scholarly journals Differential gene expression of chemokines inKRASandBRAFmutated colorectal cell lines: Role of cytokines

2014 ◽  
Vol 20 (11) ◽  
pp. 2979 ◽  
Author(s):  
Sajjad Khan
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Cell Lines ◽  
Colorectal Cell ◽  
Differential Gene

scholarly journals Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions

2018 ◽  
Author(s):  
Idan Nurick ◽  
Ron Shamir ◽  
Ran Elkon
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Cell Lines ◽  
Meta Analysis ◽  
Cell Types ◽  
Chromatin Organization ◽  
Cell Type ◽  
Differential Gene ◽  
Different Cell Types

AbstractBackgroundOur appreciation of the critical role of the 3D organization of the genome in gene regulation is steadily increasing. Recent 3C-based deep sequencing techniques elucidated a hierarchy of structures that underlie the spatial organization of the genome in the nucleus. At the top of this hierarchical organization are chromosomal territories and the megabase-scale A/B compartments that correlate with transcriptional activity within cells. Below them are the relatively cell-type invariant topologically associated domains (TADs), characterized by high frequency of physical contacts between loci within the same TAD and are assumed to function as regulatory units. Within TADs, chromatin loops bring enhancers and target promoters to close spatial proximity. Yet, we still have only rudimentary understanding how differences in chromatin organization between different cell types affect cell-type specific gene expression programs that are executed under basal and challenged conditions.ResultsHere, we carried out a large-scale meta-analysis that integrated Hi-C data from thirteen different cell lines and dozens of ChIP-seq and RNA-seq datasets measured on these cells, either under basal conditions or after treatment. Pairwise comparisons between cell lines demonstrated the strong association between modulation of A/B compartmentalization, differential gene expression and transcription factor (TF) binding events. Furthermore, integrating the analysis of transcriptomes of different cell lines in response to various challenges, we show that 3D organization of cells under basal conditions constrains not only gene expression programs and TF binding profiles that are active under the basal condition but also those induced in response to treatment.ConclusionsOur results further elucidate the role of dynamic genome organization in regulation of differential gene expression between different cell types, and indicate the impact of intra-TAD enhancer-promoter interactions that are established under basal conditions on both the basal and treatment-induced gene expression programs.

The Multikinase Inhibitor Sorafenib Inhibts Proliferation in B- and T-Lymphoblastic Cell Lines Via the PI3K/Akt Pathway.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1910-1910
Author(s):  
Catrin Schult ◽  
Meike Dahlhaus ◽  
Sonja Boldt ◽  
Änne Glass ◽  
Sabine Ruck ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Cell Lines ◽  
Metabolic Activity ◽  
Synergistic Effects ◽  
Cytotoxic Drugs ◽  
Akt Pathway ◽  
High Grade ◽  
Multikinase Inhibitor ◽  
Differential Gene

Abstract Background: The phosphatidylinositol 3 Kinase (PI3K)/Akt signalling pathway is involved in the regulation of proliferation, apoptosis and angiogenesis. Dysregulation of PI3K/Akt has been described for several solid and hematological tumors. Its role in acute lymphoblastic leukemogenesis (ALL) is unkown. Here, we investigated whether the inhibition of PI3K/Akt kinases influences apoptosis, necrosis and cell proliferation. Patients and Methods: ALL and high grade NHL cell lines with different cytogenetics and phenotypes were used (SEM, RS4;11, REH, Jurkat, DOGKIT). Phosphorylationstatus of Akt (Ser473, Thr308) and FOXO3A (Thr32) were determined by western blot (WB). Cells were incubated for 96h with LY29004 (5μM, 12.5μM, 25μM; PI3K inhibitor) or sorafenib (0.73μM, 7.3μM). In order to detect synergistic effects with other cytotoxic drugs cells were treated with combinations of sorafenib and doxorubicine, cytosin-arabinoside, and mTOR inhibitor (RAD001), respecitvely. Cell number, apoptosis, necrosis, protein phosphorylation and metabolic activity were determined at 4h, 24h, 48h, 72h, and 96h by microscopy, flow cytometry, WB and WST-1 testing. Whole genome Affymetrix gene expression arrays (U133 Plus 2.0) were performed in order to detect differential gene expression compared to controls treated with DMSO (dimethylsulfoxid) only. Results: In all ALL cell lines phosphorylated Akt (pAKT) was detected. Levels of pAkt and pFOXO3A differed between cell lines significantly, with Jurkat and SEM demonstrating high activation levels. PI3K inhibition by LY29004 led to decreased proliferation in SEM cells with only slight increases in apoptosis and moderate increase in necrosis rates (20%). Sorafenib inhibited the proliferation of SEM, Jurkat and RS4;11 significantly, with most pronounced effects at 96h. Maximal apoptosis and necrosis rates increased and ranged from 11 to 39% and 53 to 84%, respectively. Metabolic activity decreased significantly already after 24h. As early as 0.5h after treatment complete disappearance (SEM, RS4;11) or marked decrease (Jurkat) in levels of pAkt and pFOXO occurred. Combination of sorafenib with conventional cytotoxic drugs failed to demonstrate synergistic effects. Sorafenib treatment induced differential gene expression in several genes e.g. genes involved in apoptosis such as BIMBAM, caspases and CDKs. Conclusions: Inhibition of the PI3K/Akt pathway seems to be a potential therapeutic target in ALL and high grade lymphoma cells. Sorafenib as a multikinase inhibitor approved for clincial application in solid tumors displayes significant antileukemic activity in vitro and might be a potential drug for a targed therapy approach in ALL.

The PI3 Kinase (PI3K) Inhibitor, Buparlisib/BKM120, in B-Cell, T-Cell and Hodgkin Lymphoma Cell Lines: Cell Death Studies and Examination of Genomic Pathway Analyses Via a Systems Biology Approach

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1555-1555
Author(s):  
Michael E Coyle ◽  
Ravi Dashnamoorthy ◽  
Afshin Beheshti ◽  
Andrew M. Evens
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Flow Cytometry ◽  
T Cell ◽  
Cell Line ◽  
Differential Gene Expression ◽  
Cell Lines ◽  
Lymphoma Cell ◽  
Venn Diagram ◽  
Differential Gene

Abstract Introduction: The PI3K pathway plays a significant role in cell cycle, apoptosis, and DNA repair. It is commonly dysregulated in cancers making it a potential therapeutic target. BKM120 is a novel oral pan-class I PI3K inhibitor with antitumor activity and efficacy reported in solid tumors. It is in phase I/II clinical trials for treatment of relapsed-refractory NHL. There are additional data desired towards molecular mechanism of action and biological pathways of resistance for BKM120-treated lymphoma. Methods: TCL cell lines (Jurkat, Hut78, HH), HL lines (L428, L540) and DLBCL lines (SUDHL4, SUDHL6, SUDHL10, OCILY3, OCILY19) were treated with increasing concentrations of BKM120 (0.16-10uM) in 96 well plate and cell viability assessed by MTT assay. For gene expression profiling (GEP), SUDHL6, OCILY3, Jurkat, Hut78 and L540 cells were treated at IC50and analyzed on Illumina human HT12 gene chip. Gene Set Enrichment Analysis (GSEA) and biological network analysis were done using Ingenuity Pathway Analysis and Cytoscape. Apoptosis was evaluated by Annexin V and propidium iodine (AV/PI) staining and flow cytometry. For cell cycle analysis, Jurkat cells were exposed to BrdU and stained with anti-BrdU FITC and 7-AAD and analyzed by flow cytometry. Results: Cell viability showed dose-dependent growth inhibition in all lines. IC50 was between 0.316μM - 3.72μM at 72 hours (hrs). GEP analyses showed significant gene changes following BKM120 treatment with a 1.2 fold-change for OCILY3 (1886 genes), SUDHL6 (1884 genes), Hut78 (1474 genes), L540 (859 genes) and Jurkat (212 genes) (Fig 1). Differential gene expression with BKM120-treated cells showed significant overlap among DLBCL cell lines, with 991 genes of 1886 (OCILY3) and 1884 (SUDHL6). The differentially expressed genes in L540 HL cells treated with BKM120 showed better overlap with DLBCL lines than with TCL lines, with 366 and 315 of 859 L540 genes overlapping with OCILY3 and SUDHL6 lines, respectively. This may reflect the B cell of origin related response to BKM120 treatment. TCL lines had different profiles, with 52 overlapping genes of 212 for Jurkat and 1474 for Hut78. Jurkat is known to harbor a PTEN mutation with constitutively active PI3K, which may explain the differences in the GEP observed with BKM120 treatment in Jurkat and Hut78 TCL. GSEA and biological network analysis of BKM120 treated lymphoma cells showed conserved inhibitory effects on cell cycle, DNA replication and metabolic process across all lymphoma cells. However, we observed that immune signaling processes were oppositely regulated in B and T cell lymphomas. AV/PI-staining and flow cytometry revealed dose-dependent increase of apoptotic cells in all lymphoma cell lines. Analysis based on BrdU incorporation revealed induction of G2/M arrest in Jurkat cells treated with BKM120. Western blots showed decreased phosphorylation of PI3K and mTOR substrates including 4-EBP and phospho-p70S6K with BKM120 treatment. Although phosphorylation of MEK/ERK were downregulated at lower doses of BKM120, at higher doses, increased MEK/ERK phosphorylation were seen. Analysis of cell cycle regulatory proteins Cyclin, CDK and phospho-histone H3 with BKM120 treatment resulted in expression changes consistent with G2/M arrest and also resulted in increased apoptosis related PARP cleavage in all lymphoma cell lines. Conclusions: BKM120 treatment elicited biologically distinct GEP with immune functions oppositely regulated in B and T cell lymphomas, however impairment of cell cycle, DNA replication and metabolic function were the core responses/function to PI3K inhibition. Furthermore, based on GSEA, it was predicted that cell cycle arrest and MAPK activation as likely mechanisms of resistance to BKM120 treatment in these lymphoma cell lines. Additional studies are planned to examine rational combinations of BKM120 together with other targeted small molecules (e.g., Chk1-inhibitor, CDK4/6 inhibitor and MEK inhibitor). Figure 1. Differential gene expression and analysis of gene overlap. A. Point and boxplot representations of changes in gene expression following treatment with BKM120 for each cell line. B. Venn diagram of genes changing by 1.2 fold or more following treatment with BKM120 by cell line. C. Venn diagram of genes changing by 1.2 fold or more following treatment with BKM120, comparing SUDHL6 (Germinal center DLBCL) and OCI-Ly3 (ABC-DLBCL) and Hut78 and Jurkat (TCL lines). Figure 1. Differential gene expression and analysis of gene overlap. A. Point and boxplot representations of changes in gene expression following treatment with BKM120 for each cell line. B. Venn diagram of genes changing by 1.2 fold or more following treatment with BKM120 by cell line. C. Venn diagram of genes changing by 1.2 fold or more following treatment with BKM120, comparing SUDHL6 (Germinal center DLBCL) and OCI-Ly3 (ABC-DLBCL) and Hut78 and Jurkat (TCL lines). Disclosures No relevant conflicts of interest to declare.

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