scholarly journals PRC2 activates interferon-stimulated genes indirectly by repressing miRNAs in glioblastoma

2019 ◽  
Author(s):  
Haridha Shivram ◽  
Steven V. Le ◽  
Vishwanath R. Iyer
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Anaplastic Astrocytoma ◽  
Gene Expression Analysis ◽  
Histone H3 ◽  
Chromatin Binding ◽  
Chromosome 14 ◽  
Methyltransferase Activity ◽  
Polycomb Repressive Complex 2 ◽  
Interferon Stimulated Genes

AbstractPolycomb repressive complex 2 (PRC2) is a chromatin binding complex that represses gene expression by methylating histone H3 at K27 to establish repressed chromatin domains. PRC2 can either regulate genes directly through the methyltransferase activity of its component EZH2 or indirectly by regulating other gene regulators. Gene expression analysis of glioblastoma (GBM) cells lacking EZH2 showed that PRC2 regulates hundreds of interferon-stimulated genes (ISGs). We found that PRC2 directly represses several ISGs and also indirectly activates a distinct set of ISGs. Assessment of EZH2 binding proximal to miRNAs showed that PRC2 directly represses miRNAs encoded in the chromosome 14 imprinted DLK1-DIO3 locus. We found that repression of this locus by PRC2 occurs in immortalized GBM-derived cell lines as well as in primary bulk tumors from GBM and anaplastic astrocytoma patients. Through repression of these miRNAs and several other miRNAs, PRC2 activates a set of ISGs that are targeted by these miRNAs. This PRC2-miRNA-ISG network is likely to be important in regulating gene expression programs in GBM.

Comprehensive gene expression analysis after ERH gene knockdown in human bladder cancer T24 cell lines

Gene ◽  
2020 ◽  
Vol 738 ◽  
pp. 144475
Author(s):  
Kun Pang ◽  
Lin Hao ◽  
Zhenduo Shi ◽  
Bo Chen ◽  
Huiqing Pang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bladder Cancer ◽  
Cell Lines ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Gene Knockdown ◽  
Human Bladder Cancer ◽  
Human Bladder

scholarly journals Sulforaphane modulates telomerase activity via epigenetic regulation in prostate cancer cell lines

2016 ◽  
Vol 94 (1) ◽  
pp. 71-81 ◽  
Author(s):  
Ata Abbas ◽  
J. Adam Hall ◽  
William L. Patterson ◽  
Emily Ho ◽  
Anna Hsu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cancer Cells ◽  
Cell Lines ◽  
Prostate Cancer Cell ◽  
Histone H3 ◽  
Htert Promoter ◽  
Prostate Cancer Cells ◽  
Inhibitor Activity ◽  
Prostate Cancer Cell Lines

Epidemiologic studies have revealed that diets rich in sulforaphane (SFN), an isothiocyanate present in cruciferous vegetables, are associated with a marked decrease in prostate cancer incidence. The chemo-preventive role of SFN is associated with its histone de-acetylase inhibitor activity. However, the effect of SFN on chromatin composition and dynamic folding, especially in relation to HDAC inhibitor activity, remains poorly understood. In this study, we found that SFN can inhibit the expression and activity of human telomerase reverse transcriptase (hTERT), the catalytic subunit of telomerase, in 2 prostate cancer cell lines. This decrease in gene expression is correlated with SFN-induced changes in chromatin structure and composition. The SFN-mediated changes in levels of histone post-translational modifications, more specifically acetylation of histone H3 lysine 18 and di-methylation of histone H3 lysine 4, 2 modifications linked with high risk of prostate cancer recurrence, were associated with regulatory elements within the hTERT promoter region. Chromatin condensation may also play a role in SFN-mediated hTERT repression, since expression and recruitment of MeCP2, a known chromatin compactor, were altered in SFN treated prostate cancer cells. Chromatin immuno-precipitation (ChIP) of MeCP2 showed enrichment over regions of the hTERT promoter with increased nucleosome density. These combined results strongly support a role for SFN in the mediation of epigenetic events leading to the repression of hTERT in prostate cancer cells. This ability of SFN to modify chromatin composition and structure associated with target gene expression provides a new model by which dietary phytochemicals may exert their chemoprevention activity.

Bortezomib Is Effective for Down Regulation of Gene Transcriptions Specifically Expressed in Clonogenic Myeloma Side Population Cells

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3939-3939
Author(s):  
Miho Nara ◽  
Hiroyuki Tagawa ◽  
Kazuaki Teshima ◽  
Atsushi Watanabe ◽  
Mitsugu Ito ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Cell Lines ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Kinase Inhibitor ◽  
Side Population ◽  
Aurora Kinase ◽  
Aurora Kinase B ◽  
Transporter Family

Abstract Abstract 3939 Background: Multiple myeloma (MM) is characterized by the accumulation of a population of malignant plasma cells within the bone marrow. Cytotoxic chemotherapy-based treatment is not curative, and the disease eventually recurs. Although currently available anti-MM strategies are effective at targeting the bulk of tumor cells, it is not clear that these agents are targeting the tumor-initiating subpopulation, or cancer stem cells. Side Population (SP) cells are an enriched source of cancer-initiating cells with stem cell properties, which have been identified in solid tumors, as well as in hematopoietic malignancies. SP cells express high levels of various members of the ABC transporter family, which are responsible for their drug resistance. A recent our work demonstrated that SP cells in MM have shown to exhibit stem cell like characteristics as well as high tumorigenicity. Therefore, it is worthy to identify gene/proteins specifically expressed in MM SP cells, which could be essential therapeutic targets. Purpose: The aim of this study was to identify genes and transcripts that could serve as molecular markers for targeting the MM SP cells, and to identify candidate agents for the MM SP cells. Experimental design: We used Hoechst 33342 dye to detect the MM SP in five MM cell lines (RPMI 8226, AMO1, KMS-12BM, KMS-11 and JJN3) and eight primary samples. We then tested whether the MM SP cells have stem-like characteristics and performed gene expression analysis to detect genes specifically expressed in the MM SP. On that basis, we tested candidate agents such as an aurora kinase inhibitor (VX-680), a histone methyltransferase inhibitor (DZNep), lenalidomide, thalidomide and a proteasome inhibitor (bortezomib) for their ability to target MM SP cells. Results: We found that clonogenic MM SP cells exhibit “stem cell-like” properties, including self renewal, differentiation and repopulation. Gene expression analysis of MM cell lines and primary samples revealed that, in SP cells, expression of genes related to G2/M phase (e.g. CDC2, CCNB1)-, microtubule attachment (e.g. BIRC5, CENPE, SKA1)-, mitosis or centrosomes (e.g. AURKB, KIF2C, KIF11, KIF15)-, proliferation (e.g. TOP2A, ASPM)-, polycomb (e.g. EZH2, EPC1)- and proteasomes(e.g. UBE2D3, UBE3C, PSMA5)- was significantly stronger in SP than non-SP cells. On that basis, we used VX-680, DZNep, lenalidomide, thalidomide and bortezomib against MM cells. Of these, bortezomib reduced the SP fraction most effectively due to its ability to reduce levels of target gene transcripts including phospho-histone H3, aurora kinase B and EZH2. Finally we tried to examine effects of those candidate agents to “clonogenic ability of SP”, and found that bortezomib possessed the most powerful effects for reduction of SP colonies. These results suggest that bortezomib has a broader range of targets than other agents and could include cell cycle, centrosome, polycomb and proteasome genes/proteins. Conclusion: Our findings are i) the first to identify genes specifically expressed in the MM SP, ii) the first to provide a rationale for treating MM using agents against genes and encoded proteins that are specifically expressed in MM SP cells. Disclosures: Iida: Janssen Pharmaceutical K.K.: Honoraria.

Gene expression analysis of toxicological pathways in TM3 leydig cell lines treated with Ethane dimethanesulfonate

2012 ◽  
Vol 26 (6) ◽  
pp. 213-223 ◽  
Author(s):  
Eun-Hee Lee ◽  
Jung-Hwa Oh ◽  
Young-Sook Lee ◽  
Han-Jin Park ◽  
Mi-Sun Choi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Expression Analysis ◽  
Leydig Cell ◽  
Gene Expression Analysis

scholarly journals JAZF1-SUZ12 dysregulates PRC2 function and gene expression during cell differentiation

2021 ◽  
Author(s):  
Manuel Tavares ◽  
Garima Khandelwal ◽  
Joanne Mutter ◽  
Keijo Viiri ◽  
Manuel Beltran ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Differentiation ◽  
Target Genes ◽  
Histone H3 ◽  
Endometrial Stromal Sarcoma ◽  
Cell Types ◽  
Polycomb Repressive Complex 2 ◽  
Stromal Sarcoma ◽  
N Terminus ◽  
Undifferentiated Cells

Polycomb repressive complex 2 (PRC2) methylates histone H3 lysine 27 (H3K27me3) to maintain repression of genes specific for other cell types and is essential for cell differentiation. In endometrial stromal sarcoma, the PRC2 subunit SUZ12 is often fused with the NuA4/TIP60 subunit JAZF1. Here, we show that JAZF1-SUZ12 dysregulates PRC2 composition, recruitment, histone modification, gene expression and cell differentiation. The loss of the SUZ12 N-terminus in the fusion protein disrupted interaction with the PRC2 accessory factors JARID2, EPOP and PALI1 and prevented recruitment of PRC2 from RNA to chromatin. In undifferentiated cells, JAZF1-SUZ12 occupied PRC2 target genes but gained a JAZF1-like binding profile during cell differentiation. JAZF1-SUZ12 reduced H3K27me3 and increased H4Kac at PRC2 target genes, and this was associated with disruption in gene expression and cell differentiation programs. These results reveal the defects in chromatin regulation caused by JAZF1-SUZ12, which may underlie its role in oncogenesis.

scholarly journals Genome Based Search for Reference Genes for Gene Expression Analysis in Oral Cancer: a Data Science Driven Approach

2019 ◽  
Author(s):  
Nehanjali Dwivedi ◽  
Sujan K Dhar ◽  
G Charitha ◽  
Moni Abraham Kuriakose ◽  
Amritha Suresh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Expression Analysis ◽  
Reference Genes ◽  
Data Science ◽  
Gene Expression Analysis ◽  
The Cancer Genome Atlas ◽  
Experimental Conditions ◽  
Statistical Measures ◽  
Different Types

Abstract Background Quantitative real time PCR (qPCR) remains by far the most cost-effective, fast yet sensitive technique to check the gene expression levels in various systems. The traditionally used reference genes over the years were found to be regulated heavily based on sample sources and/or experimental conditions. This paper therefore presents a data science driven -omic approach for selection of reference genes from ~60,000 candidates from The Cancer Genome Atlas (TCGA) and Broad Institute Cancer Cell Line Encyclopaedia (CCLE) for gene expression studies in head and neck squamous cell carcinoma (HNSCC). mRNA-sequencing data of 500 patient samples and 33 cell lines from publicly available databases were analysed to assess stability of genes in terms of multiple statistical measures. A final set of 12 candidate genes were studied in the Indian set of data in Gene Expression Omnibus (GEO) and validated experimentally using qPCR in 35 different types of samples from platforms like drug sensitive and resistant cell lines, normal and tumor samples, fibroblast and epithelial primary culture derived from HNSCC patients from India. Result The study lead to the choice of five most stable reference genes –TYW5, RIC8B, PLEKHA3, CEP57L1 and GPR89B across three experimental platforms. Conclusion In addition to providing a set of five most stable reference genes for future gene expression analysis experiments across different types of samples in HNSCC, the study also presents an objective framework for assessing reference genes for other disease areas as well.

Identification of regulatory pathways across different cell lines (NHBE and PBMC) in COVID-19 patients using transcriptome analysis v1

2021 ◽  
Author(s):  
Lavanya not provided C ◽  
Vidya Niranjan ◽  
Aajnaa not provided Upadhyaya ◽  
Arpita not provided Guha Neogi
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Cell Lines ◽  
Expression Analysis ◽  
Pathway Analysis ◽  
Gene Expression Analysis ◽  
Reference Genome ◽  
Host Cells ◽  
Human Reference Genome ◽  
Regulatory Pathways

The Sars-CoV-2 virus is a previously uncharacterized coronavirus and causative agent of the COVID-19 pandemic. Gene expression analysis followed by pathway analysis helps researchers to find possible key targets present in biological pathways of host cells that are targeted by the SARS-CoV-2 virus. This review considers the peripheral blood mononuclear cell line (PBMC) and the normal human bronchial epithelial (NHBE) cell line, both of which support SARS-CoV-2 viral replication. Pathway analysis between the healthy and patient samples of the respective cell lines shall provide useful insights on the COVID-19 disease. Initially, the datasets from the respective cell lines were collected from the NCBI databank. These datasets underwent further analysis and were mapped and aligned to the human reference genome. This outputs the file in the BAM format. The BAM files along with the human reference genome in the GFF format were uploaded to an open-source software called OmicsBox 2.0 for differential gene expression analysis. This resulted in the generation of a table containing the differentially expressed genes which were upregulated and downregulated. These gene lists were uploaded to various pathway analyzers that map the significant genes to the most significant pathways. In this project, KOBAS 3.0 and Enrichr were used for pathway analysis. The pathways obtained from the above-mentioned pathway analyzers were further narrowed down by manual comparison. It was observed that many pathways were similar between the NHBE and PBMC cell lines. However, they were also different in terms of their overall nature. In this project, many patterns were seen through the pathways obtained, however, further optimization and functionality studies must be performed in order to establish conclusive results on the scope of the COVID-19 disease. Expanding research on the scope of the disease by going back to the basics will generate new and valuable information about the virus. This knowledge will help us combat the disease in a better and appropriate manner.

Characterization of Targets of Plitidepsin In JAK2V617F-Mutated Cells From Myeloproliferative Neoplasms

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 4093-4093
Author(s):  
Paola Guglielmelli ◽  
Costanza Bogani ◽  
Niccolò Bartalucci ◽  
Lisa Pieri ◽  
Alessandro Pancrazzi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Signaling Pathway ◽  
Cell Lines ◽  
Western Blotting ◽  
Phase Ii ◽  
Protein Level ◽  
Gene Expression Analysis ◽  
Myeloproliferative Neoplasms ◽  
Receptor Interaction

Abstract Abstract 4093 Background: In a previous study (Verrucci M et al, J. Cell Physiol, 2010, Epub May10) we reported that the cyclic depsipeptide Aplidin®, a potent cytotoxic agent currently in phase II/III clinical trials for solid and hematologic neoplasia, displayed activity in a murine model of myelofibrosis, the GATA1-low mice. In fact, Aplidin improved the proliferation of Gata1-low hematopoietic cells, corrected abnormal microvessel density and reduced bone marrow fibrosis. These effects were largely attributed to improved maturation of megakaryocytes, as suggested by the increased platelet count in thrombocytopenic Gata1-low mice. It has been previously shown that a low expression of p27 in tumor cells might correlate with their response to Aplidin; of interest, GATA1-low megakaryocytes expressed reduced levels of p27. Overall, these results suggested that Aplidin could have the potential to alter the course of myelofibrosis-like disease in Gata1-low mice and could be useful for the treatment of myelofibrosis. Aims: to evaluate activity and targets of Aplidin in cellular models of myeloproliferative neoplasms (MPN). Methods: We measured the effect of Aplidin on the proliferation of JAK2V617F-mutated cell lines (UKE-1, HEL, SET2) and of primary cells from MPN patients in liquid cultures and semisolid medium, the rate of apoptosis using Annexin V flow cytometry analysis, and the cell cycle by propidium iodide staining. Expression of mRNA was quantified by real-time PCR, while protein level was measured by western blotting. Gene expression profiling was accomplished with Agilent Whole Human Genome Oligo Microarrays (44K). Results: Aplidin reduced the proliferation of all human V617F-mutated cell lines in the low nanomolar range, with IC50 from 0.5+/−0.03nM for UKE-1 to 1.5+/−0.05nM for HEL cells. Aplidin increased the proportion of cells in the G1/G0 phase of cell cycle, up to a mean of 80+/−5% from 60+/−3% in control cells (P<0.01). Also the proportion of apoptotic cells dose-dependently increased from 20+/−3% in control cultures to 50+/−6% at 10 nM in UKE-1 cells. After 24 h of incubation with Aplidin, the level of p27 mRNA was dose-dependently increased in all cell lines evaluated, while the BCR/ABL mutated K562 cells, whose proliferative rate was inhibited at higher Aplidin concentration, did not show significant changes of p27 mRNA. By western blotting analysis, level of p27 was overtly increased in UKE-1 cells treated with 5 and 10 nM Aplidin for 24h, and at the highest concentration we also observed reduction of phosphorylated STAT5. On the other hand, there was no change in JAK2, pJAK2, STAT5, STAT3, pSTAT3, Akt, pAkt. We then measured the level of p27 mRNA in peripheral blood cells obtained from patients with polycythemia vera (PV) or primary myelofibrosis (PMF). We found that PMF patients had significantly reduced p27 mRNA and protein level compared to controls and PV patients (P<.001 for both). After incubation with 1nM Aplidin there was a 2.5+/−2.0-fold increase in the p27 mRNA level and protein in cells of PMF patients while it was substantially unaffected in controls or PV patients. Gene expression analysis was performed in SET2 and UKE-1 cells that had been treated with 3nM of Aplidin for 24 hr. Aplidin treatment of SET2 cell line resulted in the up-regulation (UR) of 268 probsets and down-regulation (DR) of 247 (in total, about 1.5% of 40,961 genes called as “present”); corresponding figures in UKE-1 cells were 261 for UR (0.6%) and 364 (0.9%) for DR genes. MAPK signalling, TGF-beta signaling pathway, Cytokine-cytokine receptor interaction, cell adhesion molecules (CAMs), neuroactive ligand-receptor interaction, T cell receptor signaling, calcium signaling pathway, and regulation of actin cytoskeleton were the most involved pathways. Conclusions: Current results suggest that Aplidin has growth inhibitory activity and induces apoptosis in MPN cells. Response to Aplidin involves increasing p27 level, similar to findings in myelofibrotic GATA1-low mice; furthermore, we have identified low p27 expression as a characteristic of PMF cells compared to normal and PV cells. Finally, gene expression analysis allowed to identify a set of genes and involved pathways undergoing differential regulation in response to Aplidin. These information could be of value also for analyzing the response to Aplidin of PMF patients enrolled in an ongoing Phase II clinical trial. Disclosures: Aracil: PharmaMar: Employment. Vannucchi:PharmaMar: Research Funding.

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