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1.
Int J Mol Sci ; 23(19)2022 Sep 27.
Article En | MEDLINE | ID: mdl-36232714

Acute myeloid leukemia (AML) is a rapidly progressing heterogeneous disease with a high mortality rate, which is characterized by hyperproliferation of atypical immature myeloid cells. The number of AML patients is expected to increase in the near future, due to the old-age-associated nature of AML and increased longevity in the human population. RUNX1 and CEBPA, key transcription factors (TFs) of hematopoiesis, are frequently and independently mutated in AML. RUNX1 and CEBPA can bind TET2 demethylase and attract it to their binding sites (TFBS) in cell lines, leading to DNA demethylation of the regions nearby. Since TET2 does not have a DNA-binding domain, TFs are crucial for its guidance to target genomic locations. In this paper, we show that RUNX1 and CEBPA mutations in AML patients affect the methylation of important regulatory sites that resulted in the silencing of several RUNX1 and CEBPA target genes, most likely in a TET2-dependent manner. We demonstrated that hypermethylation of TFBS in AML cells with RUNX1 mutations was associated with resistance to anticancer chemotherapy. Demethylation therapy restored expression of the RUNX1 target gene, BIK, and increased sensitivity of AML cells to chemotherapy. If our results are confirmed, mutations in RUNX1 could be an indication for prescribing the combination of cytotoxic and demethylation therapies.


CCAAT-Enhancer-Binding Proteins , Core Binding Factor Alpha 2 Subunit , Leukemia, Myeloid, Acute , CCAAT-Enhancer-Binding Proteins/genetics , CCAAT-Enhancer-Binding Proteins/metabolism , Core Binding Factor Alpha 2 Subunit/genetics , Core Binding Factor Alpha 2 Subunit/metabolism , DNA/genetics , DNA/metabolism , DNA Methylation/genetics , Demethylation/drug effects , Humans , Leukemia, Myeloid, Acute/drug therapy , Leukemia, Myeloid, Acute/genetics , Leukemia, Myeloid, Acute/metabolism , Mutation
2.
N Engl J Med ; 386(21): 1998-2010, 2022 05 26.
Article En | MEDLINE | ID: mdl-35613022

BACKGROUND: Although hypomethylating agents are currently used to treat patients with cancer, whether they can also reactivate and up-regulate oncogenes is not well elucidated. METHODS: We examined the effect of hypomethylating agents on SALL4, a known oncogene that plays an important role in myelodysplastic syndrome and other cancers. Paired bone marrow samples that were obtained from two cohorts of patients with myelodysplastic syndrome before and after treatment with a hypomethylating agent were used to explore the relationships among changes in SALL4 expression, treatment response, and clinical outcome. Leukemic cell lines with low or undetectable SALL4 expression were used to study the relationship between SALL4 methylation and expression. A locus-specific demethylation technology, CRISPR-DNMT1-interacting RNA (CRISPR-DiR), was used to identify the CpG island that is critical for SALL4 expression. RESULTS: SALL4 up-regulation after treatment with hypomethylating agents was observed in 10 of 25 patients (40%) in cohort 1 and in 13 of 43 patients (30%) in cohort 2 and was associated with a worse outcome. Using CRISPR-DiR, we discovered that demethylation of a CpG island within the 5' untranslated region was critical for SALL4 expression. In cell lines and patients, we confirmed that treatment with a hypomethylating agent led to demethylation of the same CpG region and up-regulation of SALL4 expression. CONCLUSIONS: By combining analysis of patient samples with CRISPR-DiR technology, we found that demethylation and up-regulation of an oncogene after treatment with a hypomethylating agent can indeed occur and should be further studied. (Funded by Associazione Italiana per la Ricerca sul Cancro and others.).


Antineoplastic Agents , Demethylation , Myelodysplastic Syndromes , Oncogenes , Up-Regulation , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Clustered Regularly Interspaced Short Palindromic Repeats , Demethylation/drug effects , Humans , Myelodysplastic Syndromes/drug therapy , Myelodysplastic Syndromes/genetics , Neoplasms/drug therapy , Neoplasms/genetics , Oncogenes/drug effects , Oncogenes/physiology , Transcription Factors/biosynthesis , Transcription Factors/genetics , Transcription Factors/metabolism , Up-Regulation/drug effects
3.
Cell Oncol (Dordr) ; 45(3): 355-365, 2022 Jun.
Article En | MEDLINE | ID: mdl-35579750

PURPOSE: N6-methyladenosine (m6A), the most prevalent mRNA modification, plays an essential role in tumorigenesis. Notably, increasing interest has been directed to bioactive peptides (BPs) with antitumor activities. Here, we set out to investigate the potential of the BP-regulated ALKBH5/MLST8/EIF4EBP1 axis on prevention and treatment of acute myeloid leukemia (AML). METHODS: The biological effects of BP on AML cells were detected by MTT and ApoLive-Glo™ multiplex assays. The role of BP in tumor growth was determined by a subcutaneous xenograft model. The ALKBH5/MLST8/EIF4EBP1 axis was identified as a potential BP target in AML via methylated RNA immunoprecipitation sequencing (MeRIP-seq) combined with RNA sequencing (RNA-seq). Western blot, RT-qPCR, MeRIP-qPCR, dual-luciferase reporter and RNA stability assays were performed to validate the function and mode of action of the BP-regulated ALKBH5/MLST8/EIF4EBP1 axis. The clinical relevance of the BP-regulated ALKBH5/MLST8/EIF4EBP1 axis in AML was confirmed by TCGA data analysis. RESULTS: We found that BP can inhibit AML cell proliferation and promote apoptosis in vitro, and repress AML tumor growth in vivo. Mechanistically, we found that BP downregulated ALKBH5 expression, which in turn repressed m6A demethylation of MLST8 and EIF4EBP1 mRNAs. Reduction of the m6A levels of MLST8 and EIF4EBP1 facilitated MLST8 and EIF4EBP1 mRNA decay, resulting in inhibition of AML cell proliferation. Furthermore, we found that the BP-regulated ALKBH5/MLST8/EIF4EBP1 axis closely correlates with AML patient prognosis. CONCLUSIONS: Our data indicate that BP can inhibit acute myeloid leukemia cell proliferation by downregulating ALKBH5-mediated m6A demethylation of EIF4EBP1 and MLST8 mRNAs, which may have potential to prevent and treat this disease.


Adaptor Proteins, Signal Transducing , AlkB Homolog 5, RNA Demethylase , Cell Cycle Proteins , Leukemia, Myeloid, Acute , Peptides , mTOR Associated Protein, LST8 Homolog , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , AlkB Homolog 5, RNA Demethylase/genetics , AlkB Homolog 5, RNA Demethylase/metabolism , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Cell Proliferation/drug effects , Demethylation/drug effects , Down-Regulation/drug effects , Humans , Leukemia, Myeloid, Acute/drug therapy , Leukemia, Myeloid, Acute/genetics , Leukemia, Myeloid, Acute/metabolism , Leukemia, Myeloid, Acute/pathology , Peptides/pharmacology , RNA, Messenger/genetics , RNA, Messenger/metabolism , mTOR Associated Protein, LST8 Homolog/genetics , mTOR Associated Protein, LST8 Homolog/metabolism
4.
J Biol Chem ; 298(2): 101563, 2022 02.
Article En | MEDLINE | ID: mdl-34998823

The cytidine deaminase APOBEC3B (A3B) is an endogenous inducer of somatic mutations and causes chromosomal instability by converting cytosine to uracil in single-stranded DNA. Therefore, identification of factors and mechanisms that mediate A3B expression will be helpful for developing therapeutic approaches to decrease DNA mutagenesis. Arsenic (As) is one well-known mutagen and carcinogen, but the mechanisms by which it induces mutations have not been fully elucidated. Herein, we show that A3B is upregulated and required for As-induced DNA damage and mutagenesis. We found that As treatment causes a decrease of N6-methyladenosine (m6A) modification near the stop codon of A3B, consequently increasing the stability of A3B mRNA. We further reveal that the demethylase FTO is responsible for As-reduced m6A modification of A3B, leading to increased A3B expression and DNA mutation rates in a manner dependent on the m6A reader YTHDF2. Our in vivo data also confirm that A3B is a downstream target of FTO in As-exposed lung tissues. In addition, FTO protein is highly expressed and positively correlates with the protein levels of A3B in tumor samples from human non-small cell lung cancer patients. These findings indicate a previously unrecognized role of A3B in As-triggered somatic mutation and might open new avenues to reduce DNA mutagenesis by targeting the FTO/m6A axis.


Adenosine/analogs & derivatives , Alpha-Ketoglutarate-Dependent Dioxygenase FTO , Arsenic , Carcinoma, Non-Small-Cell Lung , Cytidine Deaminase , Lung Neoplasms , Minor Histocompatibility Antigens , RNA, Messenger , Adenosine/genetics , Adenosine/metabolism , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/metabolism , Arsenic/toxicity , Carcinoma, Non-Small-Cell Lung/chemically induced , Carcinoma, Non-Small-Cell Lung/genetics , Cytidine Deaminase/genetics , Cytidine Deaminase/metabolism , Demethylation/drug effects , Humans , Minor Histocompatibility Antigens/genetics , Minor Histocompatibility Antigens/metabolism , Mutagenesis , RNA, Messenger/genetics , RNA, Messenger/metabolism
5.
Molecules ; 26(21)2021 Oct 20.
Article En | MEDLINE | ID: mdl-34770760

Environmental stimuli attack the skin daily resulting in the generation of reactive oxygen species (ROS) and inflammation. One pathway that regulates oxidative stress in skin involves Protein Phosphatase 2A (PP2A), a phosphatase which has been previously linked to Alzheimer's Disease and aging. Oxidative stress decreases PP2A methylation in normal human dermal fibroblasts (NHDFs). Thus, we hypothesize agents that increase PP2A methylation and activity will promote skin health and combat aging. To discover novel inhibitors of PP2A demethylation activity, we screened a library of 32 natural botanical extracts. We discovered Grape Seed Extract (GSE), which has previously been reported to have several benefits for skin, to be the most potent PP2A demethylating extract. Via several fractionation and extraction steps we developed a novel grape seed extract called Activated Grape Seed Extract (AGSE), which is enriched for PP2A activating flavonoids that increase potency in preventing PP2A demethylation when compared to commercial GSE. We then determined that 1% AGSE and 1% commercial GSE exhibit distinct gene expression profiles when topically applied to a 3D human skin model. To begin to characterize AGSE's activity, we investigated its antioxidant potential and demonstrate it reduces ROS levels in NHDFs and cell-free assays equal to or better than Vitamin C and E. Moreover, AGSE shows anti-inflammatory properties, dose-dependently inhibiting UVA, UVB and chemical-induced inflammation. These results demonstrate AGSE is a novel, multi-functional extract that modulates methylation levels of PP2A and supports the hypothesis of PP2A as a master regulator for oxidative stress signaling and aging in skin.


Flavonoids/pharmacology , Grape Seed Extract/pharmacology , Oxidative Stress/drug effects , Skin/drug effects , Skin/metabolism , Animals , Anti-Inflammatory Agents/chemistry , Anti-Inflammatory Agents/pharmacology , Antioxidants/chemistry , Antioxidants/pharmacology , Chemical Fractionation , Chromatography, High Pressure Liquid , Cytokines/biosynthesis , Demethylation/drug effects , Dose-Response Relationship, Drug , Fibroblasts/drug effects , Fibroblasts/metabolism , Flavonoids/chemistry , Flavonoids/isolation & purification , Grape Seed Extract/chemistry , Grape Seed Extract/isolation & purification , Humans , Protein Phosphatase 2/metabolism
6.
Biomed Pharmacother ; 141: 111681, 2021 Sep.
Article En | MEDLINE | ID: mdl-34139552

Renal Cell Carcinoma (RCC) is on the top 10 of the most incident cancers worldwide, being a third of patients diagnosed with advanced disease, for which no curative therapies are currently available. Thus, new effective therapeutic strategies are urgently needed. Herein, we tested the antineoplastic effect of newly synthesized 3-nitroflavanones (MLo1302) on RCC cell lines. 786-O, Caki2, and ACHN cell lines were cultured and treated with newly synthesized 3-nitroflavanones. IC50 values were calculated based on the effect on cell viability assessed by MTT assay, after 72 h of exposure. MLo1302 displayed antineoplastic properties in RCC cell lines through marked reduction of cell viability, increased apoptosis and DNA damage, and morphometric alterations indicating a less aggressive phenotype. MLo1302 induced a significant reduction of global DNA methylation and DNMT mRNA levels, increasing global DNA hydroxymethylation and TET expression. Moreover, MLo1302 decreased DNMT3A activity in RCC cell lines, demethylated and re-expressed hypermethylated genes in CAM-generated tumors. A marked in vivo decrease in tumor growth and angiogenesis was also disclosed. MLo1302 disclosed antineoplastic and demethylating activity in RCC cell lines, constituting a potential therapeutic agent for RCC patients.


Antineoplastic Agents/chemical synthesis , Carcinoma, Renal Cell/metabolism , DNA Methylation/drug effects , Demethylation/drug effects , Flavanones/chemical synthesis , Kidney Neoplasms/metabolism , Animals , Antineoplastic Agents/pharmacology , Cell Line, Tumor , Cell Survival/drug effects , Cell Survival/physiology , Chick Embryo , DNA Methylation/physiology , Dose-Response Relationship, Drug , Flavanones/pharmacology , Humans
7.
Nucleic Acids Res ; 49(10): 5779-5797, 2021 06 04.
Article En | MEDLINE | ID: mdl-34048572

Faithful genome integrity maintenance plays an essential role in cell survival. Here, we identify the RNA demethylase ALKBH5 as a key regulator that protects cells from DNA damage and apoptosis during reactive oxygen species (ROS)-induced stress. We find that ROS significantly induces global mRNA N6-methyladenosine (m6A) levels by modulating ALKBH5 post-translational modifications (PTMs), leading to the rapid and efficient induction of thousands of genes involved in a variety of biological processes including DNA damage repair. Mechanistically, ROS promotes ALKBH5 SUMOylation through activating ERK/JNK signaling, leading to inhibition of ALKBH5 m6A demethylase activity by blocking substrate accessibility. Moreover, ERK/JNK/ALKBH5-PTMs/m6A axis is activated by ROS in hematopoietic stem/progenitor cells (HSPCs) in vivo in mice, suggesting a physiological role of this molecular pathway in the maintenance of genome stability in HSPCs. Together, our study uncovers a molecular mechanism involving ALKBH5 PTMs and increased mRNA m6A levels that protect genomic integrity of cells in response to ROS.


AlkB Homolog 5, RNA Demethylase/metabolism , DNA Damage , DNA Repair , Reactive Oxygen Species/metabolism , AlkB Homolog 5, RNA Demethylase/genetics , Animals , Apoptosis/drug effects , Apoptosis/genetics , Bone Marrow Cells/drug effects , Bone Marrow Cells/metabolism , Cell Line, Tumor , DNA Damage/drug effects , DNA Repair/drug effects , DNA Repair/genetics , Demethylation/drug effects , Fanconi Anemia Complementation Group Proteins/genetics , Fanconi Anemia Complementation Group Proteins/metabolism , Gene Expression Regulation/drug effects , Gene Expression Regulation/genetics , Hematopoietic Stem Cells/drug effects , Hematopoietic Stem Cells/metabolism , Humans , Hydrogen Peroxide/pharmacology , MAP Kinase Signaling System/drug effects , Methylation/drug effects , Mice , Phosphorylation , Protein Processing, Post-Translational , RNA, Small Interfering , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , RNA-Seq , Sumoylation/drug effects , Tandem Mass Spectrometry , X-linked Nuclear Protein/genetics , X-linked Nuclear Protein/metabolism
8.
Int J Mol Sci ; 22(2)2021 Jan 18.
Article En | MEDLINE | ID: mdl-33477402

We have previously shown that the Wnt canonical pathway (WCP) is constitutively active in most cases of mantle cell lymphoma (MCL). Here, we aimed to elucidate the mechanisms underlying this biochemical deregulation. We hypothesized that gene methylation/silencing of WIF1 (Wnt inhibitory factor-1), a physiologic inhibitor of WCP, contributes to the deregulation of WCP and promotes cell growth in MCL. In support of this hypothesis, we found that the expression of WIF1 was detectable in none of the 4 MCL cell lines, and in only 2 of 5 tumors (40%) examined. Using methylation-specific PCR, we found evidence of gene methylation of WIF1 in 4 of 5 cell lines (80%) and in 24 of 29 (82%) tumors. The addition of the demethylation agent 5-aza-2'-deoxycytidine to Mino and JeKo-1, two WIF1-negative cell lines, restored the expression of WIF1 mRNA in these cells. Gene transfection of WIF1 into JeKo-1 and Mino cells significantly reduced cell growth, and this finding correlated with substantial downregulations of various proteins in WCP, such as ß-catenin and pGSK-3ß. In conclusion, our results support the concept that gene methylation/silencing of WIF1 is a frequent event in MCL, and this abnormality contributes to the aberrant activation of WCP. These results have provided further evidence that aberrant Wnt signaling is pathogenetically important in MCL and it may represent a potential therapeutic target.


Adaptor Proteins, Signal Transducing/genetics , Glycogen Synthase Kinase 3 beta/genetics , Lymphoma, Mantle-Cell/genetics , beta Catenin/genetics , Cell Line, Tumor , Cell Proliferation/genetics , DNA Methylation/genetics , Decitabine/pharmacology , Demethylation/drug effects , Epigenesis, Genetic/genetics , Gene Expression Regulation, Neoplastic/genetics , Gene Silencing , Humans , Lymphoma, Mantle-Cell/pathology , Wnt Signaling Pathway/genetics
9.
ACS Chem Biol ; 16(2): 324-333, 2021 02 19.
Article En | MEDLINE | ID: mdl-33412003

N6-methyladenosine (m6A) has emerged as the most abundant mRNA modification that regulates gene expression in many physiological processes. m6A modification in RNA controls cellular proliferation and pluripotency and has been implicated in the progression of multiple disease states, including cancer. RNA m6A methylation is controlled by a multiprotein "writer" complex including the enzymatic factor methyltransferase-like protein 3 (METTL3) that regulates methylation and two "eraser" proteins, RNA demethylase ALKBH5 (ALKBH5) and fat mass- and obesity-associated protein (FTO), that demethylate m6A in transcripts. FTO can also demethylate N6,2'-O-dimethyladenosine (m6Am), which is found adjacent to the m7G cap structure in mRNA. FTO has recently gained interest as a potential cancer target, and small molecule FTO inhibitors such as meclofenamic acid have been shown to prevent tumor progression in both acute myeloid leukemia and glioblastoma in vivo models. However, current FTO inhibitors are unsuitable for clinical applications due to either poor target selectivity or poor pharmacokinetics. In this work, we describe the structure-based design, synthesis, and biochemical evaluation of a new class of FTO inhibitors. Rational design of 20 small molecules with low micromolar IC50's and specificity toward FTO over ALKBH5 identified two competitive inhibitors FTO-02 and FTO-04. Importantly, FTO-04 prevented neurosphere formation in patient-derived glioblastoma stem cells (GSCs) without inhibiting the growth of healthy neural stem cell-derived neurospheres. Finally, FTO-04 increased m6A and m6Am levels in GSCs consistent with FTO inhibition. These results support FTO-04 as a potential new lead for treatment of glioblastoma.


Alpha-Ketoglutarate-Dependent Dioxygenase FTO/antagonists & inhibitors , Antineoplastic Agents/pharmacology , Enzyme Inhibitors/pharmacology , Pyrimidines/pharmacology , Adenosine/analogs & derivatives , Adenosine/chemistry , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/chemistry , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/metabolism , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/metabolism , Binding Sites , Demethylation/drug effects , Drug Design , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/metabolism , Humans , Molecular Docking Simulation , Neoplastic Stem Cells , Protein Binding , Pyrimidines/chemical synthesis , Pyrimidines/metabolism , RNA/chemistry , RNA/metabolism
10.
J Cell Physiol ; 236(5): 3710-3724, 2021 05.
Article En | MEDLINE | ID: mdl-33043995

Following stress, transfer RNA (tRNA) is cleaved to generate tRNA halves (tiRNAs). These tiRNAs have been shown to repress protein translation. Angiogenin was considered the main enzyme that cleaves tRNA at its anticodon to generate 35-45 nucleotide long tiRNA halves, however, the recent reports indicate the presence of angiogenin-independent cleavage. We previously observed tRNA cleavage pattern occurring away from the anticodon site. To explore this noncanonical cleavage, we analyze tRNA cleavage patterns in rat model of ischemia-reperfusion and in two rat cell lines. In vivo mitochondrial tRNAs were prone to this noncanonical cleavage pattern. In vitro, however, cytosolic and mitochondrial tRNAs could be cleaved noncanonically. Our results show an important regulatory role of mitochondrial stress in angiogenin-mediated tRNA cleavage. Neither angiogenin nor RNH1 appear to regulate the noncanonical tRNA cleavage. Finally, we verified our previous findings of the role of Alkbh1 in regulating tRNA cleavage and its impact on noncanonical tRNA cleavage.


Cells/metabolism , RNA, Transfer/metabolism , Stress, Physiological , Animals , Antimycin A/toxicity , Arsenites/toxicity , Carrier Proteins/metabolism , Cell Line , Cells/drug effects , Cytosol/drug effects , Cytosol/metabolism , Demethylation/drug effects , Humans , Male , Mitochondria/drug effects , Mitochondria/metabolism , Rats, Wistar , Ribonuclease, Pancreatic/metabolism , Stress, Physiological/drug effects
11.
Endocrinology ; 161(11)2020 11 01.
Article En | MEDLINE | ID: mdl-32865566

Thyroid hormone (T3) plays pivotal roles in vertebrate development, acting via nuclear T3 receptors (TRs) that regulate gene transcription by promoting post-translational modifications to histones. Methylation of cytosine residues in deoxyribonucleic acid (DNA) also modulates gene transcription, and our recent finding of predominant DNA demethylation in the brain of Xenopus tadpoles at metamorphosis, a T3-dependent developmental process, caused us to hypothesize that T3 induces these changes in vivo. Treatment of premetamorphic tadpoles with T3 for 24 or 48 hours increased immunoreactivity in several brain regions for the DNA demethylation intermediates 5-hydroxymethylcytosine (5-hmC) and 5-carboxylcytosine, and the methylcytosine dioxygenase ten-eleven translocation 3 (TET3). Thyroid hormone treatment induced locus-specific DNA demethylation in proximity to known T3 response elements within the DNA methyltransferase 3a and Krüppel-like factor 9 genes, analyzed by 5-hmC immunoprecipitation and methylation sensitive restriction enzyme digest. Chromatin-immunoprecipitation (ChIP) assay showed that T3 induced TET3 recruitment to these loci. Furthermore, the messenger ribonucleic acid for several genes encoding DNA demethylation enzymes were induced by T3 in a time-dependent manner in tadpole brain. A TR ChIP-sequencing experiment identified putative TR binding sites at several of these genes, and we provide multiple lines of evidence to support that tet2 contains a bona fide T3 response element. Our findings show that T3 can promote DNA demethylation in developing tadpole brain, in part by promoting TET3 recruitment to discrete genomic regions, and by inducing genes that encode DNA demethylation enzymes.


Brain/drug effects , DNA Demethylation/drug effects , Thyroid Hormones/pharmacology , Xenopus/embryology , Animals , Animals, Genetically Modified , Brain/embryology , Brain/metabolism , CpG Islands/drug effects , CpG Islands/genetics , Demethylation/drug effects , Dioxygenases/metabolism , Gene Expression Regulation, Developmental/drug effects , Larva/drug effects , Larva/genetics , Larva/growth & development , Metamorphosis, Biological/drug effects , Metamorphosis, Biological/genetics , Thyroid Hormone Receptors alpha/genetics , Xenopus/genetics , Xenopus Proteins/metabolism
12.
Int J Mol Sci ; 21(14)2020 Jul 18.
Article En | MEDLINE | ID: mdl-32708387

Multipotent human mesenchymal stem cells (MSCs) harbor clinically relevant immunomodulation, and HLA-G, a non-classical MHC class I molecule with highly restricted tissue expression, is one important molecule involved in these processes. Understanding of the natural regulatory mechanisms involved in expression of this elusive molecule has been difficult, with near exclusive reliance on cancer cell lines. We therefore studied the transcriptional control of HLA-G in primary isolated human bone marrow- (BM), human embryonic stem cell-derived (hE-), as well as placenta-derived MSCs (P-MSCs), and found that all 3 types of MSCs express 3 of the 7 HLA-G isoforms at the gene level; however, fibroblasts did not express HLA-G. Protein validation using BM- and P-MSCs demonstrated expression of 2 isoforms including a larger HLA-G-like protein. Interferon-γ (IFN-γ) stimulation upregulated both gene and protein expression in MSCs but not the constitutively expressing JEG-3 cell line. Most interestingly in human MSCs and placental tissue, hypomethylation of CpG islands not only occurs on the HLA-G proximal promoter but also on the gene body as well, a pattern not seen in either of the 2 commonly used choriocarcinoma cell lines which may contribute to the unique HLA-G expression patterns and IFN-γ-responsiveness in MSCs. Our study implicates the importance of using normal cells and tissues for physiologic understanding of tissue-specific transcriptional regulation, and highlight the utility of human MSCs in unraveling the transcriptional regulation of HLA-G for better therapeutic application.


Bone Marrow Cells/metabolism , DNA Methylation/genetics , DNA/metabolism , Embryonic Stem Cells/metabolism , HLA-G Antigens/metabolism , Mesenchymal Stem Cells/metabolism , Placenta/cytology , Azacitidine/pharmacology , Cell Line, Tumor , CpG Islands , DNA Methylation/drug effects , Demethylation/drug effects , Female , Fibroblasts/metabolism , Gene Expression Regulation/drug effects , Gene Expression Regulation/genetics , HLA-G Antigens/genetics , Humans , Interferon-gamma/pharmacology , Placenta/metabolism , Pregnancy , Promoter Regions, Genetic , Protein Isoforms , Tandem Mass Spectrometry
13.
Blood ; 136(7): 871-884, 2020 08 13.
Article En | MEDLINE | ID: mdl-32391874

Adult T-cell leukemia-lymphoma (ATL) is an aggressive hematological malignancy of CD4+ T cells transformed by human T-cell lymphotropic virus-1 (HTLV-1). Most HTLV-1-infected individuals are asymptomatic, and only 3% to 5% of carriers develop ATL. Here, we describe the contribution of aberrant DNA methylation to ATL leukemogenesis. HTLV-1-infected T-cells and their uninfected counterparts were separately isolated based on CADM1 and CD7 expression status, and differentially methylated positions (DMPs) specific to HTLV-infected T cells were identified through genome-wide DNA methylation profiling. Accumulation of DNA methylation at hypermethylated DMPs correlated strongly with ATL development and progression. In addition, we identified 22 genes downregulated because of promoter hypermethylation in HTLV-1-infected T cells, including THEMIS, LAIR1, and RNF130, which negatively regulate T-cell receptor (TCR) signaling. Phosphorylation of ZAP-70, a transducer of TCR signaling, was dysregulated in HTLV-1-infected cell lines but was normalized by reexpression of THEMIS. Therefore, we hypothesized that DNA hypermethylation contributes to growth advantages in HTLV-1-infected cells during ATL leukemogenesis. To test this idea, we investigated the anti-ATL activities of OR-1200 and OR-2100 (OR21), novel decitabine (DAC) prodrugs with enhanced oral bioavailability. Both DAC and OR21 inhibited cell growth, accompanied by global DNA hypomethylation, in xenograft tumors established by implantation of HTLV-1-infected cells. OR21 was less hematotoxic than DAC, whereas tumor growth inhibition was almost identical between the 2 compounds, making it suitable for long-term treatment of ATL patient-derived xenograft mice. Our results demonstrate that regional DNA hypermethylation is functionally important for ATL leukemogenesis and an effective therapeutic target.


Antineoplastic Agents/administration & dosage , DNA Methylation/drug effects , HTLV-I Infections/drug therapy , Leukemia-Lymphoma, Adult T-Cell/drug therapy , Pyridines/administration & dosage , Administration, Oral , Adult , Aged , Animals , Cell Transformation, Viral/drug effects , Cell Transformation, Viral/genetics , Cells, Cultured , DNA Methylation/genetics , Demethylation/drug effects , Drugs, Investigational/therapeutic use , Female , Gene Expression Regulation, Leukemic/drug effects , HTLV-I Infections/complications , HTLV-I Infections/genetics , Human T-lymphotropic virus 1/drug effects , Human T-lymphotropic virus 1/physiology , Humans , Leukemia-Lymphoma, Adult T-Cell/genetics , Mice , Mice, Inbred BALB C , Mice, Knockout , Molecular Targeted Therapy/methods , Xenograft Model Antitumor Assays , Young Adult
14.
Sci Rep ; 10(1): 6879, 2020 04 23.
Article En | MEDLINE | ID: mdl-32327675

The human genome is constantly attacked by endogenous and exogenous agents (ultraviolet light, xenobiotics, reactive oxygen species), which can induce chemical transformations leading to DNA lesions. To combat DNA damage, cells have developed several repair mechanisms; however, if the repair is defective, DNA lesions lead to permanent mutations. Single-cell gel electrophoresis (COMET assay) is a sensitive and well-established technique for quantifying DNA damage in individual cells. Nevertheless, this tool lacks relationship with mutagenesis. Therefore, to identify errors that give rise to mutations it would be convenient to test an alternative known procedure, such as next generation sequencing (NGS). Thus, the present work aims to evaluate the photomutagenicity of neuroleptic drug chlorpromazine (CPZ), and its N-demethylated metabolites using COMET assay and to test NGS as an alternative method to assess photomutagenesis. In this context, upon exposure to UVA radiation, COMET assay reveals CPZ-photosensitized DNA damage partially repaired by cells. Conversely with this result, metabolites demethylchlorpromazine (DMCPZ) and didemethylchlorpromazine (DDMCPZ) promote extensive DNA-photodamage, hardly repaired under the same conditions. Parallel assessment of mutagenesis by NGS is consistent with these results with minor discrepancies for DDMCPZ. To our knowledge, this is the first example demonstrating the utility of NGS for evaluating drug-induced photomutagenicity.


Chlorpromazine/toxicity , Demethylation , High-Throughput Nucleotide Sequencing , Metabolome , Mutagenesis/genetics , Cell Line , Chlorpromazine/chemistry , Demethylation/drug effects , Genetic Variation , Humans
15.
Cell Immunol ; 348: 104044, 2020 02.
Article En | MEDLINE | ID: mdl-32005344

We recently reported that Tregs from long-term Belatacept-treated kidney transplant patients displayed an altered phenotype and impaired suppressive function compared to Tregs from healthy controls. However, it remains unknown whether ex vivo expansion of Tregs from patients who underwent long-term immunosuppression may be feasible to be used in their treatment. In this work, Tregs from Belatacept-treated patients were polyclonally expanded in vitro in the presence of rapamycin and IL-2. After four weeks of expansion, Tregs from patients expressed high levels of FOXP3, CD25, CTLA-4, Helios and CCR7, and showed strong suppressive activity, even in the presence of pro-inflammatory cytokines. However, FOXP3 TSDR demethylation remained lower in expanded Tregs from Belatacept-treated patients compared to healthy control Tregs. These data suggest that ex vivo expansion of Tregs from patients undergoing long-term immunosuppression may require the use of epigenetic modifying agents to stabilize FOXP3 expression to be considered as treatment in kidney transplant patients.


Abatacept/therapeutic use , Immunosuppressive Agents/therapeutic use , Kidney Transplantation , T-Lymphocytes, Regulatory/drug effects , T-Lymphocytes, Regulatory/immunology , Cell Culture Techniques/methods , Demethylation/drug effects , Forkhead Transcription Factors , Humans , Immunocompromised Host , Phenotype , Sirolimus/pharmacology
16.
FEBS Open Bio ; 10(4): 525-534, 2020 04.
Article En | MEDLINE | ID: mdl-31977154

Prostate cancer (PCa) is the most prevalent cancer among men and the second leading cause of tumor-associated deaths worldwide, with increasing incidence rates over the last 10 years. Recently, miR-195 was reported to be hypermethylated at its promoter CpG island and down-regulated in hepatocellular carcinoma. However, the function of miR-195 and the underlying mechanisms in PCa remain unknown. Here, we report that a significant down-regulation of microRNA-195 (miR-195) in PCa tissues and cell lines was associated with promoter methylation status. Overexpression of miR-195 significantly suppressed cell proliferation, migration, invasion and epithelial-mesenchymal transition (increased E-cadherin and decreased N-cadherin) in PCa cells. We further demonstrated that transfection with a miR-195 inhibitor reversed the inhibitory effect of the DNA methyltransferase inhibitor 5-azacytidine on the proliferation, migration and invasion ability of PCa cells. In summary, our findings suggest that miR-195 may function as a crucial tumor suppressor in PCa.


Cell Movement/genetics , Cell Proliferation/genetics , Demethylation/drug effects , MicroRNAs/metabolism , Prostatic Neoplasms/metabolism , Prostatic Neoplasms/pathology , Signal Transduction/genetics , Apoptosis/drug effects , Apoptosis/genetics , Azacitidine/pharmacology , Cell Movement/drug effects , Cell Proliferation/drug effects , CpG Islands , DNA Methylation/drug effects , Down-Regulation , Epithelial-Mesenchymal Transition/drug effects , Epithelial-Mesenchymal Transition/genetics , Genes, Tumor Suppressor , Humans , Male , MicroRNAs/genetics , Neoplasm Invasiveness/genetics , PC-3 Cells , Promoter Regions, Genetic , Signal Transduction/drug effects , Transfection
17.
Life Sci Alliance ; 3(1)2020 01.
Article En | MEDLINE | ID: mdl-31882444

Epigenetic variation reflects the impact of a dynamic environment on chromatin. However, it remains elusive how environmental factors influence epigenetic events. Here, we show that G protein-coupled receptors (GPCRs) alter H3K4 methylation via oscillatory intracellular cAMP. Activation of Gs-coupled receptors caused a rapid decrease of H3K4me3 by elevating cAMP, whereas stimulation of Gi-coupled receptors increased H3K4me3 by diminishing cAMP. H3K4me3 gradually recovered towards baseline levels after the removal of GPCR ligands, indicating that H3K4me3 oscillates in tandem with GPCR activation. cAMP increased intracellular labile Fe(II), the cofactor for histone demethylases, through a non-canonical cAMP target-Rap guanine nucleotide exchange factor-2 (RapGEF2), which subsequently enhanced endosome acidification and Fe(II) release from the endosome via vacuolar H+-ATPase assembly. Removing Fe(III) from the media blocked intracellular Fe(II) elevation after stimulation of Gs-coupled receptors. Iron chelators and inhibition of KDM5 demethylases abolished cAMP-mediated H3K4me3 demethylation. Taken together, these results suggest a novel function of cAMP signaling in modulating histone demethylation through labile Fe(II).


Cyclic AMP/analogs & derivatives , Demethylation/drug effects , Ferrous Compounds/metabolism , Histones/metabolism , Signal Transduction/drug effects , Signal Transduction/genetics , Thionucleotides/metabolism , Animals , Cells, Cultured , Cyclic AMP/metabolism , Cyclic AMP/pharmacology , Gene Silencing , Jumonji Domain-Containing Histone Demethylases/genetics , Jumonji Domain-Containing Histone Demethylases/metabolism , Ligands , Methylation/drug effects , Oxidoreductases, N-Demethylating/genetics , Oxidoreductases, N-Demethylating/metabolism , Protein Processing, Post-Translational/drug effects , Protein Processing, Post-Translational/genetics , Rats , Receptors, G-Protein-Coupled/metabolism , Schwann Cells , Thionucleotides/pharmacology , Transfection
18.
Gynecol Endocrinol ; 36(4): 333-337, 2020 Apr.
Article En | MEDLINE | ID: mdl-31423917

Apoptosis of granulosa cells (GCs) induced by hyperandrogen plays a key role in the pathogenesis of polycystic ovary syndrome (PCOS). However, the mechanism of androgen-induced apoptosis of GCs has not been clarified to date. Recent studies have reported that PDCD4 expression is higher in PCOS patients and might be a key factor in PCOS progression. In this study, we aimed to investigate the role of PDCD4 in regulating apoptosis of human GCs and whether hyperandrogen regulate PDCD4 expression through DNA methylation. Overexpression of PDCD4 in human ovarian granulosa cell line KGN cells promoted cells apoptosis. Meanwhile, expression of caspase-3 and caspase-9 were significantly elevated. High concentration of testosterone treatment resulted in up-regulation of PDCD4 and a significant increase of apoptosis in KGN cells. In addition, knockdown of PDCD4 in KGN cells treated with high concentration of testosterone abolished the hyperandrogen-induced apoptosis. Furthermore, high concentration of testosterone down-regulated DNMT1, DNMT3A and DNMT3B expression and the methylation level in the promoter region of PDCD4 was decreased. In conclusion, PDCD4 can promote apoptosis of human ovarian GCs. The mechanism of hyperandrogen-induced apoptosis may be mediated by PDCD4. Furthermore, the up-regulation of PDCD4 induced by hyperandrogen may through demethylation of its promoter regions.


Androgens/pharmacology , Apoptosis Regulatory Proteins/genetics , Apoptosis/drug effects , Granulosa Cells/drug effects , RNA-Binding Proteins/genetics , Apoptosis/physiology , Apoptosis Regulatory Proteins/metabolism , Cells, Cultured , DNA Methylation/drug effects , Demethylation/drug effects , Female , Granulosa Cells/physiology , Humans , Hyperandrogenism/genetics , Hyperandrogenism/metabolism , Hyperandrogenism/pathology , Promoter Regions, Genetic/drug effects , RNA-Binding Proteins/metabolism , Up-Regulation/drug effects
19.
J Hazard Mater ; 389: 121885, 2020 05 05.
Article En | MEDLINE | ID: mdl-31879111

Excessive residual avermectin (AVM) in the environment can have toxic effects on non-target organisms. AVM can exert immunotoxicity by inducing genomic demethylation, but its effect on neutrophil extracellular traps (NETs) release in carp is unclear. In this study, carp neutrophils were pretreated with 5 µg/L AVM or 4 µM DNA demethylation inhibitor (aurintricarboxylic acid, ATA), alone or in combination, and then treated with 4 µM phorbol 12-myristate 13-acetate (PMA) to stimulate NETs release. The results showed that exposure of carp neutrophils to AVM significantly suppressed NETs release and MPO expression, increased ROS production, and dramatically reduced PMA-induced cellular respiratory burst. In addition, AVM could bind to the MBD2 molecule, markedly upregulate MBD2 expression to cause demethylation, and clearly activate PTEN expression, thereby inhibiting the expression of PI3K, AKT, Raf, MEK, and ERK. However, these effects were alleviated by ATA. In conclusion, our study showed that AVM could inhibit NETs release in carp by inducing demethylation of PTEN to negatively regulate NETs synthesis pathways and reducing respiratory burst level. Our findings clarify the mechanism of AVM immunotoxicity to fish and are of great significance for efforts to protect the ecological environment and human health.


Antiparasitic Agents/toxicity , Carps/immunology , Extracellular Traps/drug effects , Ivermectin/analogs & derivatives , Neutrophils/drug effects , Water Pollutants, Chemical/toxicity , Animals , Carps/metabolism , Demethylation/drug effects , Fish Proteins/metabolism , Ivermectin/toxicity , MAP Kinase Signaling System/drug effects , PTEN Phosphohydrolase/metabolism , Phosphatidylinositol 3-Kinases/metabolism , Respiratory Burst/drug effects
20.
J Immunol ; 204(1): 199-211, 2020 01 01.
Article En | MEDLINE | ID: mdl-31801817

Programmed cell death 1 (PD-1) is critical for T regulatory cells (Tregs) to maintain peripheral tolerance to self-antigens. In the tumor microenvironment, interaction between PD-1 and its ligands supports tumor immune evasion. Pembrolizumab blocks interactions of PD-1 with its ligands, enhancing antitumor and clinical responses. We and others have reported that pembrolizumab does not affect function or phenotype of thymic-derived Tregs; however, little is known about its effect on extrathymic differentiation of peripheral Tregs. In this study, we investigated the effect of pembrolizumab on in vitro-induced Tregs (iTregs). Our work showed that PD-1 blockade interferes with iTreg differentiation and has no potential effect on the stability of FOXP3 after differentiation. Additionally, we found that both nontreated and pembrolizumab-treated iTregs were suppressive. However, pembrolizumab-treated iTregs were relatively less suppressive in higher Treg ratios and failed to produce IL-10 compared with their nontreated counterparts. Different methods including transcriptomic analyses confirmed that the downregulation of FOXP3 was mediated by activating mTOR and STAT1 and inhibiting MAPK pathways, shifting the iTreg polarization in favor of Th1 and Th17 subsets. To confirm the role of mTOR activation, we found that rapamycin diminished the effect of pembrolizumab-mediated downregulation of FOXP3. Ingenuity pathway analysis revealed that pembrolizumab-treated iTregs showed upregulation of genes promoting DNA repair and immune cell trafficking, in addition to downregulation of genes supporting cellular assembly and organization. To our knowledge, this is the first study to show that pembrolizumab interferes with differentiation of human FOXP3+ iTregs and to disclose some of the molecular pathways involved.


Antibodies, Monoclonal, Humanized/pharmacology , Antineoplastic Agents, Immunological/pharmacology , Forkhead Transcription Factors/antagonists & inhibitors , T-Lymphocytes, Regulatory/drug effects , TOR Serine-Threonine Kinases/immunology , Cell Differentiation/drug effects , Cell Differentiation/immunology , Demethylation/drug effects , Forkhead Transcription Factors/immunology , Healthy Volunteers , Humans , Protein Stability/drug effects , T-Lymphocytes, Regulatory/immunology , Up-Regulation/drug effects
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