scholarly journals Promoter Demethylation Upregulates STEAP1 Gene Expression in Human Prostate Cancer: and In Silico Analysis

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1251
Author(s):  
Sandra M. Rocha ◽  
Inês Sousa ◽  
Inês M. Gomes ◽  
Patrícia Arinto ◽  
Pedro Costa-Pinheiro ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Mrna Expression ◽  
Cpg Island ◽  
Expression Patterns ◽  
Hdac Inhibitors ◽  
Gene Promoter ◽  
In Silico Analysis ◽  
Amplicon Sequencing ◽  
Negative Association

The Six Transmembrane Epithelial Antigen of the Prostate (STEAP1) is an oncogene overexpressed in several human tumors, particularly in prostate cancer (PCa). However, the mechanisms involved in its overexpression remain unknown. It is well known that epigenetic modifications may result in abnormal gene expression patterns, contributing to tumor initiation and progression. Therefore, this study aimed to analyze the methylation pattern of the STEAP1 gene in PCa versus non-neoplastic cells. Bisulfite amplicon sequencing of the CpG island at the STEAP1 gene promoter showed a higher methylation level in non-neoplastic PNT1A prostate cells than in human PCa samples. Bioinformatic analysis of the GEO datasets also showed the STEAP1 gene promoter as being demethylated in human PCa, and a negative association with STEAP1 mRNA expression was observed. These results are supported by the treatment of non-neoplastic PNT1A cells with DNMT and HDAC inhibitors, which induced a significant increase in STEAP1 mRNA expression. In addition, the involvement of HDAC in the regulation of STEAP1 mRNA expression was corroborated by a negative association between STEAP1 mRNA expression and HDAC4,5,7 and 9 in human PCa. In conclusion, our work indicates that STEAP1 overexpression in PCa can be driven by the hypomethylation of STEAP1 gene promoter.

scholarly journals High-Throughput Screening for CEBPD-Modulating Compounds in THP-1-Derived Reporter Macrophages Identifies Anti-Inflammatory HDAC and BET Inhibitors

2021 ◽  
Vol 22 (6) ◽  
pp. 3022
Author(s):  
Tatjana Ullmann ◽  
Sonja Luckhardt ◽  
Markus Wolf ◽  
Michael J. Parnham ◽  
Eduard Resch
Keyword(s):  
Gene Expression ◽  
Mrna Expression ◽  
High Throughput ◽  
Transcription Initiation ◽  
High Throughput Screening ◽  
Inflammatory Responses ◽  
Hdac Inhibitors ◽  
Screening Assay ◽  
Bet Inhibitors ◽  
Anti Inflammatory

This study aimed to identify alternative anti-inflammatory compounds that modulate the activity of a relevant transcription factor, CCAAT/enhancer binding protein delta (C/EBPδ). C/EBPδ is a master regulator of inflammatory responses in macrophages (Mϕ) and is mainly regulated at the level of CEBPD gene transcription initiation. To screen for CEBPD-modulating compounds, we generated a THP-1-derived reporter cell line stably expressing secreted alkaline phosphatase (SEAP) under control of the defined CEBPD promoter (CEBPD::SEAP). A high-throughput screening of LOPAC®1280 and ENZO®774 libraries on LPS- and IFN-γ-activated THP-1 reporter Mϕ identified four epigenetically active hits: two bromodomain and extraterminal domain (BET) inhibitors, I-BET151 and Ro 11-1464, as well as two histone deacetylase (HDAC) inhibitors, SAHA and TSA. All four hits markedly and reproducibly upregulated SEAP secretion and CEBPD::SEAP mRNA expression, confirming screening assay reliability. Whereas BET inhibitors also upregulated the mRNA expression of the endogenous CEBPD, HDAC inhibitors completely abolished it. All hits displayed anti-inflammatory activity through the suppression of IL-6 and CCL2 gene expression. However, I-BET151 and HDAC inhibitors simultaneously upregulated the mRNA expression of pro-inflammatory IL-1ß. The modulation of CEBPD gene expression shown in this study contributes to our understanding of inflammatory responses in Mϕ and may offer an approach to therapy for inflammation-driven disorders.

scholarly journals Global Histone H3 Lysine 4 Trimethylation (H3K4me3) Landscape Changes in Response to TGFβ

2021 ◽  
Vol 14 ◽  
pp. 251686572110517
Author(s):  
Ankit Naik ◽  
Nidhi Dalpatraj ◽  
Noopur Thakur
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Expression Patterns ◽  
Histone H3 ◽  
Epigenetic Mechanism ◽  
Stable Gene ◽  
Regulation Of Transcription ◽  
Functional Categories ◽  
Positive Regulation ◽  
Histone H4 Acetylation

TGFβ expression acts as a biomarker of poor prognosis in prostate cancer. It plays a dual functional role in prostate cancer. In the early stages of the tumor, it acts as a tumor suppressor while at the later stages of tumor development, it promotes metastasis. The molecular mechanisms of action of TGFβ are largely understood through the canonical and non-canonical signal transduction pathways. Our understanding of the mechanisms that establish transient TGFβ stimulation into stable gene expression patterns remains incomplete. Epigenetic marks like histone H3 modifications are directly linked with gene expression and they play an important role in tumorigenesis. In this report, we performed chromatin immunoprecipitation-sequencing (ChIP-Seq) to identify the genome-wide regions that undergo changes in histone H3 Lysine 4 trimethylation (H3K4me3) occupancy in response to TGFβ stimulation. We also show that TGFβ stimulation can induce acute epigenetic changes through the modulation of H3K4me3 signals at genes belonging to special functional categories in prostate cancer. TGFβ induces the H3K4me3 on its own ligands like TGFβ, GDF1, INHBB, GDF3, GDF6, BMP5 suggesting a positive feedback loop. The majority of genes were found to be involved in the positive regulation of transcription from the RNA polymerase II promoter in response to TGFβ. Other functional categories were intracellular protein transport, brain development, EMT, angiogenesis, antigen processing, antigen presentation via MHC class II, lipid transport, embryo development, histone H4 acetylation, positive regulation of cell cycle arrest, and genes involved in mitotic G2 DNA damage checkpoints. Our results link TGFβ stimulation to acute changes in gene expression through an epigenetic mechanism. These findings have broader implications on epigenetic bases of acute gene expression changes caused by growth factor stimulation.

scholarly journals Early Response of CD8+ T Cells in COVID-19 Patients

2021 ◽  
Vol 11 (12) ◽  
pp. 1291
Author(s):  
Deni Ramljak ◽  
Martina Vukoja ◽  
Marina Curlin ◽  
Katarina Vukojevic ◽  
Maja Barbaric ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
T Cells ◽  
Mrna Expression ◽  
Cd8 T Cells ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Effector Memory ◽  
Healthy Controls ◽  
Ifn Γ

Healthy and controlled immune response in COVID-19 is crucial for mild forms of the disease. Although CD8+ T cells play important role in this response, there is still a lack of studies showing the gene expression profiles in those cells at the beginning of the disease as potential predictors of more severe forms after the first week. We investigated a proportion of different subpopulations of CD8+ T cells and their gene expression patterns for cytotoxic proteins (perforin-1 (PRF1), granulysin (GNLY), granzyme B (GZMB), granzyme A (GZMA), granzyme K (GZMK)), cytokine interferon-γ (IFN-γ), and apoptotic protein Fas ligand (FASL) in CD8+ T cells from peripheral blood in first weeks of SARS-CoV-2 infection. Sixteen COVID-19 patients and nine healthy controls were included. The absolute counts of total lymphocytes (p = 0.007), CD3+ (p = 0.05), and CD8+ T cells (p = 0.01) in COVID-19 patients were significantly decreased compared to healthy controls. In COVID-19 patients in CD8+ T cell compartment, we observed lower frequency effector memory 1 (EM1) (p = 0.06) and effector memory 4 (EM4) (p < 0.001) CD8+ T cells. Higher mRNA expression of PRF1 (p = 0.05) and lower mRNA expression of FASL (p = 0.05) at the fifth day of the disease were found in COVID-19 patients compared to healthy controls. mRNA expression of PRF1 (p < 0.001) and IFN-γ (p < 0.001) was significantly downregulated in the first week of disease in COVID-19 patients who progressed to moderate and severe forms after the first week, compared to patients with mild symptoms during the entire disease course. GZMK (p < 0.01) and FASL (p < 0.01) mRNA expression was downregulated in all COVID-19 patients compared to healthy controls. Our results can lead to a better understanding of the inappropriate immune response of CD8+ T cells in SARS-CoV2 with the faster progression of the disease.

scholarly journals Protein structure-based gene expression signatures

2020 ◽  
Author(s):  
R. Rahman ◽  
Y. Xiong ◽  
J. G. C. van Hasselt ◽  
J. Hansen ◽  
E. A. Sobie ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Structure ◽  
Mrna Expression ◽  
Expression Patterns ◽  
Drug Effects ◽  
Tissue Expression ◽  
Structural Features ◽  
Biological Phenomena ◽  
Gene Expression Signatures ◽  
Cellular Phenotypes

AbstractGene expression signatures (GES) connect phenotypes to mRNA expression patterns, providing a powerful approach to define cellular identity, function, and the effects of perturbations. However, the use of GES has suffered from vague assessment criteria and limited reproducibility. The structure of proteins defines the functional capability of genes, and hence, we hypothesized that enrichment of structural features could be a generalizable representation of gene sets. We derive structural gene expression signatures (sGES) using features from various levels of protein structure (e.g. domain, fold) encoded by the transcribed genes in GES, to describe cellular phenotypes. Comprehensive analyses of data from the Genotype-Tissue Expression Project (GTEx), ARCHS4, and mRNA expression of drug effects on cardiomyocytes show that structural GES (sGES) are useful for identifying robust signatures of biological phenomena. sGES also enables the characterization of signatures across experimental platforms, facilitates the interoperability of expression datasets, and can describe drug action on cells.

In Silico Analysis of the CST6 Tumor Suppressor Gene

2013 ◽  
Vol 2 (3) ◽  
pp. 42-58
Author(s):  
Athanasia Pavlopoulou ◽  
Georgios Tsaramirsis
Keyword(s):  
Tumor Suppressor ◽  
Splice Variants ◽  
Cpg Island ◽  
Mammalian Species ◽  
Gene Promoter ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Suppressor Gene ◽  
Differentially Expressed ◽  
Gene Encoding

The gene encoding cystatin E/M, CST6, is a Class II tumor suppressor. Using bioinformatics tools for database mining and virtual gene expression profiling, the authors showed that CST6 is differentially expressed in various types of cancer. Moreover, epigenetic silencing mediated by hypermethylation of the CpG island located at the CST6 promoter was found to be conserved in mammalian species. Comprehensive analyses of animal genomes led to the identification of novel CST6 transcript orthologs and splice variants that enabled us to trace the evolutionary origin of CST6. Moreover, eight novel and potentially regulatory SNPs were identified in CST6 gene. Conserved cancer-relevant regulatory elements were identified in the CST6 gene promoter. In addition, miRNAs that are differentially expressed in human cancers were identified as putative posttranscriptional regulators of CST6. Collectively, the authors suggest that expression of CST6 in normal and cancer cells is coordinately regulated by genomic, transcriptional and post-transcriptional mechanisms.

Gene set based systematic analysis of prostate cancer and its subtypes

2020 ◽  
Vol 16 (2) ◽  
pp. 4381-4393
Author(s):  
Senlin Ye ◽  
Haohui Wang ◽  
Kancheng He ◽  
Hongwei Shen ◽  
Mou Peng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Expression Patterns ◽  
Methylation Status ◽  
Gene Expression Patterns ◽  
Biological Functions ◽  
Systematic Analysis ◽  
Gene Set ◽  
Analysis Strategy ◽  
Similarities And Differences

Aim: A gene set based systematic analysis strategy is used to investigate prostate tumors and its subclusters with focuses on similarities and differences of biological functions. Results: Dysregulation of methylation status, as well as RAS/RAF/ERK and PI3K-ATK signaling pathways, were found to be the most dramatic changes during prostate cancer tumorigenesis. Besides, neural and inflammation microenvironment is also significantly divergent between tumor and adjacent tissues. Insights of subclasses within prostate tumor cohorts revealed four different clusters with distinct gene expression patterns. We found that samples are mainly clustered by immune environments and proliferation traits. Conclusion: The findings of this article may help to advance the progress of identifying better diagnosis biomarkers and therapeutic targets.

scholarly journals Silencing of MBD1 and MeCP2 in prostate-cancer-derived PC3 cells produces differential gene expression profiles and cellular phenotypes

2008 ◽  
Vol 28 (6) ◽  
pp. 319-326 ◽  
Author(s):  
Ahmed Yaqinuddin ◽  
Farhat Abbas ◽  
Syed Z. Naqvi ◽  
Mohammad U. Bashir ◽  
Romena Qazi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Mrna Expression ◽  
Cellular Proliferation ◽  
Expression Profiles ◽  
Boyden Chamber ◽  
Invasion And Migration ◽  
Pc3 Cells ◽  
And Migration

Alterations in genomic CpG methylation patterns have been found to be associated with cell transformation and neoplasia. Although it is recognized that methylation of CpG residues negatively regulates gene expression, how the various MBPs (methyl-binding proteins) contribute to this process remains elusive. To determine whether the two well characterized proteins MeCP2 (methyl-CpG-binding protein 2) and MBD1 (methyl-CpG-binding domain 1) have distinct or redundant functions, we employed RNAi (RNA interference) to silence their expression in the prostate cancer-derived PC3 cell line, and subsequently compared cell growth, invasion and migration properties of these cell lines in addition to their respective mRNA-expression profiles. Cells devoid of MeCP2 proliferated more poorly compared with MBD1-deficient cells and the parental PC3 cells. Enhanced apoptosis was observed in MeCP2-deficient cells, whereas apoptosis in parental and MBD1-deficient cells appeared to be equivalent. Boyden chamber invasion and wound-healing migration assays showed that MBD1-silenced cells were both more invasive and migratory compared with MeCP2-silenced cells. Finally, gene chip microarray analyses showed striking differences in the mRNA-expression profiles obtained from MeCP2- and MBD1-depleted cells relative to each other as well as when compared with control cells. The results of the present study suggest that MeCP2 and MBD1 silencing appear to affect cellular processes independently in vivo and that discrete sets of genes involved in cellular proliferation, apoptosis, invasion and migration are targeted by each protein.

Correlation of messenger RNA expression patterns of ERCC1, TS, EGFR, and VEGFR2 with KRAS and BRAF mutational status in advanced colorectal cancer: Implications for targeted therapies.

2013 ◽  
Vol 31 (4_suppl) ◽  
pp. 383-383
Author(s):  
Martin K. H. Maus ◽  
Craig Stephens ◽  
Stephanie H. Astrow ◽  
Peter Philipp Grimminger ◽  
Dongyun Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Mrna Expression ◽  
Advanced Colorectal Cancer ◽  
Expression Patterns ◽  
Mrna Levels ◽  
Expression Levels ◽  
Mutational Status ◽  
Mrna Expression Levels ◽  
Gene Expression Levels

383 Background: Gene expression levels of ERCC1, TS, EGFR and VEGFR2 may have predictive value for the personalized use of standard chemotherapeutics as well as agents targeting the EGFR and VEGF pathways and the efficacy of EGFR directed monoclonal antibodies like panitumumab and cetuximab has been confirmed to be dependent on wt KRAS and wt BRAF in patients with advanced colorectal cancer. We investigated the correlations between KRAS/BRAF mutational status and the mRNA expression levels of these genes. Methods: Formalin-fixed paraffin-embedded tumor specimens from 600 patients with advanced colorectal adenocarcinoma were microdissected and DNA and RNA was extracted. Specifically designed primers and probes were used to detect 7 different base substitutions in codon 12 and 13 of KRAS, V600E mutations in BRAF and the expression levels of ERCC1, TS, EGFR and VEGFR2 by RT-PCR. Results: Mt KRAS tumors had significantly lower TS and EGFR gene expression levels compared with wt KRAS (p<0,001), whereas mt BRAF tumors showed significantly increased TS and EGFR mRNA levels compared to wt BRAF (p<0,001). Mt BRAF tumors showed significantly higher mRNA levels than mt KRAS tumors (p<0,001). ERCC1 and VEGFR2 mRNA levels were significantly down-regulated in mt KRAS specimen (p<0,001), but showed no significant correlation with BRAF mutational status. Conclusions: KRAS and BRAF mutations are associated with opposite mRNA expression levels for TS and EGFR. Recently, resistance to BRAF inhibition in mt BRAF colorectal tumors has been shown in preclinical models to be associated with up-regulation of EGFR. Our data suggests that BRAF mutants are associated with high EGFR levels at the time of diagnosis, and not necessarily part of an acquired mechanism of resistance. Significantly lower mRNA expression levels of VEGFR2 in mt KRAS tumors may explain lower response to angiogenesis inhibition seen in the TML study.

scholarly journals Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Xin Du ◽  
Leng Han ◽  
An-Yuan Guo ◽  
Zhongming Zhao
Keyword(s):  
Gene Expression ◽  
Methylation Level ◽  
Cpg Island ◽  
Expression Patterns ◽  
Cpg Islands ◽  
Gc Content ◽  
Gene Markers ◽  
A Genome ◽  
Genome Level ◽  
Lower Ratio

CpG islands are typically located in the 5′end of genes and considered as gene markers because they play important roles in gene regulation via epigenetic change. In this study, we compared the features of CpG islands identified by several major algorithms by setting the parameter cutoff values in order to obtain a similar number of CpG islands in a genome. This approach allows us to systematically compare the methylation and gene expression patterns in the identified CpG islands. We found that Takai and Jones’ algorithm tends to identify longer CpG islands but with weaker CpG island features (e.g., lower GC content and lower ratio of the observed over expected CpGs) and higher methylation level. Conversely, the CpG clusters identified by Hackenberg et al.’s algorithm using stringent criteria are shorter and have stronger features and lower methylation level. In addition, we used the genome-wide base-resolution methylation profile in two cell lines to show that genes with a lower methylation level at the promoter-associated CpG islands tend to express in more tissues and have stronger expression. Our results validated that the DNA methylation of promoter-associated CpG islands suppresses gene expression at the genome level.

Sign in / Sign up

Export Citation Format

Share Document