scholarly journals Profiling of Epigenetic Features in Clinical Samples Reveals Novel Widespread Changes in Cancer

Cancers ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 723 ◽  
Author(s):  
Roberta Noberini ◽  
Camilla Restellini ◽  
Evelyn Oliva Savoia ◽  
Francesco Raimondi ◽  
Lavinia Ghiani ◽  
...  

Aberrations in histone post-translational modifications (PTMs), as well as in the histone modifying enzymes (HMEs) that catalyze their deposition and removal, have been reported in many tumors and many epigenetic inhibitors are currently under investigation for cancer treatment. Therefore, profiling epigenetic features in cancer could have important implications for the discovery of both biomarkers for patient stratification and novel epigenetic targets. In this study, we employed mass spectrometry-based approaches to comprehensively profile histone H3 PTMs in a panel of normal and tumoral tissues for different cancer types, identifying various changes, some of which appear to be a consequence of the increased proliferation rate of tumors, while others are cell-cycle independent. Histone PTM changes found in tumors partially correlate with alterations of the gene expression profiles of HMEs obtained from publicly available data and are generally lost in culture conditions. Through this analysis, we identified tumor- and subtype-specific histone PTM changes, but also widespread changes in the levels of histone H3 K9me3 and K14ac marks. In particular, H3K14ac showed a cell-cycle independent decrease in all the seven tumor/tumor subtype models tested and could represent a novel epigenetic hallmark of cancer.

2018 ◽  
Vol 44 (1) ◽  
pp. 86-97
Author(s):  
Ceren Sucularli ◽  
Ugur Toprak ◽  
Melda Arslantas

Abstract Background Comparing gene expression profiles using gene expression datasets of different types of tumors is frequently used to identify molecular mechanisms of cancer. This study aimed to find shared and type specific gene expression profiles of hepatocellular carcinoma (HCC) and B-cell chronic lymphocytic leukemia (B-CLL). Material and methods Gene expression microarrays for HCC and B-CLL and RNA-sequencing expression data for liver HCC and lymphoid neoplasm diffuse large B-cell lymphoma (DLBC) were analyzed and differentially expressed probe sets or genes for each cancer type were detected. Probe sets and genes that were shared or specifically expressed in both cancer types were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) terms for Biological Process (BP) annotations were performed. Results According to our analysis shared upregulated genes were mainly annotated in cell cycle processes. Some of the genes that changed only in HCC were annotated in cell cycle and metabolic processes, and some of the genes, altered only in B-CLL, were annotated in immune response and hemopoiesis. Conclusion These results contribute to cancer research that aim to find the conserved gene expression profiles in different cancer types and widen the knowledge of HCC and B-CLL specific mechanisms.


BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanan Ren ◽  
Ting-You Wang ◽  
Leah C. Anderton ◽  
Qi Cao ◽  
Rendong Yang

Abstract Background Long non-coding RNAs (lncRNAs) are a growing focus in cancer research. Deciphering pathways influenced by lncRNAs is important to understand their role in cancer. Although knock-down or overexpression of lncRNAs followed by gene expression profiling in cancer cell lines are established approaches to address this problem, these experimental data are not available for a majority of the annotated lncRNAs. Results As a surrogate, we present lncGSEA, a convenient tool to predict the lncRNA associated pathways through Gene Set Enrichment Analysis of gene expression profiles from large-scale cancer patient samples. We demonstrate that lncGSEA is able to recapitulate lncRNA associated pathways supported by literature and experimental validations in multiple cancer types. Conclusions LncGSEA allows researchers to infer lncRNA regulatory pathways directly from clinical samples in oncology. LncGSEA is written in R, and is freely accessible at https://github.com/ylab-hi/lncGSEA.


Cancers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 816
Author(s):  
Priya Ramarao-Milne ◽  
Olga Kondrashova ◽  
Sinead Barry ◽  
John D. Hooper ◽  
Jason S. Lee ◽  
...  

Genetic and epigenetic factors contribute to the development of cancer. Epigenetic dysregulation is common in gynaecological cancers and includes altered methylation at CpG islands in gene promoter regions, global demethylation that leads to genome instability and histone modifications. Histones are a major determinant of chromosomal conformation and stability, and unlike DNA methylation, which is generally associated with gene silencing, are amenable to post-translational modifications that induce facultative chromatin regions, or condensed transcriptionally silent regions that decondense resulting in global alteration of gene expression. In comparison, other components, crucial to the manipulation of chromatin dynamics, such as histone modifying enzymes, are not as well-studied. Inhibitors targeting DNA modifying enzymes, particularly histone modifying enzymes represent a potential cancer treatment. Due to the ability of epigenetic therapies to target multiple pathways simultaneously, tumours with complex mutational landscapes affected by multiple driver mutations may be most amenable to this type of inhibitor. Interrogation of the actionable landscape of different gynaecological cancer types has revealed that some patients have biomarkers which indicate potential sensitivity to epigenetic inhibitors. In this review we describe the role of epigenetics in gynaecological cancers and highlight how it may exploited for treatment.


Author(s):  
Jitka Holcakova ◽  
Pavla Ceskova ◽  
Roman Hrstka ◽  
Petr Muller ◽  
Lenka Dubska ◽  
...  

Abstractp73, a member of the p53 family, exhibits activities similar to those of p53, including the ability to induce growth arrest and apoptosis. p73 influences chemotherapeutic responses in human cancer patients, in association with p53. Alternative splicing of the TP73 gene produces many p73 C- and N-terminal isoforms, which vary in their transcriptional activity towards p53-responsive promoters. In this paper, we show that the C-terminal spliced isoforms of the p73 protein differ in their DNA-binding capacity, but this is not an accurate predictor of transcriptional activity. In different p53-null cell lines, p73β induces either mitochondrial-associated or death receptor-mediated apoptosis, and these differences are reflected in different gene expression profiles. In addition, p73 induces cell cycle arrest and p21WAF1 expression in H1299 cells, but not in Saos-2. This data shows that TAp73 isoforms act differently depending on the tumour cell background, and have important implications for p73-mediated therapeutic responses in individual human cancer patients.


2021 ◽  
Author(s):  
Yuting Liu ◽  
Kehui Wang ◽  
Li Huang ◽  
Jicheng Zhao ◽  
Xinpeng Chen ◽  
...  

Centromere identity is defined by nucleosomes containing CENP-A, a histone H3 variant. The deposition of CENP-A at centromeres is tightly regulated in a cell-cycle-dependent manner. We previously reported that the spatiotemporal control of centromeric CENP-A incorporation is mediated by the phosphorylation of CENP-A Ser68. However, a recent report argued that Ser68 phosphoregulation is dispensable for accurate CENP-A loading. Here, we report that the substitution of Ser68 of endogenous CENP-A with either Gln68 or Glu68 severely impairs CENP-A deposition and cell viability. We also find that mice harboring the corresponding mutations are lethal. Together, these results indicate that the dynamic phosphorylation of Ser68 ensures cell-cycle-dependent CENP-A deposition and cell viability.


2019 ◽  
Vol 47 (16) ◽  
pp. 8439-8451 ◽  
Author(s):  
Alberto González-Medina ◽  
Elena Hidalgo ◽  
José Ayté

Abstract In fission yeast, MBF-dependent transcription is inactivated at the end of S phase through a negative feedback loop that involves the co-repressors, Yox1 and Nrm1. Although this repression system is well known, the molecular mechanisms involved in MBF activation remain largely unknown. Compacted chromatin constitutes a barrier to activators accessing promoters. Here, we show that chromatin regulation plays a key role in activating MBF-dependent transcription. Gcn5, a part of the SAGA complex, binds to MBF-regulated promoters through the MBF co-activator Rep2 in a cell cycle-dependent manner and in a reverse correlation to the binding of the MBF co-repressors, Nrm1 or Yox1. We propose that the co-repressors function as physical barriers to SAGA recruitment onto MBF promoters. We also show that Gcn5 acetylates specific lysine residues on histone H3 in a cell cycle-regulated manner. Furthermore, either in a gcn5 mutant or in a strain in which histone H3 is kept in an unacetylated form, MBF-dependent transcription is downregulated. In summary, Gcn5 is required for the full activation and correct timing of MBF-regulated gene transcription.


2008 ◽  
Vol 82 (7) ◽  
pp. 3428-3437 ◽  
Author(s):  
Charles M. Chau ◽  
Zhong Deng ◽  
Hyojueng Kang ◽  
Paul M. Lieberman

ABSTRACT The Epstein-Barr virus C promoter (Cp) regulates the major multicistronic transcript encoding the EBNA-LP, 1, 2, and 3 genes required for B-cell proliferation during latency. The growth-transforming potential of these viral genes suggests that they must be tightly regulated with the host cell cycle and differentiation process. To better understand Cp regulation, we used DNA affinity purification to identify cellular and viral proteins that bind to Cp in latently infected cells. Several previously unknown factors were identified, including the cell cycle regulatory proteins E2F1 and Rb. E2F1 bound to a specific site in Cp located in the core Cp region 3′ of the known EBNA2-responsive RBP-Jk (CSL, CBF1) binding site. The histone H3 K4 demethylase LSD1 (BCC110) was also identified by DNA affinity and was shown to form a stable complex with Rb. Coimmunoprecipitation assays demonstrated that E2F1, Rb, and LSD1 bind to Cp in a cell cycle-dependent manner. Rb and LSD1 binding to Cp increased after the S phase, corresponding to a decrease in histone H3 K4 methylation and Cp transcription. Coimmunoprecipitation and immunofluorescence assays reveal that LSD1 interacts with Rb. Surprisingly, LSD1 did not coimmunoprecipitate with E2F1, suggesting that it associates with Rb independently of E2F1. Depletion of LSD1 by small interfering RNAs inhibited Cp basal transcription levels, and overexpression of LSD1 altered the cell cycle profile in p53-positive (p53+), but not p53-negative (p53−), HCT cells. These findings indicate that Cp is a cell cycle-regulated promoter that is under the control of Rb and the histone demethylase LSD1 in multiple latency types.


2002 ◽  
Vol 277 (51) ◽  
pp. 49504-49510 ◽  
Author(s):  
Ji Li ◽  
Peili Chen ◽  
Natasha Sinogeeva ◽  
Myriam Gorospe ◽  
Robert P. Wersto ◽  
...  

Arsenic trioxide (As2O3) is highly effective for the treatment of acute promyelocytic leukemia, even in patients who are unresponsive to all-trans-retinoic acid therapy. As2O3is believed to function primarily by promoting apoptosis, but the underlying molecular mechanisms remain largely unknown. In this report, using cDNA arrays, we have examined the changes in gene expression profiles triggered by clinically achievable doses of As2O3in acute promyelocytic leukemia NB4 cells.CASPASE-10expression was found to be potently induced by As2O3. Accordingly, caspase-10 activity also substantially increased in response to As2O3treatment. A selective inhibitor of caspase-10, Z-AEVD-FMK, effectively blocked caspase-3 activation and significantly attenuated As2O3-triggered apoptosis. Interestingly, the treatment of NB4 cells with As2O3markedly increased histone H3 phosphorylation at serine 10, an event that is associated with acetylation of the lysine 14 residue. Chromatin immunoprecipitation assays revealed that As2O3potently enhances histone H3 phosphoacetylation at theCASPASE-10locus. These results suggest that the effect of As2O3on histone H3 phosphoacetylation at theCASPASE-10gene may play an important role in the induction of apoptosis and thus contribute to its therapeutic effects on acute promyelocytic leukemia.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 2798-2798
Author(s):  
Kenneth H Shain ◽  
Vasco Oliveira ◽  
Danielle Yarde ◽  
Linda Mathews ◽  
William S. Dalton

Abstract Abstract 2798 Poster Board II-774 Multiple Myeloma (MM) is an incurable malignancy of mature clonal B cells. The refractory nature of MM has long been attributed to the acquisition of drug resistance. Traditionally, mechanisms of drug resistance have been defined by acquired changes in the expression or function of specific gene products. To this end, we have recently demonstrated that selected resistance to the cytotoxic agent melphalan correlated with increased expression of components of the Fanconi Anemia (FA)/BRCA DNA repair pathway and a concomitant increase in repair of DNA interstrand cross-links (ICLs).(Hazlehurst et al Cancer Res 2003; Chen et al Blood 2005) Further, the exogenous expression of specific FANC components in RPMI 8226 cell lines enhanced ICL repair, favored the release from melphalan-induced S-phase delay, and rendered these cells partially resistant to melphalan treatment. Together, these results suggest a causal relationship between increased expression of FA DNA repair components, increased DNA repair, and acquired resistance to melphalan. Over the past decade a large body of evidence has emerged demonstrating that in addition to drug resistance mechanisms intrinsic to the cancer cell, there exist dynamic, de novo mechanisms coordinated by the tumor microenvironment resulting in an environment-mediated drug resistance (EM-DR). As such, we examined the potential role of the microenvironment in regulating the FA/BRCA DNA repair pathway. FA pathway protein expression was evaluated with anti-sera to FANCD1/BRCA2, FANCC, FANCD2, FANCI, FANCG and BRCA1 in drug sensitive RPMI 8226 cells and melphalan resistant 8226/LR5 cells in co-culture with the HS-5 bone marrow stromal cell line. With these preliminary results we present three novel findings. First, we demonstrate that expression of FA/BRCA pathway components is regulated by intracellular interactions in both MM cells and bone marrow stromal cells (BMSCs). Second, we show that the acquisition of drug resistance alters FANC protein expression profiles upon co-culture. Third, in the HS-5 BMSCs, mono-ubiquitinated FANCD2 is observed in the absence of detectable FANCG. In RPMI 8226 cells, Western blot analysis demonstrated an acute (within 30minutes) and prolonged (up to 48hours) time-dependent increase in expression of FANCD2/BRCA2, FANCC, FANCD2, and BRCA1 upon incubation with BMSCs relative to MM cells incubated alone. However, no appreciated increases in FANCI or FANCG were noted under the same conditions. Incubation of 8226/LR5s with HS-5 BMSCs demonstrated a slightly different up-regulation of FA/BRCA pathway protein expression with addition of increased FANCI expression and no increase in FANCD2 or FANCC expression. We also examined FANC protein expression in the HS-5 cells. Interestingly, in the BMSCs significant differences were noted in the FANC expression profiles. Co-culture of RPMI 8226 cells with HS-5 cells demonstrated only modest elevations in FANCD2; however, co-culture with drug-resistant 8226/LR5s resulted in increased levels of FANCD2, FANCI and BRCA1. These data indicate that different tumor cells may alternately influence FA/BRCA-mediated DNA repair and potentially drug resistance in juxtaposed bone marrow stroma. Curiously, we also observed mono-ubiquitinated FANCD2 in the absence of any detectable levels of FANCG protein under co-culture conditions. As the FA/BRCA DNA repair pathway has been associated with cell cycle progression, we evaluated cell cycle kinetics under the co-culture conditions. The results of BrdU analysis demonstrated that the observed changes in FA/BRCA protein expression in MM and BMSC could not be fully explained by cell-cycle distribution. Therefore, within this report we demonstrate for the first time that microenvironmental interactions can modulate the FA/BRCA DNA repair pathway in MM and BMSCs. These results suggest that the FA/BRCA DNA damage repair pathway may be an important modulatory component of EM-DR. Importantly, the potential de novo drug resistance likely involves both the MM tumor cell and adjacent stromal cells. Current and future studies will attempt to examine a causal relationship between increased FANC expression and melphalan (and other drug) resistance seen in co-culture conditions, as well as to identify specific signaling molecules and mechanisms controlling the enhanced expression in both cell models. Disclosures: No relevant conflicts of interest to declare.


Plant Science ◽  
2005 ◽  
Vol 168 (3) ◽  
pp. 789-795 ◽  
Author(s):  
Tamás Kapros ◽  
Zsolt Kelemen ◽  
Jakob H. Waterborg ◽  
Dénes Dudits

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