhibition since its activation induces apoptosis in lymphomas. To validate and extend our findings, we queried public expression datasets of primary DLBCL. First, we used our cell lines expression data to confirm that the BIC probe in the Affymetrix chip reliably reflected the expression of miR155. Since DLBCL entails at least two groups of tumors reflecting distinct normal B-cells (GC and ABC) and the expression of miRNA and its targets are highly tissue/cell specific, we compartmentalized these analyses within the groups of ABC and GC tumors. We selected the tumors within each group with the highest and lowest levels of BIC (20% percentile) and performed unsupervised hierarchical clustering analysis (filtering parameters 0.5<SD/mean<10). In agreement with our data in the GC-type miR155-expressing cell lines, we found that in GC-, but not in ABC tumors, the expression of BIC inversely correlated with that of the genes related to the immune response. Notably, the pro-apoptotic molecule CD24 was significantly downregulated (p<0.02) in BIC overexpressing primary DLBCL, underscoring the need for further characterization of the signals relayed by this surface molecule and its potential as a rational drug target. Our data start to delineate the effects of miR155 in DLBCL and show the potential of expression arrays to identify miRNA targets modified by mRNA cleavage.

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