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1.
EMBO J ; 40(20): e107680, 2021 10 18.
Article in English | MEDLINE | ID: mdl-34532864

ABSTRACT

Cell plasticity is a crucial hallmark leading to cancer metastasis. Upregulation of Rho/ROCK pathway drives actomyosin contractility, protrusive forces, and contributes to the occurrence of highly invasive amoeboid cells in tumors. Cancer stem cells are similarly associated with metastasis, but how these populations arise in tumors is not fully understood. Here, we show that the novel oncogene RASSF1C drives mesenchymal-to-amoeboid transition and stem cell attributes in breast cancer cells. Mechanistically, RASSF1C activates Rho/ROCK via SRC-mediated RhoGDI inhibition, resulting in generation of actomyosin contractility. Moreover, we demonstrate that RASSF1C-induced amoeboid cells display increased expression of cancer stem-like markers such as CD133, ALDH1, and Nanog, and are accompanied by higher invasive potential in vitro and in vivo. Further, RASSF1C-induced amoeboid cells employ extracellular vesicles to transfer the invasive phenotype to target cells and tissue. Importantly, the underlying RASSF1C-driven biological processes concur to explain clinical data: namely, methylation of the RASSF1C promoter correlates with better survival in early-stage breast cancer patients. Therefore, we propose the use of RASSF1 gene promoter methylation status as a biomarker for patient stratification.


Subject(s)
Breast Neoplasms/genetics , Extracellular Vesicles/metabolism , Neoplastic Stem Cells/metabolism , Tumor Suppressor Proteins/genetics , rhoA GTP-Binding Protein/genetics , src-Family Kinases/genetics , AC133 Antigen/genetics , AC133 Antigen/metabolism , Aldehyde Dehydrogenase 1 Family/genetics , Aldehyde Dehydrogenase 1 Family/metabolism , Animals , Breast Neoplasms/metabolism , Breast Neoplasms/mortality , Breast Neoplasms/pathology , Cell Line, Tumor , Cell Movement , Cell Proliferation , CpG Islands , DNA Methylation , Extracellular Vesicles/chemistry , Female , Gene Expression Regulation, Neoplastic , Humans , MCF-7 Cells , Mice , Mice, SCID , Nanog Homeobox Protein/genetics , Nanog Homeobox Protein/metabolism , Neoplastic Stem Cells/pathology , Signal Transduction , Spheroids, Cellular/metabolism , Spheroids, Cellular/pathology , Survival Analysis , Tumor Suppressor Proteins/metabolism , Xenograft Model Antitumor Assays , rhoA GTP-Binding Protein/metabolism , src-Family Kinases/metabolism
2.
Plant J ; 115(3): 846-865, 2023 08.
Article in English | MEDLINE | ID: mdl-37310200

ABSTRACT

Precise gene-editing using CRISPR/Cas9 technology remains a long-standing challenge, especially for genes with low expression and no selectable phenotypes in Chlamydomonas reinhardtii, a classic model for photosynthesis and cilia research. Here, we developed a multi-type and precise genetic manipulation method in which a DNA break was generated by Cas9 nuclease and the repair was mediated using a homologous DNA template. The efficacy of this method was demonstrated for several types of gene editing, including inactivation of two low-expression genes (CrTET1 and CrKU80), the introduction of a FLAG-HA epitope tag into VIPP1, IFT46, CrTET1 and CrKU80 genes, and placing a YFP tag into VIPP1 and IFT46 for live-cell imaging. We also successfully performed a single amino acid substitution for the FLA3, FLA10 and FTSY genes, and documented the attainment of the anticipated phenotypes. Lastly, we demonstrated that precise fragment deletion from the 3'-UTR of MAA7 and VIPP1 resulted in a stable knock-down effect. Overall, our study has established efficient methods for multiple types of precise gene editing in Chlamydomonas, enabling substitution, insertion and deletion at the base resolution, thus improving the potential of this alga in both basic research and industrial applications.


Subject(s)
Chlamydomonas reinhardtii , Chlamydomonas , CRISPR-Cas Systems , Chlamydomonas/genetics , Gene Editing/methods , Chlamydomonas reinhardtii/genetics
3.
Proc Biol Sci ; 290(1999): 20230368, 2023 05 31.
Article in English | MEDLINE | ID: mdl-37221849

ABSTRACT

Hibernation consists of alternating torpor-arousal phases, during which animals cope with repetitive hypothermia and ischaemia-reperfusion. Due to limited transcriptomic and methylomic information for facultative hibernators, we here conducted RNA and whole-genome bisulfide sequencing in liver of hibernating Syrian hamster (Mesocricetus auratus). Gene ontology analysis was performed on 844 differentially expressed genes and confirmed the shift in metabolic fuel utilization, inhibition of RNA transcription and cell cycle regulation as found in seasonal hibernators. Additionally, we showed a so far unreported suppression of mitogen-activated protein kinase (MAPK) and protein phosphatase 1 pathways during torpor. Notably, hibernating hamsters showed upregulation of MAPK inhibitors (dual-specificity phosphatases and sproutys) and reduced levels of MAPK-induced transcription factors (TFs). Promoter methylation was found to modulate the expression of genes targeted by these TFs. In conclusion, we document gene regulation between hibernation phases, which may aid the identification of pathways and targets to prevent organ damage in transplantation or ischaemia-reperfusion.


Subject(s)
Hibernation , Transcriptome , Animals , Cricetinae , Mesocricetus , Liver , Gene Expression Profiling
4.
Int J Mol Sci ; 24(22)2023 Nov 16.
Article in English | MEDLINE | ID: mdl-38003603

ABSTRACT

Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by a constant accumulation of lipids in the liver. This hepatic lipotoxicity is associated with a dysregulation of the first step in lipid catabolism, known as beta oxidation, which occurs in the mitochondrial matrix. Eventually, this dysregulation will lead to mitochondrial dysfunction. To evaluate the possible involvement of mitochondrial DNA methylation in this lipid metabolic dysfunction, we investigated the functional metabolic effects of mitochondrial overexpression of CpG (MSssI) and GpC (MCviPI) DNA methyltransferases in relation to gene expression and (mito)epigenetic signatures. Overall, the results show that mitochondrial GpC and, to a lesser extent, CpG methylation increase bile acid metabolic gene expression, inducing the onset of cholestasis through mito-nuclear epigenetic reprogramming. Moreover, both increase the expression of metabolic nuclear receptors and thereby induce basal overactivation of mitochondrial respiration. The latter promotes mitochondrial swelling, favoring lipid accumulation and metabolic-stress-induced mitophagy and autophagy stress responses. In conclusion, both mitochondrial GpC and CpG methylation create a metabolically challenging environment that induces mitochondrial dysfunction, which may contribute to the progression of MASLD.


Subject(s)
Fatty Liver , Mitophagy , Humans , Mitophagy/genetics , Mitochondria/genetics , Mitochondria/metabolism , DNA, Mitochondrial/metabolism , Fatty Liver/metabolism , Stress, Physiological , Lipids
5.
Adv Exp Med Biol ; 1389: 515-533, 2022.
Article in English | MEDLINE | ID: mdl-36350521

ABSTRACT

DNA methylation is an essential epigenetic mark, strongly associated with gene expression regulation. Aberrant DNA methylation patterns underlie various diseases and efforts to intervene with DNA methylation signatures are of great clinical interest. Technological developments to target writers or erasers of DNA methylation to specific genomic loci by epigenetic editing resulted in successful gene expression modulation, also in in vivo models. Application of epigenetic editing in human health could have a huge impact, but clinical translation is still challenging. Despite successes for a wide variety of genes, not all genes mitotically maintain their (de)methylation signatures after editing, and reprogramming requires further understanding of chromatin context-dependency. In addition, difficulties of current delivery systems and off-target effects are hurdles to be tackled. The present review describes findings towards effective and sustained DNA (de)methylation by epigenetic editing and discusses the need for multi-effector approaches to achieve highly efficient long-lasting reprogramming.


Subject(s)
DNA Methylation , Gene Editing , Humans , DNA Methylation/genetics , Gene Editing/methods , CRISPR-Cas Systems , Epigenesis, Genetic , Gene Expression
6.
Int J Mol Sci ; 23(4)2022 Feb 16.
Article in English | MEDLINE | ID: mdl-35216315

ABSTRACT

Mutations in either mitochondrial DNA (mtDNA) or nuclear genes that encode mitochondrial proteins may lead to dysfunctional mitochondria, giving rise to mitochondrial diseases. Some mitochondrial myopathies, however, present without a known underlying cause. Interestingly, methylation of mtDNA has been associated with various clinical pathologies. The present study set out to assess whether mtDNA methylation could explain impaired mitochondrial function in patients diagnosed with myopathy without known underlying genetic mutations. Enhanced mtDNA methylation was indicated by pyrosequencing for muscle biopsies of 14 myopathy patients compared to four healthy controls, at selected cytosines in the Cytochrome B (CYTB) gene, but not within the displacement loop (D-loop) region. The mtDNA methylation patterns of the four healthy muscle biopsies were highly consistent and showed intriguing tissue-specific differences at particular cytosines with control skin fibroblasts cultured in vitro. Within individual myopathy patients, the overall mtDNA methylation pattern correlated well between muscle and skin fibroblasts. Despite this correlation, a pilot analysis of four myopathy and five healthy fibroblast samples did not reveal a disease-associated difference in mtDNA methylation. We did, however, detect increased expression of solute carrier family 25A26 (SLC25A26), encoding the importer of S-adenosylmethionine, together with enhanced mtDNA copy numbers in myopathy fibroblasts compared to healthy controls. To confirm that pyrosequencing indeed reflected DNA methylation and not bisulfite accessibility, mass spectrometry was employed. Although no myopathy-related differences in total amount of methylated cytosines were detected at this stage, a significant contribution of contaminating nuclear DNA (nDNA) was revealed, and steps to improve enrichment for mtDNA are reported. In conclusion, in this explorative study we show that analyzing the mitochondrial genome beyond its sequence opens novel avenues to identify potential molecular biomarkers assisting in the diagnosis of unexplained myopathies.


Subject(s)
Epigenome , Muscular Diseases , Amino Acid Transport Systems/genetics , Calcium-Binding Proteins/metabolism , Cytosine/metabolism , DNA Methylation , DNA, Mitochondrial/metabolism , Humans , Mitochondria/metabolism , Muscular Diseases/genetics , Muscular Diseases/metabolism
7.
Cell Biol Toxicol ; 37(4): 497-513, 2021 08.
Article in English | MEDLINE | ID: mdl-33040242

ABSTRACT

Cadmium (Cd), a highly toxic heavy metal, is widespreadly distributed in the environment. Chronic exposure to Cd is associated with the development of several diseases including cancers. Over the decade, many researches have been carried on various models to examine the acute effects of Cd; yet, limited knowledge is known about the long-term Cd exposure, especially in the human lung cells. Previously, we showed that chronic Cd-exposed human bronchial epithelial BEAS-2B cells exhibited transformed cell properties, such as anchorage-independent growth, augmented cell migration, and epithelial-mesenchymal transition (EMT). To study these Cd-transformed cells more comprehensively, here, we further characterized their subproteomes. Overall, a total of 63 differentially expressed proteins between Cd-transformed and passage-matched control cells among the five subcellular fractions (cytoplasmic, membrane, nuclear-soluble, chromatin-bound, and cytoskeletal) were identified by mass spectrometric analysis and database searching. Interestingly, we found that the thiol protease ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCHL1) is one of the severely downregulated proteins in the Cd-transformed cells. Notably, the EMT phenotype of Cd-transformed cells can be suppressed by forced ectopic expression of UCHL1, suggesting UCHL1 as a crucial modulator in the maintenance of the proper differentiation status in lung epithelial cells. Since EMT is considered as a critical step during malignant cell transformation, finding novel cellular targets that can antagonize this transition may lead to more efficient strategies to inhibit cancer development. Our data report for the first time that UCHL1 may play a function in the suppression of EMT in Cd-transformed human lung epithelial cells, indicating that UCHL1 might be a new therapeutic target for chronic Cd-induced carcinogenesis. Graphical abstract.


Subject(s)
Cadmium , Ubiquitin Thiolesterase , Cadmium/toxicity , Cell Movement , Epithelial Cells , Epithelial-Mesenchymal Transition , Humans , Ubiquitin Thiolesterase/genetics
8.
J Inherit Metab Dis ; 43(1): 63-70, 2020 01.
Article in English | MEDLINE | ID: mdl-30916397

ABSTRACT

Gene therapy is currently considered as the optimal treatment for inborn errors of metabolism (IEMs), as it aims to permanently compensate for the primary genetic defect. However, emerging gene editing approaches such as CRISPR-Cas9, in which the DNA of the host organism is edited at a precise location, may have outperforming therapeutic potential. Gene editing strategies aim to correct the actual genetic mutation, while circumventing issues associated with conventional compensation gene therapy. Such strategies can also be repurposed to normalize gene expression changes that occur secondary to the genetic defect. Moreover, besides the genetic causes of IEMs, it is increasingly recognized that their clinical phenotypes are associated with epigenetic changes. Because epigenetic alterations are principally reversible, this may offer new opportunities for treatment of IEM patients. Here, we present an overview of the promises of epigenetics in eventually treating IEMs. We discuss the concepts of gene and epigenetic editing, and the advantages and disadvantages of current and upcoming gene-based therapies for treatment of IEMs.


Subject(s)
Gene Editing/methods , Genetic Therapy/methods , Metabolism, Inborn Errors/genetics , Metabolism, Inborn Errors/therapy , CRISPR-Cas Systems , Epigenomics/methods , Humans , Metabolism, Inborn Errors/diagnosis
9.
Int J Mol Sci ; 21(10)2020 May 21.
Article in English | MEDLINE | ID: mdl-32455614

ABSTRACT

Epigenetic editing, an emerging technique used for the modulation of gene expression in mammalian cells, is a promising strategy to correct disease-related gene expression. Although epigenetic reprogramming results in sustained transcriptional modulation in several in vivo models, further studies are needed to develop this approach into a straightforward technology for effective and specific interventions. Important goals of current research efforts are understanding the context-dependency of successful epigenetic editing and finding the most effective epigenetic effector(s) for specific tasks. Here we tested whether the fibrosis- and cancer-associated PLOD2 gene can be repressed by the DNA methyltransferase M.SssI, or by the non-catalytic Krüppel associated box (KRAB) repressor directed to the PLOD2 promoter via zinc finger- or CRISPR-dCas9-mediated targeting. M.SssI fusions induced de novo DNA methylation, changed histone modifications in a context-dependent manner, and led to 50%-70% reduction in PLOD2 expression in fibrotic fibroblasts and in MDA-MB-231 cancer cells. Targeting KRAB to PLOD2 resulted in the deposition of repressive histone modifications without DNA methylation and in almost complete PLOD2 silencing. Interestingly, both long-term TGFß1-induced, as well as unstimulated PLOD2 expression, was completely repressed by KRAB, while M.SssI only prevented the TGFß1-induced PLOD2 expression. Targeting transiently expressed dCas9-KRAB resulted in sustained PLOD2 repression in HEK293T and MCF-7 cells. Together, these findings point to KRAB outperforming DNA methylation as a small potent targeting epigenetic effector for silencing TGFß1-induced and uninduced PLOD2 expression.


Subject(s)
Gene Silencing , Heterochromatin/metabolism , Kruppel-Like Transcription Factors/metabolism , Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase/genetics , Adult , Cells, Cultured , DNA-Cytosine Methylases/genetics , DNA-Cytosine Methylases/metabolism , Epigenesis, Genetic , HEK293 Cells , Humans , Kruppel-Like Transcription Factors/genetics , MCF-7 Cells , Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase/metabolism , Promoter Regions, Genetic , Transcriptional Activation , Transforming Growth Factor beta/metabolism
10.
Bioorg Med Chem Lett ; 29(15): 1922-1927, 2019 08 01.
Article in English | MEDLINE | ID: mdl-31155430

ABSTRACT

A major challenge in the application of cytotoxic anti-cancer drugs is their general lack of selectivity, which often leads to systematic toxicity due to their inability to discriminate between malignant and healthy cells. A particularly promising target for selective targeting are the folate receptors (FR) that are often over-expressed on cancer cells. Here, we report on a conjugate of the pentadentate nitrogen ligand N4Py to folic acid, via a cleavable disulphide linker, which shows selective cytotoxicity against folate receptor expressing cancer cells.


Subject(s)
Antineoplastic Agents/therapeutic use , Bleomycin/therapeutic use , Folic Acid/therapeutic use , Neoplasms/drug therapy , Antineoplastic Agents/pharmacology , Bleomycin/pharmacology , Folic Acid/pharmacology , Humans
11.
Trends Genet ; 31(7): 353-6, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25891224

ABSTRACT

Despite decades of research, mitochondrial epigenetics remains a controversial notion. Recent findings, however, indicate that dysfunctional mitochondrial DNA (mtDNA) methylation could underlie aging and disease. Unraveling such a level of regulation will be essential in the understanding of and in interfering with the role of mitochondria in many physiological and pathophysiological processes.


Subject(s)
Epigenesis, Genetic , Mitochondria/genetics , Animals , DNA Methylation , DNA, Mitochondrial/genetics , Genes, Mitochondrial , Humans , Mitochondria/enzymology
12.
Inorg Chem ; 57(13): 7748-7756, 2018 Jul 02.
Article in English | MEDLINE | ID: mdl-29916702

ABSTRACT

Metal coordination complexes can display interesting biological activity, as illustrated by the bleomycins (BLMs), a family of natural antibiotics that when coordinated to a redox-active metal ion, show antitumor activity. Yet, which metal ion is required for the activity in cells is still subject to debate. In this study, we described how different metal ions affect the intracellular behavior and activity of the synthetic BLM-mimic N, N-bis(2-pyridylmethyl)- N-bis(2-pyridyl)methylamine (N4Py). Our study shows that a mixture of iron(II), copper(II), and zinc(II) complexes can be generated when N4Py is added to cell cultures but that the metal ion can also be exchanged by other metal ions present in cells. Moreover, the combination of chemical data, together with the performed biological experiments, shows that the active complex causing oxidative damage to cells is the FeII-N4Py complex and not per se the metal complex that was initially added to the cell culture medium. Finally, it is proposed that the high activity observed upon the addition of the free N4Py ligand is the result of a combination of scavenging of biologically relevant metals and oxidative damage caused by the iron(II) complex.


Subject(s)
Coordination Complexes/chemistry , Coordination Complexes/pharmacology , Metals, Heavy/chemistry , Pyridines/chemistry , Pyridines/pharmacology , Cell Line, Tumor , Humans , Intracellular Space/drug effects , Intracellular Space/metabolism , Ligands , Models, Molecular , Molecular Conformation , Structure-Activity Relationship
13.
Brain ; 140(12): 3252-3268, 2017 Dec 01.
Article in English | MEDLINE | ID: mdl-29155979

ABSTRACT

The Dlg4 gene encodes for post-synaptic density protein 95 (PSD95), a major synaptic protein that clusters glutamate receptors and is critical for plasticity. PSD95 levels are diminished in ageing and neurodegenerative disorders, including Alzheimer's disease and Huntington's disease. The epigenetic mechanisms that (dys)regulate transcription of Dlg4/PSD95, or other plasticity genes, are largely unknown, limiting the development of targeted epigenome therapy. We analysed the Dlg4/PSD95 epigenetic landscape in hippocampal tissue and designed a Dlg4/PSD95 gene-targeting strategy: a Dlg4/PSD95 zinc finger DNA-binding domain was engineered and fused to effector domains to either repress (G9a, Suvdel76, SKD) or activate (VP64) transcription, generating artificial transcription factors or epigenetic editors (methylating H3K9). These epi-editors altered critical histone marks and subsequently Dlg4/PSD95 expression, which, importantly, impacted several hippocampal neuron plasticity processes. Intriguingly, transduction of the artificial transcription factor PSD95-VP64 rescued memory deficits in aged and Alzheimer's disease mice. Conclusively, this work validates PSD95 as a key player in memory and establishes epigenetic editing as a potential therapy to treat human neurological disorders.


Subject(s)
Alzheimer Disease/genetics , Behavior, Animal , Cognition , Disks Large Homolog 4 Protein/genetics , Epigenetic Repression , Hippocampus/metabolism , Memory , Transcriptional Activation , Alzheimer Disease/pathology , Alzheimer Disease/physiopathology , Alzheimer Disease/psychology , Amyloid beta-Protein Precursor/genetics , Animals , Disease Models, Animal , Epigenesis, Genetic , Histone Code , Humans , Mice , Mice, Transgenic , Rats , Zinc Fingers
14.
J Appl Toxicol ; 38(6): 888-895, 2018 06.
Article in English | MEDLINE | ID: mdl-29423916

ABSTRACT

Cadmium (Cd), a carcinogenic toxic metal, is pervasively distributed in the soil, water and air. Chronic exposure to Cd has been correlated to lung disease development including cancers. Although many studies have been conducted to investigate the proteome response of cells challenged with Cd, the epiproteomic responses (i.e., global histone post-translational modifications [PTMs]), particularly in human lung cells, are largely unexplored. Here, we provide an epiproteome profiling of human bronchial epithelial cells (BEAS-2B) chronically treated with cadmium chloride (CdCl2 ), with the aim of identifying global epiproteomic signatures in response to Cd epigenotoxicity. Total histone proteins from Cd-treated and untreated BEAS-2B cells were isolated and subject to quantitative histone PTM-enzyme-linked immunosorbent assay using 18 histone PTM antibodies. Our results unveiled that chronic Cd treatment led to the marked downregulation of H3K4me2 and H3K36me3 and upregulation of H3K9acS10ph, H4K5ac, H4K8ac and H4K12ac PTM marks. Cd-treated cells exhibit transformed cell properties as evidenced by enhanced cell migration and the ability of anchorage-independent growth on soft agar. Notably, treatment of Cd-transformed cells with C646, a potent histone acetyltransferase inhibitor, suppressed the expression of mesenchymal marker genes and cell migration ability of these cells. Taken together, our studies provide for the first time the global epiproteomic interrogation of chronic Cd-exposed human lung cells. The identified aberrant histone PTM alterations associated with Cd-induced epigenotoxicity likely account for the epithelial-mesenchymal transition and neoplastic survival of these cells.


Subject(s)
Bronchi/drug effects , Cadmium Chloride/toxicity , Enzyme-Linked Immunosorbent Assay , Epithelial Cells/drug effects , Histones/metabolism , Protein Processing, Post-Translational/drug effects , Proteomics/methods , Acetylation , Bronchi/metabolism , Bronchi/pathology , Cell Line , Cell Movement/drug effects , Cell Proliferation/drug effects , Enzyme Inhibitors/pharmacology , Epithelial Cells/metabolism , Epithelial Cells/pathology , Epithelial-Mesenchymal Transition/drug effects , Histone Acetyltransferases/antagonists & inhibitors , Histone Acetyltransferases/metabolism , Humans , Methylation
15.
Am J Physiol Lung Cell Mol Physiol ; 312(3): L334-L347, 2017 03 01.
Article in English | MEDLINE | ID: mdl-28011616

ABSTRACT

Airway mucus hypersecretion contributes to the morbidity and mortality in patients with chronic inflammatory lung diseases. Reducing mucus production is crucial for improving patients' quality of life. The transcription factor SAM-pointed domain-containing Ets-like factor (SPDEF) plays a critical role in the regulation of mucus production and, therefore, represents a potential therapeutic target. This study aims to reduce lung epithelial mucus production by targeted silencing SPDEF using the novel strategy, epigenetic editing. Zinc fingers and CRISPR/dCas platforms were engineered to target repressors (KRAB, DNA methyltransferases, histone methyltransferases) to the SPDEF promoter. All constructs were able to effectively suppress both SPDEF mRNA and protein expression, which was accompanied by inhibition of downstream mucus-related genes [anterior gradient 2 (AGR2), mucin 5AC (MUC5AC)]. For the histone methyltransferase G9A, and not its mutant or other effectors, the obtained silencing was mitotically stable. These results indicate efficient SPDEF silencing and downregulation of mucus-related gene expression by epigenetic editing, in human lung epithelial cells. This opens avenues for epigenetic editing as a novel therapeutic strategy to induce long-lasting mucus inhibition.


Subject(s)
Epigenesis, Genetic , Epithelial Cells/metabolism , Gene Editing , Lung/cytology , Mucus/metabolism , Proto-Oncogene Proteins c-ets/genetics , Base Sequence , Cell Line , DNA (Cytosine-5-)-Methyltransferases/genetics , DNA (Cytosine-5-)-Methyltransferases/metabolism , DNA Methylation/genetics , DNA Methyltransferase 3A , Down-Regulation/genetics , Gene Silencing , Histocompatibility Antigens/genetics , Histocompatibility Antigens/metabolism , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Humans , Models, Biological , Mucin 5AC/metabolism , Promoter Regions, Genetic/genetics , Protein Domains , Proto-Oncogene Proteins c-ets/metabolism , Zinc Fingers
16.
Mol Ther ; 24(3): 536-47, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26686387

ABSTRACT

DNA hypermethylation is extensively explored as therapeutic target for gene expression modulation in cancer. Here, we re-activated hypermethylated candidate tumor suppressor genes (TSGs) (C13ORF18, CCNA1, TFPI2, and Maspin) by TET2-induced demethylation in cervical cancer cell lines. To redirect TET2 to hypermethylated TSGs, we engineered zinc finger proteins (ZFPs), which were first fused to the transcriptional activator VP64 to validate effective gene re-expression and confirm TSG function. ChIP-Seq not only revealed enriched binding of ZFPs to their intended sequence, but also considerable off-target binding, especially at promoter regions. Nevertheless, results obtained by targeted re-expression using ZFP-VP64 constructs were in line with cDNA overexpression; both revealed strong growth inhibition for C13ORF18 and TFPI2, but not for CCNA1 and Maspin. To explore effectivity of locus-targeted demethylation, ZFP-TET2 fusions were constructed which efficiently demethylated genes with subsequent gene re-activation. Moreover, targeting TET2 to TFPI2 and C13ORF18, but not CCNA1, significantly decreased cell growth, viability, and colony formation in cervical cancer cells compared to a catalytically inactive mutant of TET2. These data underline that effective re-activation of hypermethylated genes can be achieved through targeted DNA demethylation by TET2, which can assist in realizing sustained re-expression of genes of interest.


Subject(s)
DNA-Binding Proteins/metabolism , Epigenesis, Genetic , Gene Expression Regulation, Neoplastic , Gene Silencing , Genes, Tumor Suppressor , Proto-Oncogene Proteins/metabolism , Uterine Cervical Neoplasms/genetics , Uterine Cervical Neoplasms/metabolism , Cell Line, Tumor , DNA Methylation , Dioxygenases , Female , Gene Editing , Humans , Protein Binding , Recombinant Fusion Proteins , Zinc Fingers
17.
J Biol Chem ; 290(47): 28465-28476, 2015 Nov 20.
Article in English | MEDLINE | ID: mdl-26432637

ABSTRACT

PLOD2 (procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2) hydroxylates lysine residues in collagen telopeptides and is essential for collagen pyridinoline cross-link formation. PLOD2 expression and subsequent pyridinoline cross-links are increased in fibrotic pathologies by transforming growth factor ß-1 (TGFß1). In this report we examined the molecular processes underlying TGFß1-induced PLOD2 expression. We found that binding of the TGFß1 pathway related transcription factors SMAD3 and SP1-mediated TGFß1 enhanced PLOD2 expression and could be correlated to an increase of acetylated histone H3 and H4 at the PLOD2 promoter. Interestingly, the classical co-activators of SMAD3 complexes, p300 and CBP, were not responsible for the enhanced H3 and H4 acetylation. Depletion of SMAD3 reduced PLOD2 acetylated H3 and H4, indicating that another as of yet unidentified histone acetyltransferase binds to SMAD3 at PLOD2. Assessing histone methylation marks at the PLOD2 promoter depicted an increase of the active histone mark H3K79me2, a decrease of the repressive H4K20me3 mark, but no role for the generally strong transcription-related modifications: H3K4me3, H3K9me3 and H3K27me3. Collectively, our findings reveal that TGFß1 induces a SP1- and SMAD3-dependent recruitment of histone modifying enzymes to the PLOD2 promoter other than the currently known TGFß1 downstream co-activators and epigenetic modifications. This also suggests that additional activation strategies are used downstream of the TGFß1 pathway, and hence their unraveling could be of great importance to fully understand TGFß1 activation of genes.


Subject(s)
Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase/metabolism , Transforming Growth Factor beta1/metabolism , Acetylation , Cells, Cultured , Histones/metabolism , Humans , Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase/genetics , Promoter Regions, Genetic , Protein Serine-Threonine Kinases/metabolism , Receptor, Transforming Growth Factor-beta Type I , Receptors, Transforming Growth Factor beta/metabolism , Smad3 Protein/metabolism , Sp1 Transcription Factor/metabolism
18.
Nucleic Acids Res ; 42(3): 1563-74, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24194590

ABSTRACT

Increasing evidence indicates that active DNA demethylation is involved in several processes in mammals, resulting in developmental stage-specificity and cell lineage-specificity. The recently discovered Ten-Eleven Translocation (TET) dioxygenases are accepted to be involved in DNA demethylation by initiating 5-mC oxidation. Aberrant DNA methylation profiles are associated with many diseases. For example in cancer, hypermethylation results in silencing of tumor suppressor genes. Such silenced genes can be re-expressed by epigenetic drugs, but this approach has genome-wide effects. In this study, fusions of designer DNA binding domains to TET dioxygenase family members (TET1, -2 or -3) were engineered to target epigenetically silenced genes (ICAM-1, EpCAM). The effects on targeted CpGs' methylation and on expression levels of the target genes were assessed. The results indicated demethylation of targeted CpG sites in both promoters for targeted TET2 and to a lesser extent for TET1, but not for TET3. Interestingly, we observed re-activation of transcription of ICAM-1. Thus, our work suggests that we provided a mechanism to induce targeted DNA demethylation, which facilitates re-activation of expression of the target genes. Furthermore, this Epigenetic Editing approach is a powerful tool to investigate functions of epigenetic writers and erasers and to elucidate consequences of epigenetic marks.


Subject(s)
DNA-Binding Proteins/metabolism , DNA/metabolism , Dioxygenases/metabolism , Epigenesis, Genetic , Intercellular Adhesion Molecule-1/genetics , Promoter Regions, Genetic , Proto-Oncogene Proteins/metabolism , Animals , Antigens, Neoplasm/genetics , Cell Adhesion Molecules/genetics , Cell Line, Tumor , DNA Methylation , Epithelial Cell Adhesion Molecule , HEK293 Cells , Humans , Intercellular Adhesion Molecule-1/biosynthesis , Mice , Transcriptional Activation , Zinc Fingers
19.
Adv Exp Med Biol ; 945: 475-490, 2016.
Article in English | MEDLINE | ID: mdl-27826848

ABSTRACT

Epigenetic regulation of gene expression is vital for the maintenance of genome integrity and cell phenotype. In addition, many different diseases have underlying epigenetic mutations, and understanding their role and function may unravel new insights for diagnosis, treatment, and even prevention of diseases. It was an important breakthrough when epigenetic alterations could be gene-specifically manipulated using epigenetic regulatory proteins in an approach termed epigenetic editing. Epigenetic editors can be designed for virtually any gene by targeting effector domains to a preferred sequence, where they write or erase the desired epigenetic modification. This chapter describes the tools for editing DNA methylation signatures and their applications. In addition, we explain how to achieve targeted DNA (de)methylation and discuss the advantages and disadvantages of this approach. Silencing genes directly at the DNA methylation level instead of targeting the protein and/or RNA is a major improvement, as repression is achieved at the source of expression, potentially eliminating the need for continuous administration. Re-expression of silenced genes by targeted demethylation might closely represent the natural situation, in which all transcript variants might be expressed in a sustainable manner. Altogether epigenetic editing, for example, by rewriting DNA methylation, will assist in realizing the curable genome concept.


Subject(s)
DNA Methylation/genetics , DNA/genetics , Epigenesis, Genetic , Gene Expression Regulation/genetics , Gene Editing , Gene Silencing , Genome, Human , Humans , Molecular Targeted Therapy , RNA
20.
Biochim Biophys Acta ; 1846(2): 494-509, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25270772

ABSTRACT

Ovarian cancer is the most lethal gynecological tumor type in the world due to late stage detection, and resistance to chemotherapy. Therefore, alternative additional therapies are required. The etiology of ovarian cancer remains largely unknown, but risk factors point toward an important role for oxidative stress. Both healthy and tumor cells can cope with oxidative stress by activating the transcription factor Nrf2 (also known as Nfe2l2), the master regulator of antioxidant and cytoprotective genes. Indeed, for most ovarian cancers, aberrant activation of Nrf2 is observed, which is often associated with a copy number loss within the Nrf2-inhibitory complex KEAP1-CUL3-RBX1. A key role for Nrf2 in ovarian carcinogenesis has been validated by siRNA studies. However, to exploit the Nrf2 pathway for therapeutic interventions, potential side-effects should be minimized. In this review, we explore ovarian cancer specific factors with links to aberrant activity of Nrf2, to be exploited in future combination strategies, synergistic with direct Nrf2 inhibitory drugs. Particularly, we propose to stratify patients based on common ovarian cancer mutations (KRAS, BRAF, ERBB2, BRCA1 and its link with estradiol, TP53) for future NRF2 targeting strategies.


Subject(s)
NF-E2-Related Factor 2/physiology , Ovarian Neoplasms/etiology , Animals , Female , Genes, Tumor Suppressor , Humans , Mutation , NF-E2-Related Factor 2/antagonists & inhibitors , Oncogenes , Ovarian Neoplasms/genetics , Oxidative Stress
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