scholarly journals Transcriptional analysis of sodium valproate in a serotonergic cell line reveals gene regulation through both HDAC inhibition-dependent and independent mechanisms

2019 ◽  
Author(s):  
Priyanka Sinha ◽  
Simone Cree ◽  
Allison L. Miller ◽  
John F. Pearson ◽  
Martin A. Kennedy
Keyword(s):  
Cell Line ◽  
Sodium Valproate ◽  
Cell Model ◽  
Hdac Inhibitors ◽  
Transcriptional Analysis ◽  
Hdac Inhibition ◽  
Genes Expression ◽  
Gene Regulatory ◽  
Regulatory Effects ◽  
Serotonergic Cell

AbstractSodium valproate (VPA) is a histone deacetylase (HDAC) inhibitor, widely prescribed in the treatment of bipolar disorder, and yet the precise modes of therapeutic action for this drug are not fully understood. After exposure of the rat serotonergic cell line RN46A to VPA, RNA-sequencing (RNA-Seq) analysis showed widespread changes in gene expression. Analysis by multiple pipelines revealed as many as 230 genes were significantly upregulated and 72 genes were significantly downregulated. A subset of 23 differentially expressed genes was selected for validation using the nCounter® platform, and of these we obtained robust validation for ADAM23, LSP1, MAOB, MMP13, PAK3, SERPINB2, SNAP91, WNT6, and ZCCHC12. We investigated the effect of lithium on this subset and found four genes, CDKN1C, LSP1, SERPINB2 and WNT6 co-regulated by lithium and VPA. We also explored the effects of other HDAC inhibitors and the VPA analogue valpromide on the subset of 23 selected genes. Expression of eight of these genes, CDKN1C, MAOB, MMP13, NGFR, SHANK3, VGF, WNT6 and ZCCHC12, was modified by HDAC inhibition, whereas others did not appear to respond to several HDAC inhibitors tested. These results suggest VPA may regulate genes through both HDAC-dependent and independent mechanisms. Understanding the broader gene regulatory effects of VPA in this serotonergic cell model should provide insights into how this drug works and whether other HDACi compounds may have similar gene regulatory effects, as well as highlighting molecular processes that may underlie regulation of mood.

scholarly journals Chemical Genomics Reveals JAK STAT Activation As a Mechanism of Resistance to HDAC Inhibitors in B Cell Lymphomas

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 271-271
Author(s):  
Matthew S. McKinney ◽  
Anne W Beaven ◽  
Andrea Moffitt ◽  
Jason Landon Smith ◽  
Eric Lock ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cell ◽  
Cell Line ◽  
Cell Lines ◽  
Hdac Inhibitors ◽  
Resistant Cell ◽  
Hdac Inhibition ◽  
Stat Pathway

Abstract Background: HDAC inhibitors (HDACi) are being investigated as treatment for relapsed/refractory non Hodgkin lymphoma (NHL) and other cancers. However, the mechanisms underlying sensitivity and resistance to HDAC inhibition in lymphomas have not been fully characterized. We probed the cellular and molecular response to HDACi in vitro and in vivo in order to determine factors that dictate the response to HDACi and to enable design of approaches to incorporate HDACi into novel combination therapeutics. Methods: High-throughput cytotoxicity screening was performed using two different HDAC inhibitors, LBH589 (panobinostat) and SAHA (vorinostat) in 52 lymphoid cell lines characterized through RNA-seq and microarray gene expression profiling. This screen revealed a greater than 50-fold range in concentration needed to induce cytotoxicity for the 2 different HDAC inhibitors and there was moderate correlation between the 2 compounds in this panel (Pearson correlation r = 0.76, p < 0.01). By pairing this chemosensitivity data with gene expression profiles of the screened cell lines, we developed a gene expression classifier for LBH589 that identified resistant and sensitive cell line groups. This predictor was applied to B-cell NHL cell lines tested with LBH589 in the Cancer Cell Line Encyclopedia (CCLE) and we found that the sensitive and resistant cell line groups distinguished by this method differed more than 5-fold in IC50 (0.021 vs. 1.24 nM, P < 0.01 by Wilcoxon rank sum), thus validating the ability of this approach to distinguish HDACi resistant cell lines. We further initiated a clinical trial of LBH589 in relapsed/refractory diffuse large B cell lymphoma patients combined with RNAseq profiling of their tumors prior to embarking on treatment. We treated nine patients with LBH589, and application of our response predictor to scaled RNAseq gene expression data revealed 4 predicted responders and 5 predicted non-responders. Two of the predicted responders had a clinical response to LBH589, whereas none of the predicted non-responders had a clinical response, thus our classifier was able to identify all of the LBH589-responsive patients from this cohort (P = 0.08 by Fisher's exact test). Analysis of differentially expressed molecular pathways in HDACi sensitive and resistant samples by gene set enrichment revealed the JAK-STAT pathway as the most differentially expressed pathway associated with HDACi resistance (at P < 0.001 and FDR < 0.20). We further identified a number of distinct mutations including STAT3, SOCS1 and JAK1 that were associated with activation of the JAK-STAT pathway by gene expression signatures and the LBH589 response signature in DLBCL cell lines and patient samples by analysis of RNA-seq data. Phosphoprotein analysis by Western blot and Sis-inducible-element (SIE) luciferase reporter assays were used to confirm JAK-STAT activation in these samples and we found that overexpression of STAT3 Src-homology domain mutations activated JAK-STAT3 signaling in isogenic cell lines and fostered resistance to LBH589 in vitro. Conversely, using in vivo DLBCL xenograft models, we found that combining JAK-STAT and HDAC inhibition by treatment with LBH589 and ruxolitinib resulted in synergistic reduction of tumor cell viability and tumor growth with tolerable toxicity in mice. Conclusions: Sustained JAK-STAT activation appears to mediate resistance to HDAC inhibition in DLBCL and other NHLs and several recurrent genetic lesions drive JAK-STAT activation in these diseases. This process can be overcome by JAK 1/2 inhibition with ruxolitinib and these findings demonstrate a role for combination therapy with HDAC inhibitors and small molecules targeting the JAK-STAT pathway in lymphoid malignancies. Disclosures No relevant conflicts of interest to declare.

The Histone Deacetylase Inhibitor Depsipeptide Mediates Distinct Patterns of Histone Acetylation in Cells Overexpressing Bcl-2.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2802-2802
Author(s):  
David M. Lucas ◽  
Liwen Zhang ◽  
Melanie E. Davis ◽  
Xiaodan Su ◽  
Amy Sklenar ◽  
...  
Keyword(s):  
B Cells ◽  
Growth Inhibition ◽  
Histone Acetylation ◽  
Cell Line ◽  
Hdac Inhibitors ◽  
Hdac Inhibition ◽  
Histone Proteins ◽  
Post Translational Modifications ◽  
Over Expression ◽  
Empty Vector

Abstract Post-translational modifications of histone proteins including acetylation and methylation are known to be important in the regulation of gene expression, and histone modification patterns are found to be altered in many tumor types. We have established a liquid chromatography/mass spectrometry (LC/MS) analysis technique that allows for detailed interrogation of histone protein post-translational patterns. Application of this technique to histone proteins isolated from Chronic Lymphocytic Leukemia (CLL) patient cells and CD19-selected normal B cells has demonstrated that primary CLL cells have a pattern of H2A modification distinct from normal B cells, and that changes in each of the histone proteins H2A, H2B, H3 and H4 occur following treatment with HDAC inhibitors. We have used this and other techniques to understand how factors that influence apoptotic threshold, such as Bcl-2, can also cause changes in histone post-translational modifications induced by depsipeptide and other HDAC inhibitors. To initially explore this, we utilized the 697 lymphoblastoid cell line transfected either with an empty vector (697-neo) or a vector driving a ten-fold overexpression of Bcl-2 protein (697-Bcl-2). Cells were exposed to varying concentrations of depsipeptide for 4 or 24 hours and analyzed for growth inhibition, cell death, HDAC inhibition, and p21 induction. The results of these studies are summarized in the following table: Effects of Depsipeptide Treatment on 697 Cells at 24 Hours Relative % Cell Growth Apoptotic Cells (%) Relative HDAC Inhibition (%) p21, fold increase 697-neo untreated 100 8.2 0 1.0 697-neo 3.8 nM DDP 66.3 9.0 74.0 1.5 697-neo 38 nM DDP 41.0 57.5 97.0 2.3 697-Bcl-2 untreated 100 7.6 0 1.0 697-Bcl-2 3.8 nM DDP 90.4 7.5 77.3 1.9 697-Bcl-2 38 nM DDP 80.6 10.4 94.6 3.9 Over-expression of Bcl-2 completely blocked apoptosis induced by depsipeptide, as compared to the empty vector cell line. Despite this, growth inhibition, HDAC inhibition and p21 protein induction was observed in the Bcl-2 over-expressing cell line. Specific acetylation of H4 was analyzed by LC/MS and demonstrated that baseline histone acetylation patterns were identical between the 697-neo and 697-Bcl-2 cell lines. With depsipeptide treatment, however, distinct differences were noted in the pattern of acetylation between the two cell lines at 24 hours. Specifically, 697-neo showed increases in the di-, tri-, and tetra-acetylated H4 forms, with the tri-acetylated form predominating. In the 697-Bcl-2 cells the di-acetylated form was the most abundant followed closely by tri- and tetra- acetylated forms, and in contrast to the 697-neo cells, a penta-acetylated form is strongly detected. Our data suggest that molecular characteristics of tumor cells that alter apoptotic thresholds may influence changes in histone acetylation following HDAC inhibitor treatment. Exploration of the relationship between histone acetylation and Bcl-2 over-expression is currently under study.

Novel Conjugated Quinazolinone-Based Hydroxamic Acids: Design, Synthesis and Biological Evaluation

2020 ◽  
Vol 16 ◽  
Author(s):  
Tran Khac Vu ◽  
Nguyen Thi Thanh ◽  
Nguyen Van Minh ◽  
Nguyen Huong Linh ◽  
Nguyen Thi Phương Thao ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Cell Lines ◽  
Cancer Cell ◽  
Hdac Inhibitors ◽  
Cancer Cell Lines ◽  
Hydroxamic Acids ◽  
Biological Evaluation ◽  
Hdac Inhibition ◽  
Ic50 Value ◽  
Mcf 7

Background: Target-based approach to drug discovery currently attracts a great deal of interest from medicinal chemists in anticancer drug discovery and development. Histone deacetylase (HDAC) inhibitors represent an extensive class of targeted anti-cancer agents. Among the most explored structure moieties, hydroxybenzamides and hydroxypropenamides have been demonstrated to have potential HDAC inhibitory effects. Several compounds of these structural classes have been approved for clinical uses to treat different types of cancer, such as vorinostat and belinostat. Aims: This study aims at developing novel HDAC inhibitors bearing conjugated quinazolinone scaffolds with potential cytotoxicity against different cancer cell lines. Method: A series of novel N-hydroxyheptanamides incorporating conjugated 6-hydroxy-2 methylquinazolin-4(3H)- ones (15a-l) was designed, synthesized and evaluated for HDAC inhibitory potency as well as cytotoxicity against three human cancer cell lines, including HepG-2, MCF-7 and SKLu-1. Molecular simulations were finally performed to gain more insight into the structure-activity. relationships. Results: It was found that among novel conjugated quinazolinone-based hydroxamic acids synthesized, compounds 15a, 15c and 15f were the most potent, both in terms of HDAC inhibition and cytotoxicity. Especially, compound 15f displayed up to nearly 4-fold more potent than SAHA (vorinostat) in terms of cytotoxicity against MCF-7 cell line with IC50 value of 1.86 µM, and HDAC inhibition with IC50 value of 6.36 µM. Docking experiments on HDAC2 isozyme showed that these compounds bound to HDAC2 with binding affinities ranging from -10.08 to -14.93 kcal/mol compared to SAHA (-15.84 kcal/mol). It was also found in this research that most of the target compounds seemed to be more cytotoxic toward SKLu-1than MCF-7 and HepG-2. Conclusion: The resesrch results suggest that some hydroxamic acids could emerge for further evaluation and the results are well served as basics for further design of more potent HDAC inhibitors and antitumor agents.

Continuous Hypoxia and Glucose Metabolism, The Effects on Genes Expression in Mcf7 Breast Cancer Cell Line

2020 ◽  
Vol 20 ◽  
Author(s):  
Abdel Qader Al Bawab ◽  
Malek Zihlif ◽  
Yazan Jarrar ◽  
Ahmad Saleh
Keyword(s):  
Breast Cancer ◽  
Glucose Metabolism ◽  
Cancer Cells ◽  
Cell Line ◽  
Breast Cancer Cell Line ◽  
Warburg Effect ◽  
Cancer Cell Line ◽  
Mcf7 Cells ◽  
Genetic Changes ◽  
Genes Expression

Background: Hypoxia (deprived oxygen in tissues) may induce molecular and genetic changes in cancer cells. Objective: Investigating the genetic changes of glucose metabolism in breast cancer cell line (MCF7) after exposure to continuous hypoxia (10 and 20 cycles exposure of 72 hours continuously on a weekly basis). Method: Gene expression of MCF7 cells was evaluated using real-time polymerase chain reaction- array method. Furthermore, cell migration and wound healing assays were also applied. Results: It was found that 10 episodes of continuous hypoxia activated Warburg effect in MCF7 cells via the significant up-regulation of genes involved in glycolysis (ANOVA, p value < 0.05). The molecular changes were associated with the ability of MCF7 cells to divide and migrate. Interestingly, after 20 episodes of continuous hypoxia, the expression glycolysis mediated genes has dropped significantly (from 30 to 9 folds). This could be attributed to the adaptive ability of cancer cells. Conclusion: It is concluded that 10 hypoxic episodes increased the survival rate and the aggressiveness of MCF7 cells and induced Warburg effect by up-regulation of the glycolysis mediating genes expression.

scholarly journals 3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome

2020 ◽  
Vol 49 (D1) ◽  
pp. D38-D46
Author(s):  
Kyukwang Kim ◽  
Insu Jang ◽  
Mooyoung Kim ◽  
Jinhyuk Choi ◽  
Min-Seo Kim ◽  
...  
Keyword(s):  
Cell Line ◽  
Large Scale ◽  
Three Dimensional ◽  
Cancer Cell Line ◽  
Cancer Genome ◽  
Structural Variations ◽  
3D Genome ◽  
Tightly Coupled ◽  
Regulatory Effects ◽  
The Impact

Abstract Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (i) the collection of 401 samples including 220 cancer cell line/tumor Hi-C data, 153 normal cell line/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. ‘3DIV’ is freely available at http://3div.kr.

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