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| Differences and enrichment analysis of continuously changed genes in DNA methylation. (A) Heatmap shows the methylation differences of continuously changed genes in the three stages. Scale from blue to red indicates the log 2 FC from low to high. (B) Stemness enrichment analysis of continuously changed genes. The significant terms (FDR < 0.01) are shown in the figure.
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BackgroundDNA methylation plays essential roles in tumor occurrence and stemness maintenance. Tumor-repopulating cells (TRCs) are cancer stem cell (CSC)-like cells with highly tumorigenic and self-renewing abilities, which were selected from tumor cells in soft three-dimensional (3D) fibrin gels.Methods
Here, we presented a genome-wide map of methy...
Contexts in source publication
Context 1
... modifications of continuously hyper-or hypomethylated CG dinucleotides provide a biomarker for replicative senescence (Franzen et al., 2018). We identified 54 genes whose methylation levels were continuously increased or decreased from 0 h to 5 days in at least one methylation type ( Figure 7A). Thirtyeight genes belonging to them were continuously changed (5 genes continuously increased, and 33 genes continuously decreased) in mCG, 20 genes continuously changed in mCHG, and only 2 genes (JAZF1 and XKR4) continuously changed in mCHH. ...
Context 2
... genes belonging to them were continuously changed (5 genes continuously increased, and 33 genes continuously decreased) in mCG, 20 genes continuously changed in mCHG, and only 2 genes (JAZF1 and XKR4) continuously changed in mCHH. The methylation altered in these genes may affect tumor proliferation; for instance, the CREB5 continuously decreased in mCG ( Figure 7A) was hypomethylated in Graves' disease (Cai et al., 2015). Hypermethylation of ADAMTS6 is identified in multiple cancers ( Kordowski et al., 2018), and its methylation level continuously decreased in mCHG (Figure 7A), while LMX1A continuously increased in mCHG and serve as a DNA methylation marker in cervical cancer (Lai et al., 2008). ...
Context 3
... methylation altered in these genes may affect tumor proliferation; for instance, the CREB5 continuously decreased in mCG ( Figure 7A) was hypomethylated in Graves' disease (Cai et al., 2015). Hypermethylation of ADAMTS6 is identified in multiple cancers ( Kordowski et al., 2018), and its methylation level continuously decreased in mCHG (Figure 7A), while LMX1A continuously increased in mCHG and serve as a DNA methylation marker in cervical cancer (Lai et al., 2008). ...
Context 4
... of continuously changed genes, differences in non-CG methylation were more significant (| log 2 FC| > 20) than in mCG (| log 2 FC| < 5). None of the continuously changed genes were CSCs marker genes, but were notably enriched in five stemnessrelated gene sets (Figure 7B), indicating their importance in cancer cell stemness. ...
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Background
Dilution of color in rabbits is associated with many different genetic mechanisms that form different color groups. A number of previous studies have revealed potential regulatory mechanisms by which epigenetics regulate pigmentation. However, the genome-wide DNA methylation involved in animal coat-color dilution remains unknown.
Results...
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Citations
... In a special mode, DNMT3A, 3B, and nucleosome core particles form a complex with catalytic activity resulting to the interaction with DNA. This function reported previously is involved in mechanical microenvironment stimulated tumor-repopulating cells (TRCs) (cancer stem cell-like cells) selection and further indicates that the complex, especially the core members DNMT3A and DNMT 3B, is sensitive to biomechanical cues [17]. In CpG mode of methylation regulation, although the methylation status of each CpG site under mechanical stimuli is a complex event, the score of cytosine region is an overall evaluation of the compound methylation of multiple cells. ...
The occurrence and development of tumors depend on a complex regulation by not only biochemical cues, but also biomechanical factors in tumor microenvironment. With the development of epigenetic theory, the regulation of biomechanical stimulation on tumor progress genetically is not enough to fully illustrate the mechanism of tumorigenesis. However, biomechanical regulation on tumor progress epigenetically is still in its infancy. Therefore, it is particularly important to integrate the existing relevant researches and develop the potential exploration. This work sorted out the existing researches on the regulation of tumor by biomechanical factors through epigenetic means, which contains summarizing the tumor epigenetic regulatory mode by biomechanical factors, exhibiting the influence of epigenetic regulation under mechanical stimulation, illustrating its existing applications, and prospecting the potential. This review aims to display the relevant knowledge through integrating the existing studies on epigenetic regulation in tumorigenesis under mechanical stimulation so as to provide theoretical basis and new ideas for potential follow-up research and clinical applications.
Graphical Abstract
Mechanical factors under physiological conditions stimulate the tumor progress through epigenetic ways, and new strategies are expected to be found with the development of epidrugs and related delivery systems.
... In this sense, it is believed that DNA methylation has an important role in regulating the expression of genes such as OCT4, NANOG, SOX2, and KLF4, which are essential for maintaining stem cells' characteristics. Significant changes have been reported when this process has been studied in 2D-and 3D-cultured cells, the results obtained regarding altered methylation patterns in 3D cell cultures were more comparable with tissue-based analysis [32][33][34]. ...
... Therefore, many studies have highlighted the influence of the rigidity or softness of the ECM on changes in the epigenetic landscape. Thus, it has been proposed to optimize 3D culture systems to control the aforementioned factors, among others, and thus better reflect what happens in tumors in vivo [20,33,34]. ...
Simple Summary
Genome-wide DNA methylation is a regulatory mechanism that is frequently altered in human cancers. Remarkably, these epigenetic marks on DNA are greatly influenced by microenvironmental factors, so to study them better, it is necessary to use novel cell cultures that faithfully reflect what happens in tumor cells in vivo. In this review, we highlight the importance of three-dimensional (3D) cell culture models, relative to traditional two-dimensional (2D) monolayer cell cultures, for the study of epigenetic DNA methylation in cancer. Moreover, we highlight how research approaches, by optimizing the 3D culture systems, can obtain a more realistic overview of the epigenetic landscape. The implications of the discovery of potential targets for cancer therapies are also discussed.
Abstract
During the last century, 2D cell cultures have been the tool most widely used to study cancer biology, drug discovery, genomics, and the regulation of gene expression at genetic/epigenetic levels. However, this experimental approach has limitations in faithfully recreating the microenvironment and cellular processes occurring in tumors. For these reasons, 3D cell cultures have recently been implemented to optimize the conditions that better recreate the biological and molecular features of tumors, including cell–cell and cell–extracellular matrix (ECM) interactions, growth kinetics, metabolic activities, and the development of gradients in the cellular microenvironment affecting the availability of oxygen and nutrients. In this sense, tumor cells receive stimuli from the local environment, resulting in significant changes in their signaling pathways, gene expression, and transcriptional and epigenetic patterns. In this review, we discuss how different types of 3D cell culture models can be applied to characterize the epigenetic footprints of cancer cell lines, emphasizing that DNA methylation patterns play an essential role in the emergence and development of cancer. However, how 3D cancer cell cultures remodel the epigenetic programs is poorly understood, with very few studies in this emerging topic. Here, we have summarized the studies on the reprogramming of the epigenetic landscape of DNA methylation during tumorigenesis and discuss how it may be affected by microenvironmental factors, specifically in 3D cell cultures.
... Genetic and epigenetic mechanisms function cooperatively to regulate tumorigenesis, progression and therapeutic resistance [5][6][7]. DNA methylation has been recognized as a key mechanism of tumorigenesis, progression, and resistance, which can modulate gene expression by controlling access to regulatory regions and affecting transcription factor binding in DNA [8][9][10][11]. ...
Epigenetic alterations, including DNA methylation, play crucial roles in the tumor. Epigenetic drugs like DNA methyltransferase-1 (DNMT1) inhibitors have been exhibited positive effects in cancer treatment. However, the role of DNMT1 in oral squamous cell carcinoma (OSCC) is less clearly described. What is more, the effects on the immune microenvironment of DNMT1 have not become appreciated. In this research, we determine the expression levels of DNMT1 and the association of prognosis by analyzing human OSCC tissue microarrays. Two different types of immunocompetent mouse OSCC models were established to explore the effects of DNMT1 inhibitor on the tumor microenvironment(TME). We identified DNMT1 was highly expressed both in human and mouse OSCC tissues. The expression levels of DNMT1 was also correlated with the immunosuppressive molecules and tumor-promoter such as VISTA, PD-L1, B7-H4, and PAK2, indicating a worse prognosis. Of particular concern is that DNMT1 inhibition improved TME and delayed tumor growth by decreasing myeloid-derived suppressor cells (MDSCs) and increasing tumor-infiltrating T cells. Our data suggests that DNMT1 play a key role in OSCC and has a possible immunotherapeutic marker treatment.
... 25 Another study pointed out that genes with continuously increasing or decreasing methylation, such as CREB5, may also affect the tumor-repopulating cell screening process. 26 Moreover, DNAm levels of CREB5 (cg11301281) are related to metabolic syndrome traits [8], so its expression may be involved in the process of blood glucose control and metabolic response. ...
Purpose
Clopidogrel resistance (CR) is mostly caused by interindividual variability of the platelet inhibition of clopidogrel, which may induce cardiovascular events. The aim of this research was to evaluate whether DNAm levels of CREB5 (cg01534253) are involved in CR among acute coronary syndrome (ACS) patients treated with clopidogrel.
Methods
72 patients(36 CR and 36 non‐CR) who underwent ACS were included in this study. The VerifyNow P2Y12 assay was selected to evaluate residual platelet reactivity, and bisulfite pyrosequencing methods was used to examine DNA methylation levels on cg01534253. Secondly, CREB5 mRNA expression was analyzed via quantitative real‐time PCR. Last, we employed logistic regression to test the interaction between genetic factors of CREB5 methylation and multiple clinical variables in CR patients.
Results
Subunit analysis indicated that for patients whose HbA1c levels were ≥6.5% or whose GLU levels were ≥7 mmol/L, lower methylation of cg01534253 indicated a poorer clopidogrel response. In addition, CREB5 mRNA expression was increased in CR patients with GLU levels ≥7 mmol/L. Moreover, regression analysis indicated that the values of albumin and uric acid were correlated with the incidence of CR.
Conclusions
Our findings were likely to provide fresh understanding for the new mechanism of platelet inhibition failure and promote individualized antiplatelet therapy.
... This is essential for the self-renewal and maintenance of liver CSCs through activation of Wnt/β-catenin signaling [51]. Huang W et al. performed whole-genome bisulfite sequencing on tumor-repopulating cells (TRC), which are cancer stem cell (CSC)-like cells with highly tumorigenic and self-renewing abilities, their results showed that CSCs markers were biased toward altering their methylation in non-CG methylation and enriched in the gene body region, indicating non-CG DNA methylation plays a vital role in TRC selection [52]. ...
Distinct regions harboring cancer stem cells (CSCs) have been identified within the microenvironment of various tumors, and as in the case of their healthy counterparts, these anatomical regions are termed “niche.” Thus far, a large volume of studies have shown that CSC niches take part in the maintenance, regulation of renewal, differentiation and plasticity of CSCs. In this review, we summarize and discuss the latest findings regarding CSC niche morphology, physical terrain, main signaling pathways and interactions within them. The cellular and molecular components of CSCs also involve genetic and epigenetic modulations that mediate and support their maintenance, ultimately leading to cancer progression. It suggests that the crosstalk between CSCs and their niche plays an important role regarding therapy resistance and recurrence. In addition, we updated diverse therapeutic strategies in different cancers in basic research and clinical trials in this review. Understanding the complex heterogeneity of CSC niches is a necessary pre-requisite for designing superior therapeutic strategies to target CSC-specific factors and/or components of the CSC niche.
... Here, we used colorectal cancer to demonstrate as a proof of principle that the expression of stemness signature is highly heterogeneous not only intertumorally, but also at the level of individual cancer cells, with a larger contribution from intratumoral heterogeneity. Additionally, it was reported that specific patterns of hyper/hypo methylation follow the stem phenotype in cancer cells [95,96]. Therefore, another source of stemness heterogeneity may come from the epigenetic component or from other factors such as variability in pre-mRNA splicing [97] and expression of non-coding genes, e.g. ...
Significant alterations in signaling pathways and transcriptional regulatory programs together represent major hallmarks of many cancers. These, among all, include the reactivation of stemness, which is registered by the expression of pathways that are active in the embryonic stem cells (ESCs). Here, we assembled gene sets that reflect the stemness and proliferation signatures and used them to analyze a large panel of RNA-seq data from The Cancer Genome Atlas (TCGA) Consortium in order to specifically assess the expression of stemness-related and proliferation-related genes across a collection of different tumor types. We introduced a metric that captures the collective similarity of the expression profile of a tumor to that of ESCs, which showed that stemness and proliferation signatures vary greatly between different tumor types. We also observed a high degree of intertumoral heterogeneity in the expression of stemness- and proliferation-related genes, which was associated with increased hazard ratios in a fraction of tumors and mirrored by high intratumoral heterogeneity and a remarkable stemness capacity in metastatic lesions across cancer cells in single cell RNA-seq datasets. Taken together, these results indicate that the expression of stemness signatures is highly heterogeneous and cannot be used as a universal determinant of cancer. This calls into question the universal validity of diagnostic tests that are based on stem cell markers.
The self-renewing cancer stem cells (CSCs) represent one of the distinct cell populations occurring in a tumour that can differentiate into multiple lineages. This group of sparsely abundant cells play a vital role in tumour survival and resistance to different treatments during cancer. The lack of exclusive markers associated with CSCs makes diagnosis and prognosis in cancer patients extremely difficult. This calls for the identification of unique regulators and markers for CSCs. Various signalling pathways like the Wnt/β-catenin pathway, Hedgehog pathway, Notch pathway, and TGFβ/BMP play a major role in the regulation and maintenance of CSCs. Epigenetic regulatory mechanisms add another layer of complexity to control these signalling pathways. In this chapter, we discuss about the role of epigenetic mechanisms in regulating the cellular signalling pathways in CSCs. The epigenetic regulatory mechanisms such as DNA methylation, histone modification and microRNAs can modulate the diverse effectors of signalling pathways and consequently the growth, differentiation and tumorigenicity of CSCs. In the end, we briefly discuss the therapeutic potential of targeting these epigenetic regulators and their target genes in CSCs.
DNA methylation, as an epigenetic mechanism, occurs by adding a methyl group of cytosines in position 5 by DNA methyltransferases and has essential roles in cellular function, especially in the transcriptional regulation of embryonic and adult stem cells. Hypomethylation and hypermethylation cause either the expression or inhibition of genes, and there is a tight balance between regulating the activation or repression of genes in normal cellular activity. Abnormal methylation is well-known hallmark of cancer development and progression and can switch normal stem cells into cancer stem cells. Cancer Stem Cells (CSCs) are minor populations of tumor cells that exhibit unique properties such as self-regeneration, resistance to chemotherapy, and high ability of metastasis. The purpose of this paper is to show how aberrant DNA methylation accumulation affects self-renewal, differentiation, multidrug-resistant, and metastasis processes in cancer stem cells.
