scholarly journals Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to Oesophageal Adenocarcinoma

2020 ◽  
Author(s):  
Connor Rogerson ◽  
Samuel Ogden ◽  
Edward Britton ◽  
Yeng Ang ◽  
Andrew D. Sharrocks ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Prognostic Significance ◽  
Gene Expression Signature ◽  
Chromatin Accessibility ◽  
Oesophageal Adenocarcinoma ◽  
Cell Cycle Gene ◽  
A Cell

AbstractOesophageal adenocarcinoma (OAC) is one of the most common causes of cancer deaths and yet compared to other common cancers, we know relatively little about the underlying molecular mechanisms. Barrett’s oesophagus (BO) is the only known precancerous precursor to OAC, but our understanding about the specific events leading to OAC development is limited. Here, we have integrated gene expression and chromatin accessibility profiles of human biopsies of BO and OAC and identified a strong cell cycle gene expression signature in OAC compared to BO. Through analysing associated chromatin accessibility changes, we have implicated the transcription factor KLF5 in the transition from BO to OAC. Importantly, we show that KLF5 expression is unchanged during this transition, but instead, KLF5 is redistributed across chromatin in OAC cells to directly regulate cell cycle genes specifically in OAC. Our findings have potential prognostic significance as the survival of patients with high expression of KLF5 target genes is significantly lower. We have provided new insights into the gene expression networks in OAC and the mechanisms behind progression to OAC, chiefly the repurposing of KLF5 for novel regulatory activity in OAC.

scholarly journals Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Connor Rogerson ◽  
Samuel Ogden ◽  
Edward Britton ◽  
Yeng Ang ◽  
Andrew D Sharrocks ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Prognostic Significance ◽  
Gene Expression Signature ◽  
Chromatin Accessibility ◽  
Oesophageal Adenocarcinoma ◽  
Cell Cycle Gene ◽  
Molecular Events ◽  
Common Causes ◽  
A Cell

Oesophageal adenocarcinoma (OAC) is one of the most common causes of cancer deaths. Barrett’s oesophagus (BO) is the only known precancerous precursor to OAC, but our understanding about the molecular events leading to OAC development is limited. Here, we have integrated gene expression and chromatin accessibility profiles of human biopsies and identified a strong cell cycle gene expression signature in OAC compared to BO. Through analysing associated chromatin accessibility changes, we have implicated the transcription factor KLF5 in the transition from BO to OAC. Importantly, we show that KLF5 expression is unchanged during this transition, but instead, KLF5 is redistributed across chromatin to directly regulate cell cycle genes specifically in OAC cells. This new KLF5 target gene programme has potential prognostic significance as high levels correlate with poorer patient survival. Thus, the repurposing of KLF5 for novel regulatory activity in OAC provides new insights into the mechanisms behind disease progression.

scholarly journals Oncogenic B-Myb Is Associated With Deregulation of the DREAM-Mediated Cell Cycle Gene Expression Program in High Grade Serous Ovarian Carcinoma Clinical Tumor Samples

2021 ◽  
Vol 11 ◽  
Author(s):  
Audra N. Iness ◽  
Lisa Rubinsak ◽  
Steven J. Meas ◽  
Jessica Chaoul ◽  
Sadia Sayeed ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Ovarian Carcinoma ◽  
Treatment Response ◽  
Target Genes ◽  
Gene Expression Signature ◽  
Cell Cycle Gene ◽  
High Grade ◽  
Serous Ovarian Carcinoma ◽  
Cell Cycle Gene Expression

Cell cycle control drives cancer progression and treatment response in high grade serous ovarian carcinoma (HGSOC). MYBL2 (encoding B-Myb), an oncogene with prognostic significance in several cancers, is highly expressed in most HGSOC cases; however, the clinical significance of B-Myb in this disease has not been well-characterized. B-Myb is associated with cell proliferation through formation of the MMB (Myb and MuvB core) protein complex required for transcription of mitotic genes. High B-Myb expression disrupts the formation of another transcriptional cell cycle regulatory complex involving the MuvB core, DREAM (DP, RB-like, E2F, and MuvB), in human cell lines. DREAM coordinates cell cycle dependent gene expression by repressing over 800 cell cycle genes in G0/G1. Here, we take a bioinformatics approach to further evaluate the effect of B-Myb expression on DREAM target genes in HGSOC and validate our cellular model with clinical specimens. We show that MYBL2 is highly expressed in HGSOC and correlates with expression of DREAM and MMB target genes in both The Cancer Genome Atlas (TCGA) as well as independent analyses of HGSOC primary tumors (N = 52). High B-Myb expression was also associated with poor overall survival in the TCGA cohort and analysis by a DREAM target gene expression signature yielded a negative impact on survival. Together, our data support the conclusion that high expression of MYBL2 is associated with deregulation of DREAM/MMB-mediated cell cycle gene expression programs in HGSOC and may serve as a prognostic factor independent of its cell cycle role. This provides rationale for further, larger scale studies aimed to determine the clinical predictive value of the B-Myb gene expression signature for treatment response as well as patient outcomes.

scholarly journals Identification of Core Genes Related to Progression and Prognosis of Hepatocellular Carcinoma and Small-Molecule Drug Predication

2021 ◽  
Vol 12 ◽  
Author(s):  
Nan Jiang ◽  
Xinzhuo Zhang ◽  
Dalian Qin ◽  
Jing Yang ◽  
Anguo Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Cell Cycle ◽  
Small Molecule ◽  
Molecular Mechanisms ◽  
Cox Regression ◽  
Disease Free Survival ◽  
Gene Expression Signature ◽  
Cox Regression Analysis ◽  
Small Molecule Drugs

BackgroundHepatocellular carcinoma (HCC) is one of the most leading causes of cancer death with a poor prognosis. However, the underlying molecular mechanisms are largely unclear, and effective treatment for it is limited. Using an integrated bioinformatics method, the present study aimed to identify the key candidate prognostic genes that are involved in HCC development and identify small-molecule drugs with treatment potential.Methods and ResultsIn this study, by using three expression profile datasets from Gene Expression Omnibus database, 1,704 differentially expressed genes were identified, including 671 upregulated and 1,033 downregulated genes. Then, weighted co-expression network analysis revealed nine modules are related with pathological stage; turquoise module was the most associated module. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analyses (KEGG) indicated that these genes were enriched in cell division, cell cycle, and metabolic related pathways. Furthermore, by analyzing the turquoise module, 22 genes were identified as hub genes. Based on HCC data from gene expression profiling interactive analysis (GEPIA) database, nine genes associated with progression and prognosis of HCC were screened, including ANLN, BIRC5, BUB1B, CDC20, CDCA5, CDK1, NCAPG, NEK2, and TOP2A. According to the Human Protein Atlas and the Oncomine database, these genes were highly upregulated in HCC tumor samples. Moreover, multivariate Cox regression analysis showed that the risk score based on the gene expression signature of these nine genes was an independent prognostic factor for overall survival and disease-free survival in HCC patients. In addition, the candidate small-molecule drugs for HCC were identified by the CMap database.ConclusionIn conclusion, the nine key gene signatures related to HCC progression and prognosis were identified and validated. The cell cycle pathway was the core pathway enriched with these key genes. Moreover, several candidate molecule drugs were identified, providing insights into novel therapeutic approaches for HCC.

scholarly journals Identification of a Gene Signature Associated to Treatment Response to Palbociclib in Multiple Myeloma

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5666-5666
Author(s):  
Angelique Bruyer ◽  
Alboukadel Kassambara ◽  
Paul Anziani ◽  
Donia El Bahlagui ◽  
Nicolas Robert ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Multiple Myeloma ◽  
Rna Sequencing ◽  
Cell Lines ◽  
Molecular Mechanisms ◽  
Conflicts Of Interest ◽  
Gene Expression Signature ◽  
G1 Arrest ◽  
Expression Signature

Abstract Background: Inpatients with relaspsed/refractoryMultiple Myeloma (MM), outcomes are far from optimal, especially in patients refractory to current treatments Recent studies and clinical trials have highlighted the therapeutic potential of Palbociclib, a CDK4/6 inhibitor, in various cancers including MM. Deregulation of CDK4/6 is involved in the loss of cell cycle control in MM. Response to Palbociclib combined with bortezomib and dexamethasone was acquired in 20% of the relapsed/refractory MM patients, suggesting that biomarkers to identify patients that could benefit from this treatment are needed. Additional studies are required to understand the biological pathways associated with sensitivity or resistance of MM cells to Palbociclib. Methods: 14 human MM cell lines and 12 primary MM samples were tested for response to Palbociclib treatment. The concentration required to inhibit growth by 50% (IC50) was calculated. Gene expression signature associated with multiple myeloma response to Palbociclib, as well as, genes deregulated by the treatment have been analyzed using microarray and RNA-sequencing methods. Results: Palbociclib had an heterogeneous in vitro activity among the 14 human myeloma cell lines tested, which aggregated into three groups based on the distribution of the IC50 values: sensitive (n = 5, IC50: 0.2 - 0.3µM), intermediate (n = 3, IC50: 0.5 - 0.7µM) or more resistant group (n = 6, IC50: 0.9 - 2.4µM). The same holds true when testing the Palbociclib on primary multiple myeloma samples. The evaluation of the Palbociclib effect on cell cycle progression and the induction of the apoptosis, reveals that Palbociclib is essentially cytostatic, inducing prolonged G1 arrest in sensitive cell lines with a strong reduction of the percentage of cells in S phase. To better understand the molecular mechanisms associated with Palbociclib response, we identified a gene expression signature correlated with the response in both MM cell lines and primary myeloma cells from patients. Additionally, we have analyzed differentially expressed genes after Palbociclib treatment in human MM cell lines using RNA sequencing (n = 4). The physiological role of the downregulated genes after Palbociclib treatment is associated with cell cycle, mitosis and E2F mediated regulation of DNA replication. Significantly upregulated genes, after Palbociclib treatment, were enriched in genes encoding proteins involved in glutathione synthesis and recycling, and biological oxidations. Conclusion: Altogether, our data demonstrated a high heterogeneity in the response of MM cells to Palbociclib. We identified a gene expression signature associated with Palbociclib response in MM. These genes could help to identify MM patients that could benefit from Palbociclib treatment and provide novel targets for efficient combination therapy. Disclosures No relevant conflicts of interest to declare.

scholarly journals The coordination of terminal differentiation and cell cycle exit is mediated through the regulation of chromatin accessibility

2018 ◽  
Author(s):  
Yiqin Ma ◽  
Daniel J McKay ◽  
Laura Buttitta
Keyword(s):  
Cell Cycle ◽  
Terminal Differentiation ◽  
Chromatin Accessibility ◽  
Cell Cycle Gene ◽  
Cell Cycle Regulators ◽  
Cell Cycle Exit ◽  
Cell Cycle Genes ◽  
Repressor Complex ◽  
Pupal Wing ◽  
A Cell

During terminal differentiation most cells will exit the cell cycle and enter into a prolonged or permanent G0. Cell cycle exit is usually initiated through the repression of cell cycle gene expression by formation of a transcriptional repressor complex called DREAM. However when DREAM repressive function is compromised during terminal differentiation, additional unknown mechanisms act to stably repress cycling and ensure robust cell cycle exit. Here we provide evidence that developmentally programmed, temporal changes in chromatin accessibility at a subset of critical cell cycle genes acts to enforce cell cycle exit during terminal differentiation in the Drosophila melanogaster wing. We show that during terminal differentiation, chromatin closes at a set of pupal wing enhancers for the key rate-limiting cell cycle regulators cycE, e2f1 and stg. This closing coincides with wing cells entering a robust postmitotic state that is strongly refractory to cell cycle re-activation. When cell cycle exit is genetically disrupted, chromatin accessibility at cell cycle genes remains largely unaffected and the closing of enhancers at cycE, e2f1 and stg proceeds independent of the cell cycling status. Instead, disruption of cell cycle exit leads to changes in accessibility and expression of a subset of hormone-induced transcription factors involved in the progression of terminal differentiation. Our results uncover a mechanism that acts as a cell cycle-independent timer to limit aberrant cycling in terminally differentiating tissues. In addition, we provide a new molecular description of the cross-talk between cell cycle exit and terminal differentiation during metamorphosis.

scholarly journals Visualization and sequencing of accessible chromatin reveals cell cycle and post romidepsin treatment dynamics

2020 ◽  
Author(s):  
Pierre-Olivier Estève ◽  
Udayakumar S. Vishnu ◽  
Hang Gyeong Chin ◽  
Sriharsa Pradhan
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Histone Deacetylases ◽  
Mammalian Cells ◽  
Chromatin Accessibility ◽  
Cell Type Specificity ◽  
Myc Oncogene ◽  
Genome Wide ◽  
A Cell ◽  
Accessible Chromatin

AbstractChromatin accessibility is a predictor of gene expression, cell division and cell type specificity. NicE-viewSeq (Nicking Enzyme assisted viewing and Sequencing) allows accessible chromatin visualization and sequencing with overall lower mitochondrial DNA and duplicated sequences interference relative to ATAC-see. Using NicE-viewSeq, we interrogated the accessibility of chromatin in a cell cycle (G1, S and G2/M) - specific manner using mammalian cells. Despite DNA replication and subsequent condensation of chromatin to chromosomes, chromatin accessibility remained generally preserved with minimal subtle alterations. Genome-wide alteration of chromatin accessibility within TSS and enhancer elements gradually decreased as cells progressed from G1 to G2M, with distinct differential accessibility near consensus transcription factors sites. Inhibition of histone deacetylases promoted accessible chromatin within gene bodies, correlating with apoptotic gene expression. In addition, reduced chromatin accessibility for the MYC oncogene pathway correlated with down regulation of pertinent genes. Surprisingly, repetitive RNA loci expression remained unaltered following histone acetylation-mediated increased accessibility. Therefore, we suggest that subtle changes in chromatin accessibility is a prerequisite during cell cycle and histone deacetylase inhibitor mediated therapeutics.

824 MOLECULAR UNDERPINNINGS OF NEUROENDOCRINE DIFFERENTIATION IN ESOPHAGEAL ADENOCARCINOMA AND ITS PROGNOSTIC SIGNIFICANCE

2021 ◽  
Vol 34 (Supplement_1) ◽  
Author(s):  
G Wilson ◽  
E Elimova ◽  
J Yeung ◽  
G Darling ◽  
S N Kalimuthu
Keyword(s):  
Gene Expression ◽  
Esophageal Adenocarcinoma ◽  
Molecular Mechanisms ◽  
Prognostic Significance ◽  
Neuroendocrine Differentiation ◽  
Gene Expression Signature ◽  
Gene Signature ◽  
Ordinary Least Squares ◽  
Least Squares Regression ◽  
Morphological Pattern

Abstract   The presence of neuroendocrine (NE) differentiation has been previously reported in both morphological subtypes, (intestinal and diffuse), of esophageal adenocarcinoma, (EAC). This is more commonly seen in the post-treatment setting and is thought to confer a more aggressive phenotype. However, the molecular underpinning and therapeutic implications of NE differentiation within EAC is poorly understood. Herein, the goal is to understand the molecular mechanisms, evolution and the prognostic significance of NE development in EAC tumours. Methods We interrogated a previously published transcriptome dataset with matched H&E slides, TCGA EAC (N = 86). Moreover, we have begun reviewing H&E slides from EAC patients from UHN (N = 50). We created a NE gene expression signature (N = 25 genes) from the literature as an initial proof of concept. We quantified the presence of a NET-like/organoid morphology in the matched H&E slides and correlated it with the average z-score of the NE gene signature calculated from the matched transcriptome data. Results NE differentiation was present in 27/86 cases with a mean of 21.01% +/− 20.9 within the tumour area. We compared the expression of our NE gene signature with the proportion of NE morphology and observed a moderate correlation between morphology with the gene expression (R^2 = 0.546, P < 0.001 ordinary least squares regression), providing validation that the organoid/NET-like morphological pattern correlates with NE differentiation. Furthermore, we have validated the presence of NE morphology in a subset of the UHN samples using electron microscopy and immunohistochemistry (chromogranin and synaptophysin). Conclusion This is a first of a kind study to profile a specific morphology with a transcriptional signature within EAC across a large cohort of patient samples. Correlation of NE-features with clinical outcome together with treatment resistant implications is currently underway.

scholarly journals Yeast cell cycle protein CDC48p shows full-length homology to the mammalian protein VCP and is a member of a protein family involved in secretion, peroxisome formation, and gene expression.

1991 ◽  
Vol 114 (3) ◽  
pp. 443-453 ◽  
Author(s):  
K U Fröhlich ◽  
H W Fries ◽  
M Rüdiger ◽  
R Erdmann ◽  
D Botstein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Fusion Protein ◽  
Intracellular Transport ◽  
Consensus Sequence ◽  
Cell Cycle Gene ◽  
Cell Cycle Protein ◽  
A Cell ◽  
Yeast Mutants ◽  
Mammalian Protein

Yeast mutants of cell cycle gene cdc48-1 arrest as large budded cells with microtubules spreading aberrantly throughout the cytoplasm from a single spindle plaque. The gene was cloned and disruption proved it to be essential. The CDC48 sequence encodes a protein of 92 kD that has an internal duplication of 200 amino acids and includes a nucleotide binding consensus sequence. Vertebrate VCP has a 70% identity over the entire length of the protein. Yeast Sec18p and mammalian N-ethylmaleimide-sensitive fusion protein, which are involved in intracellular transport, yeast Pas1p, which is essential for peroxisome assembly, and mammalian TBP-1, which influences HIV gene expression, are 40% identical in the duplicated region. Antibodies against CDC48 recognize a yeast protein of apparently 115 kD and a mammalian protein of 100 kD. Both proteins are bound loosely to components of the microsomal fraction as described for Sec18p and N-ethylmaleimide-sensitive fusion protein. This similarity suggests that CDC48p participates in a cell cycle function related to that of N-ethylmaleimide-sensitive fusion protein/Sec18p in Golgi transport.

Sign in / Sign up

Export Citation Format

Share Document