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1.
Article in English | WPRIM | ID: wpr-880692

ABSTRACT

RNA methylation is of great significance in the regulation of gene expression, among which the more important methylation modifiers are N6-methyladenosine (m6A) and 5-methylcytosine (m5C). The methylation process is mainly regulated by 3 kinds of proteins: methyltransferase, demethylase, and reader. m6A, m5C, and their related proteins have high abundance in the brain, and they have important roles in the development of the nervous system and the repair and remodeling of the vascular system. The neurovascular unit (NVU) is a unit of brain structure and function composed of neurons, capillaries, astrocytes, supporting cells, and extracellular matrix. The local microenvironment for NVU has an important role in nerve cell function repair, and the remodeling of NVU is of great significance in the prognosis of various neurological diseases.


Subject(s)
5-Methylcytosine , Adenosine/metabolism , Methylation , Methyltransferases/metabolism , RNA
2.
Article in Chinese | WPRIM | ID: wpr-878987

ABSTRACT

To investigate the effect of Gegen Qinlian Decoction(GQD) on enzyme activity, gene expression and methylation level of fatty acid synthase(FASN) in adipose tissue from rats with insulin resistance induced by high-fat diet. The 60% fat-powered high-fat diet was continuously given to male SD rats to induce the insulin resistance model. Then, they were divided into five groups randomly and administrated by gavage every day for 16 weeks with following drugs respectively: 10 mL·kg~(-1)water for control group(C) and insulin resistance model control group(IR), 1.65 g·kg~(-1)GQD per day for low-dose group(GQDL), 4.95 g·kg~(-1)GQD per day for medium-dose group(GQDM), 14.85 g·kg~(-1)GQD per day for high-dose group(GQDH), and 5 mg·kg~(-1) rosiglitazone per day for rosiglitazone group(RGN). Epididymal adipose tissue was taken to determine enzyme activity of FASN by colorimetric method, mRNA expression level of Fasn by quantitative Real-time PCR(Q-PCR) and CpGs methylation level between +313 and +582 by bisulfite sequencing PCR(BSP). These results showed that Fasn expression was significantly lowered in IR model rats compared with the control rats(P<0.01). Enzymatic activity and CpGs methylation level of Fasn in IR group showed downward trends. Low and medium-dose GQD can increase enzyme activity of FASN(P<0.05). Moreover, low-dose GQD increased the total CpGs methylation level of Fasn fragment between +313 and +582 in insulin resistance rats(P<0.05). For GQDM group, the methylation frequency of CpGs at positions +506 and +508(P<0.01) as well as the methylation frequency of CpGs on the binding sites of transcription factorzinc finger protein 161(P<0.05) were significantly increased. The methylation frequency of CpG at +442 position was positively correlated with Fasn expression(P<0.01, r=0.735), and methylation frequencies of CpGs at +345 and +366 positions were positively associated to enzyme activity of FASN respectively(P<0.05, r=0.479; P<0.01, r=0.640). In conclusion, GQD can reverse enzyme activity of FASN and methylation level of Fasn in adipose tissue of insulin resistant rats, and CpG sites at positions +506 and +508 may be the targets of GQD. The methylation level of CpGs at + 345 and + 366 sites were possibly related to FASN activity, while methylation of CpG at + 442 site may be closely correlated with mRNA level of Fasn. In addition, GQD did not significantly change mRNA expression level of Fasn, but effectively reversed enzymatic activity, suggesting that GQD may regulate the post transcriptional expression of Fasn.


Subject(s)
Adipose Tissue , Animals , Drugs, Chinese Herbal , Fatty Acid Synthases/genetics , Gene Expression , Insulin Resistance/genetics , Male , Methylation , Rats , Rats, Sprague-Dawley
3.
Electron. j. biotechnol ; 45: 19-29, May 15, 2020. tab, ilus, graf
Article in English | LILACS | ID: biblio-1177401

ABSTRACT

BACKGROUND: Long non-coding RNAs (lncRNAs), as post-transcriptional regulators, were thought to function in the inductive property of dermal papilla cells (DPCs) in cashmere goat. Previously, lncRNA-599554 was identified in secondary hair follicle (SHF) of cashmere goat, but its functional significance is unknown. RESULTS: In the present investigation, we verified that lncRNA-599554 had significantly higher expression at the anagen dermal papilla of cashmere goat SHF than that at telogen. Based on overexpression and knockdown techniques, we found that lncRNA-599554 contributes the inductive property of DPCs of cashmere goat, which was assessed by detecting the changes in the expression of several typical indictor genes in DPCs including ET-1, SCF, Versican, ALP, Lef1 and Ptc-1. Based on RNA pull-down assay, we verified that lncRNA-599554 directly interacted with chi-miR-15a-5p. Also, we showed that lncRNA-599554 positively regulated the Wnt3a expression in DPCs but which did not appear to involve its modulating of promoter methylation. Based on the use of Dual-luciferase reporter assays, our data indicated that lncRNA-599554 regulated the Wnt3a expression through chi-miR-15a-5p-mediated post-transcriptional level. CONCLUSIONS: We showed that lncRNA-599554 contributes the inductive property of DPCs in cashmere goat which might be achieved through sponging chi-miR-15b-5p to promote the Wnt3a expression. The results from the present investigation provided a novel insight into the functional mechanism of lncRNA-599554 in the SHF regeneration of cashmere goat along with the formation and growth of cashmere fiber.


Subject(s)
Animals , Hair Follicle/cytology , Hair Follicle/metabolism , Dermis/cytology , Wnt3A Protein/metabolism , RNA, Long Noncoding/metabolism , Biological Assay/methods , Goats , RNA, Long Noncoding/genetics , Luciferases , Methylation
4.
Article in Chinese | WPRIM | ID: wpr-879490

ABSTRACT

With the in-depth exploration of all stages in early-stage embryos, in particular zygotic genome activation and first cell lineage differentiation, researchers have found that early embryonic epigenetics follows a strict pattern of temporal and spatial modification. Previous studies have determined the inhibitory effect of H3K9me3 and H3K27me3 on genomic expression, and found that they are involved in many core biological events in the genome such as chromatin reprogramming, genomic imprinting, maintenance of embryonic stem cell pluripotency and somatic cell nuclear transfer, though the detailed molecular mechanism has remained elusive. From the point of developmental biology and epigenetics, this article has expounded the research progress on the methylation of H3K9 and H3K27 histones in early-stage embryos, which may provide a clue for the complex mechanism of embryonic development and improvement of culture method for embryos in vitro.


Subject(s)
Chromatin , Embryonic Development , Epigenesis, Genetic , Female , Gene Expression Regulation, Developmental , Histones/metabolism , Humans , Methylation , Pregnancy
5.
Annals of Dermatology ; : 122-129, 2020.
Article in English | WPRIM | ID: wpr-811086

ABSTRACT

BACKGROUND: Loss-of-function mutations in the filaggrin gene (FLG), which encodes an epidermal protein crucial for the formation of a functional skin barrier, have been identified as a major predisposing factor in the etiopathogenesis of atopic dermatitis (AD). Recent reports of relatively low frequencies of FLG-null mutations among specific ethnic groups with AD necessitated analysis of the epigenetic regulation which may control FLG expression without altering its DNA sequence.OBJECTIVE: The study aimed to identify DNA methylation-dependent regulation of FLG expression.METHODS: Quantitative polymerase chain reaction was performed to determine the restoration of FLG mRNA expression in normal human epidermal keratinocyte (NHEK) cells after treatment with epigenetic modulating agents. Bisulfite genomic sequencing and pyrosequencing analyses of the FLG promoter region were conducted to identify the citical CpG sites relevant to FLG expression. We performed small-scale pilot study for epidermal tissues obtained from Korean patients with severe AD.RESULTS: We here show that DNA methylation in the FLG with non-CpG island promoter is responsible for the transcriptional regulation of FLG in undifferentiated NHEK cells. The methylation frequencies in a single CpG site of the FLG promoter were significantly higher in lesional epidermis than those in matched nonlesional epidermis of subjects with severe AD.CONCLUSION: Our in vitro and clinical studies point to this unique CpG site as a potential DNA methylation marker of FLG, which can be a promising therapeutic target in the complications of filaggrin-related skin barrier dysfunction as well as in AD.


Subject(s)
Base Sequence , Causality , Dermatitis, Atopic , DNA , DNA Methylation , Epidermis , Epigenomics , Ethnic Groups , Gene Expression , Humans , In Vitro Techniques , Keratinocytes , Methylation , Pilot Projects , Polymerase Chain Reaction , Promoter Regions, Genetic , RNA, Messenger , Skin
7.
Yonsei Medical Journal ; : 186-191, 2020.
Article in English | WPRIM | ID: wpr-782192

ABSTRACT

0.2 and p<0.05. NOTCH1 was identified as a candidate network hub gene in cases. NOTCH1 transcripts significantly increased in lung tissues from HDLI cases compared to unexposed controls (p=0.05). NOTCH1 may play an important role in pulmonary fibrosis of HDLI.


Subject(s)
Child , DNA Methylation , Gene Expression Profiling , Humans , Humidifiers , Korea , Lung Injury , Lung , Methylation , Pulmonary Fibrosis
8.
Article in Chinese | WPRIM | ID: wpr-828630

ABSTRACT

OBJECTIVE@#To study the clinical screening and genetic diagnosis of children suspected of Prader-Willi syndrome (PWS), as well as the differences in the scores of clinical diagnostic criteria among the children with a confirmed diagnosis of PWS.@*METHODS@#A total of 94 children suspected of PWS who were admitted from July 2016 to December 2018 were enrolled as subjects. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) was performed to confirm the diagnosis. For the children with a confirmed diagnosis of PWS, the scores of clinical diagnostic criteria were determined, and the perinatal characteristics were analyzed.@*RESULTS@#A total of 11 children with PWS were confirmed by MS-MLPA, with a detection rate of 12%, among whom there were 7 boys and 4 girls, with a median age of 3 years and 4 months (range 25 days to 6 years and 8 months) at the time of confirmed diagnosis. Among the 11 children with PWS, only 5 children (45%) met the criteria for clinical diagnosis. The main perinatal characteristics of the children with PWS were decreased fetal movement (9 cases, 82%), cesarean section birth (11 cases, 100%), hypotonia (11 cases, 100%), feeding difficulties (11 cases, 100%), and weak crying (11 cases, 100%).@*CONCLUSIONS@#Gene testing should be performed as early as possible for children suspected of PWS by clinical screening. PWS may be missed if only based on the scores of clinical diagnostic criteria.


Subject(s)
Cesarean Section , Child , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Male , Methylation , Muscle Hypotonia , Prader-Willi Syndrome , Pregnancy
9.
Blood Research ; : 17-26, 2020.
Article in English | WPRIM | ID: wpr-820807

ABSTRACT

BACKGROUND: DNMT3A mutations occur in approximately 20% of AML cases and are associated with changes in DNA methylation. CDKN2B plays an important role in the regulation of hematopoietic progenitor cells and DNMT3A mutation is associated with CDKN2B promoter methylation. We analyzed the characteristics of DNMT3A mutations including their clinical significance in AML and their influence on promoter methylation and CDKN2B expression.METHODS: A total of 142 adults, recently diagnosed with de novo AML, were enrolled in the study. Mutations in DNMT3A, CEBPA, and NPM1 were analyzed by bidirectional Sanger sequencing. We evaluated CDKN2B promoter methylation and expression using pyrosequencing and RT-qPCR.RESULTS: We identified DNMT3A mutations in 19.7% (N=28) of enrolled patients with AML, which increased to 29.5% when analysis was restricted to cytogenetically normal-AML. Mutations were located on exons from 8–23, and the majority, including R882, were found to be present on exon 23. We also identified a novel frameshift mutation, c.1590delC, in AML with biallelic mutation of CEBPA. There was no significant difference in CDKN2B promoter methylation according to the presence or type of DNMT3A mutations. CDKN2B expression inversely correlated with CDKN2B promoter methylation and was significantly higher in AML with R882H mutation in DNMT3A. We demonstrated that DNMT3A mutation was associated with poor AML outcomes, especially in cytogenetically normal-AML. The DNMT3A mutation remained as the independent unfavorable prognostic factor after multivariate analysis.CONCLUSION: We characterized DNMT3A mutations in AML and revealed the association between the DNMT3A mutation and CDKN2B expression and clinical outcome.


Subject(s)
Adult , DNA Methylation , Exons , Frameshift Mutation , Hematopoietic Stem Cells , Humans , Leukemia, Myeloid, Acute , Methylation , Multivariate Analysis
10.
Arch. endocrinol. metab. (Online) ; 63(4): 438-444, July-Aug. 2019. tab, graf
Article in English | LILACS | ID: biblio-1019366

ABSTRACT

ABSTRACT Pubertal timing in humans is determined by complex interactions including hormonal, metabolic, environmental, ethnic, and genetic factors. Central precocious puberty (CPP) is defined as the premature reactivation of the hypothalamic-pituitary-gonadal axis, starting before the ages of 8 and 9 years in girls and boys, respectively; familial CPP is defined by the occurrence of CPP in two or more family members. Pioneering studies have evidenced the participation of genetic factors in pubertal timing, mainly identifying genetic causes of CPP in sporadic and familial cases. In this context, rare activating mutations were identified in genes of the kisspeptin excitatory pathway (KISS1R and KISS1 mutations). More recently, loss-of-function mutations in two imprinted genes (MKRN3 and DLK1) have been identified as important causes of familial CPP, describing novel players in the modulation of the hypothalamic-pituitary-gonadal axis in physiological and pathological conditions. MKRN3 mutations are the most common cause of familial CPP, and patients with MKRN3 mutations present clinical features indistinguishable from idiopathic CPP. Meanwhile, adult patients with DLK1 mutations present high frequency of metabolic alterations (overweight/obesity, early onset type 2 diabetes and hyperlipidemia), indicating that DLK1 may be a novel link between reproduction and metabolism. Arch Endocrinol Metab. 2019;63(4):438-44


Subject(s)
Humans , Puberty, Precocious/genetics , Phenotype , Puberty, Precocious/etiology , Ribonucleoproteins/genetics , Calcium-Binding Proteins , Gene Silencing , Intercellular Signaling Peptides and Proteins/genetics , Intercellular Signaling Peptides and Proteins/metabolism , Kisspeptins/genetics , Receptors, Kisspeptin-1/genetics , Membrane Proteins/genetics , Membrane Proteins/metabolism , Methylation , Mutation
11.
Electron. j. biotechnol ; 38: 1-9, Mar. 2019. tab, graf
Article in English | LILACS | ID: biblio-1051273

ABSTRACT

BACKGROUND: Microbial oils produced by diverse microorganisms are being considered as alternative sources of triglycerides for biodiesel production. However, the standalone production of biodiesel from microorganisms is not currently economically feasible. In case of yeasts, the use of low-value nutrient sources in microbial production and the implementation of cost-efficient downstream processes could reduce costs and make microbial lipids competitive with other commodity-type oils in biodiesel production. Industrial biodiesel synthesis from oleaginous seeds is currently based on a multistep process. However, a simple process called in situ transesterification (ISTE), which takes place within the biomass without a previous lipid extraction step, is receiving increasing interest. In this work, the optimal conditions for an ISTE process to obtain biodiesel from previously selected oleaginous yeast (Rhodotorula graminis S1/S2) were defined using the response surface methodology (RSM). RESULTS: Using the RSM approach, the optimal conditions for the maximum yield with minimum reaction time included a methanol-to-biomass ratio of 60:1, 0.4 M H2SO4, and incubation at 70°C for 3 h. The optimized in situ process yield was significantly higher (123%) than that obtained with a two-step method in which fatty acids from saponifiable lipids were first extracted and then esterified with methanol. The composition of the fatty acid methyl ester mixture obtained from R. graminis S1/S2 by ISTE met Uruguayan standards for biodiesel. CONCLUSION: The characteristics achieved by the optimized method make microbial oil a potential alternative for biodiesel production from yeast at an industrial scale.


Subject(s)
Yeasts/metabolism , Biofuels , Reaction Time , Rhodotorula , Biomass , Environment , Esterification , Esters , Fatty Acids , Renewable Energy , Lipids , Methylation
12.
Rev. colomb. gastroenterol ; 34(1): 1-9, ene.-mar. 2019. tab, graf
Article in Spanish | LILACS | ID: biblio-1003831

ABSTRACT

Resumen El cáncer colorrectal es una enfermedad heterogénea, en cuya aparición se involucran factores hereditarios y ambientales. En las formas heredadas existen genes responsables de incrementar el desarrollo tumoral en los portadores, y se consideran a los factores medioambientales como responsables de gran parte de las formas esporádicas. El objetivo de este estudio fue analizar el estado de metilación de 5 genes implicados en la carcinogénesis colorrectal y su relación con los distintos estadios clínicos de estos tumores. Por una parte, nuestro análisis reveló que el estado de metilación de los promotores de los genes HMLH1 (human mut homologue 1), APC (adenomatous poliposis coli), P15, P16 y CDH1, considerados como unas de las alteraciones más tempranas en este proceso; fluctuaron entre 13,3 % para hMLH1 y 56,6 % para APC. También reveló que la inactivación epigenética de los genes APC y P16 podrían ser responsables de la aparición y de la progresión de los tumores ya que se encontraron en pacientes con estadio II. Por otra parte, los genes APC y p15 resultaron estar mutados en todas las etapas de la carcinogénesis, por lo que se involucrarían en todos los procesos tanto de inicio como de invasión y metástasis. Por último, nuestros resultados apoyan la utilización de la identificación de la metilación de los genes supresores ya que se están identificando dianas epigenéticas para el desarrollo de nuevos tratamientos de quimioterapia y está emergiendo como una estrategia con gran potencial dado que, en principio, las alteraciones epigenéticas son potencialmente reversibles.


Abstract Colorectal cancer is a heterogeneous disease which involves hereditary and environmental factors. The inherited forms have genes which are responsible for increasing the tumor development in carriers. Environmental factors are considered responsible for many sporadic forms. The objective of this study was to analyze the methylation status of five genes involved in colorectal carcinogenesis and their relationships with the various clinical stages of these tumors. Our analysis revealed that the methylation status of the promoters of genes HMLH1, APC, P15, P16 and CDH1, considered to be among the earliest alterations in this process, ranged from 13.3% for HMLH1 to 56.6% for APC. In addition, epigenetic inactivation of APC and P16 genes could be responsible for the appearance and progression of tumors since inactivation was found in stage II patients. On the other hand, the APC and p15 gene were mutated in all stages of carcinogenesis, so they could be involved throughout the processes of initiation, invasion and metastasis. Finally, our results support using identification of methylation of suppressor genes since they identify epigenetic targets for development of new chemotherapy treatments. This is emerging as a strategy with great potential since epigenetic alterations are, in principle, potentially reversible.


Subject(s)
Humans , Male , Female , Colorectal Neoplasms , Genes, p16 , Methylation , Therapeutics , Epigenomics
13.
Article in English | WPRIM | ID: wpr-719425

ABSTRACT

PURPOSE: Helicobacter pylori infection induces phenotype-stabilizing methylation and promotes gastric mucosal atrophy that can inhibit CpG-island methylation. Relationship between the progression of gastric mucosal atrophy and the initiation of CpG-island methylation was analyzed to delineate epigenetic period for neoplastic transformation. MATERIALS AND METHODS: Normal-appearing gastric mucosa was biopsied from 110 H. pylori–positive controls, 95 H. pylori–negative controls, 99 gastric cancer patients, and 118 gastric dysplasia patients. Gastric atrophy was assessed using endoscopic-atrophic-border score. Methylation-variable sites of eight CpG-island genes adjacent to Alu (CDH1, ARRDC4, PPARG, and TRAPPC2L) or LTR (MMP2, CDKN2A, RUNX2, and RUNX3) retroelements and stomach-specific TFF3 gene were analyzed using radioisotope-labeled methylation-specific polymerase chain reaction. RESULTS: Mean ages of H. pylori–positive controls with mild, moderate, and severe atrophy were 51, 54, and 65 years and those of H. pylori–associated TFF3 overmethylation at the three atrophic levels (51, 58, and 63 years) tended to be periodic. Alu-adjacent overmethylation (50 years) was earlier than TFF3 overmethylation (58 years) in H. pylori–positive controls with moderate atrophy. Cancer patients with moderate atrophy showed late Alu-adjacent (58 years) overmethylation and frequent LTR-adjacent overmethylation. LTR-adjacent overmethylation was frequent in cancer (66 years) and dysplasia (68 years) patients with severe atrophy. CONCLUSION: Atrophic progression is associated with gastric cancer at moderate level by impeding the initiation of Alu-adjacent methylation. LTR-adjacent methylation is increased in cancer patients and subsequently in dysplasia patients.


Subject(s)
Atrophy , DNA Methylation , Epigenomics , Gastric Mucosa , Gastritis, Atrophic , Genes, Essential , Helicobacter pylori , Housekeeping , Humans , Methylation , Polymerase Chain Reaction , Retroelements , Stomach Neoplasms
14.
Clinical Endoscopy ; : 235-238, 2019.
Article in English | WPRIM | ID: wpr-763437

ABSTRACT

Conventional adenomas have historically been considered to be the only screening-relevant colorectal cancer (CRC) precursor lesion. The prevailing paradigm was that most CRCs arise along the chromosomal instability pathway, where adenomas accumulate incremental genetic alterations over time, leading eventually to malignancy. However, it is now recognized that this “conventional” pathway accounts for only about two-thirds of CRCs. The serrated pathway is responsible for most of the remainder, and is a disproportionate contributor to postcolonoscopy CRC. Hallmarks of the serrated pathway are mutations in the BRAF gene, high levels of methylation of promoter CpG islands, and the sessile serrated polyp (SSP). Accumulating evidence shows that SSPs can be considered adenoma-equivalent from the standpoint of CRC screening. SSPs have a higher prevalence than previously thought, and appear to have a relatively long dwell time similar to that of conventional adenomas. In addition, SSPs, whether sporadic or as part of the serrated polyposis syndrome, are associated with increased risk of synchronous and metachronous neoplasia. These features collectively support that SSPs are highly relevant to CRC prevention.


Subject(s)
Adenoma , Chromosomal Instability , Colonoscopy , Colorectal Neoplasms , CpG Islands , Mass Screening , Methylation , Polyps , Prevalence
15.
Article in English | WPRIM | ID: wpr-763126

ABSTRACT

PURPOSE: Glioblastoma, the most common brain tumor in adults, has poor prognosis. The purpose of this study was to determine the effect of disulfiram (DSF), an aldehyde dehydrogenase inhibitor, on in vitro radiosensitivity of glioblastoma cells with different methylation status of O⁶-methylguanine-DNA methyltransferase (MGMT) promoter and the underlying mechanism of such effect. MATERIALS AND METHODS: Five human glioblastoma cells (U138MG, T98G, U251MG, U87MG, and U373MG) and one normal human astrocyte (NHA) cell were cultured and treated with DSF or 6MV X-rays (0, 2, 4, 6, and 8 Gy). For combined treatment, cells were treated with DSF before irradiation. Surviving fractions fit from cell survival based on colony forming ability. Apoptosis, DNA damage repair, and cell cycle distributionwere assayed bywestern blot for cleaved caspase-3, γH2AX staining, and flow cytometry, respectively. RESULTS: DSF induced radiosensitization in most of the glioblastoma cells, especially, in the cells with radioresistance as wildtype unmethylated promoter (MGMT-wt), but did not in normal NHA cell. DSF augmented or induced cleavage of caspase-3 in all cells after irradiation. DSF inhibited repair of radiation-induced DNA damage in MGMT-wt cells, but not in cells with methylated MGMT promoter. DSF abrogated radiation-induced G2/M arrest in T98G and U251MG cells. CONCLUSION: Radiosensitivity of glioblastoma cells were preferentially enhanced by pre-irradiation DSF treatment compared to normal cell, especially radioresistant cells such as MGMT-wt cells. Induction of apoptosis or inhibition of DNA damage repair may underlie DSF-induced radiosensitization. Clinical benefit of combining DSF with radiotherapy should be investigated in the future.


Subject(s)
Adult , Aldehyde Dehydrogenase , Apoptosis , Astrocytes , Brain Neoplasms , Caspase 3 , Cell Cycle , Cell Survival , Disulfiram , DNA Damage , Flow Cytometry , Glioblastoma , Humans , In Vitro Techniques , Methylation , Prognosis , Radiation Tolerance , Radiotherapy
16.
Blood Research ; : 144-148, 2019.
Article in English | WPRIM | ID: wpr-763057

ABSTRACT

BACKGROUND: Ikaros family zinc finger 1 (IKZF1) is a transcription factor with an important role in controlling hematopoietic proliferation and function, particularly lymphoid cell differentiation. It was previously shown that various mechanisms and expression patterns of Ikaros are linked to a variety of cancers. We hypothesized that aberrant methylation (hypomethylation) of the IKZF1 promoter region might be one of the causes of B-cell acute lymphoblastic leukemia (B-ALL). In B-ALL patients, an increased expression of this gene is a potential cause of B-cell differentiation arrest and proliferation induction. Therefore, as more than 90% of patients with ALL are <15 years old, we investigated the methylation pattern of the IKZF1 promoter in childhood B-ALL. METHODS: Twenty-five newly diagnosed B-ALL cases were included (all younger than 15 yr). In addition, we selected 25 healthy age- and sex-matched children as the control group. We collected the blood samples in EDTA-containing tubes and isolated lymphocytes from whole blood using Ficoll 1.077 Lymphosep. Next, we extracted genomic DNA with the phenol/chloroform method. Two microgram of DNA per sample was treated with sodium bisulfite using the EpiTect Bisulfite Kit, followed by an assessment of DNA methylation by polymerase chain reaction (PCR) analysis of the bisulfite-modified genomic DNA. RESULTS: Our data highlighted a hypomethylated status of the IKZF1 promoter in the ALL cases (96% of the cases were unmethylated). In contrast, the control group samples were partially methylated (68%). CONCLUSION: This study demonstrated a hypomethylated pattern of the IKZF1 promoter region in childhood B-ALL, which might underlie the aberrant Ikaros expression patterns that were previously linked to this malignancy.


Subject(s)
B-Lymphocytes , Child , DNA , DNA Methylation , Ficoll , Hematologic Neoplasms , Humans , Leukemia , Lymphocytes , Methods , Methylation , Polymerase Chain Reaction , Precursor Cell Lymphoblastic Leukemia-Lymphoma , Promoter Regions, Genetic , Sodium , Transcription Factors , Zinc Fingers
17.
Article in English | WPRIM | ID: wpr-765956

ABSTRACT

The mammalian intestine contains many different cell types but is comprised of 2 main cell types: epithelial cells and smooth muscle cells. Recent in vivo and in vitro evidence has revealed that various alterations to the DNA methylation apparatus within both of these cell types can result in a variety of cellular phenotypes including modified differentiation status, apoptosis, and uncontrolled growth. Methyl groups added to cytosines in regulatory genomic regions typically act to repress associated gene transcription. Aberrant DNA methylation patterns are often found in cells with abnormal growth/differentiation patterns, including those cells involved in burdensome intestinal pathologies including inflammatory bowel diseases and intestinal pseudo-obstructions. The altered methylation patterns being observed in various cell cultures and DNA methyltransferase knockout models indicate an influential connection between DNA methylation and gastrointestinal cells' development and their response to environmental signaling. As these modified DNA methylation levels are found in a number of pathological gastrointestinal conditions, further investigations into uncovering the causative nature, and controlled regulation, of this epigenetic modification is of great interest.


Subject(s)
Apoptosis , Cell Culture Techniques , Cell Differentiation , DNA Methylation , DNA , Epigenomics , Epithelial Cells , In Vitro Techniques , Inflammatory Bowel Diseases , Intestinal Mucosa , Intestinal Pseudo-Obstruction , Intestines , Methylation , Muscle, Smooth , Myocytes, Smooth Muscle , Pathology , Phenotype
18.
Article in English | WPRIM | ID: wpr-765052

ABSTRACT

BACKGROUND: Tauopathies, a class of neurodegenerative diseases that includes Alzheimer's disease (AD), are characterized by the deposition of neurofibrillary tangles composed of hyperphosphorylated tau protein in the human brain. As abnormal alterations in histone acetylation and methylation show a cause and effect relationship with AD, we investigated the role of several Jumonji domain-containing histone demethylase (JHDM) genes, which have yet to be studied in AD pathology. METHODS: To examine alterations of several JHDM genes in AD pathology, we performed bioinformatics analyses of JHDM gene expression profiles in brain tissue samples from deceased AD patients. Furthermore, to investigate the possible relationship between alterations in JHDM gene expression profiles and AD pathology in vivo, we examined whether tissue-specific downregulation of JHDM Drosophila homologs (kdm) can affect tauR406W-induced neurotoxicity using transgenic flies containing the UAS-Gal4 binary system. RESULTS: The expression levels of JHDM1A, JHDM2A/2B, and JHDM3A/3B were significantly higher in postmortem brain tissue from patients with AD than from non-demented controls, whereas JHDM1B mRNA levels were downregulated in the brains of patients with AD. Using transgenic flies, we revealed that knockdown of kdm2 (homolog to human JHDM1), kdm3 (homolog to human JHDM2), kdm4a (homolog to human JHDM3A), or kdm4b (homolog to human JHDM3B) genes in the eye ameliorated the tauR406W-engendered defects, resulting in less severe phenotypes. However, kdm4a knockdown in the central nervous system uniquely ameliorated tauR406W-induced locomotion defects by restoring heterochromatin. CONCLUSION: Our results suggest that downregulation of kdm4a expression may be a potential therapeutic target in AD.


Subject(s)
Acetylation , Alzheimer Disease , Brain , Central Nervous System , Computational Biology , Diptera , Down-Regulation , Drosophila melanogaster , Drosophila , Heterochromatin , Histones , Humans , Locomotion , Methylation , Neurodegenerative Diseases , Neurofibrillary Tangles , Pathology , Phenotype , RNA, Messenger , tau Proteins , Tauopathies , Transcriptome
19.
Article in English | WPRIM | ID: wpr-764980

ABSTRACT

BACKGROUND: Little is known about epigenetic silencing of genes by promoter hypermethylation in renal cell carcinoma (RCC). The aim of this study was to identify prognostic methylation markers in surgically treated clear cell RCC (ccRCC). METHODS: Methylation patterns were assayed using the Infinium HumanMethylation450 BeadChip array on pairs of ccRCC and normal tissue from 12 patients. Using quantitative PSQ analysis, tumor-specific hypermethylated genes were validated in 25 independent cohorts and their clinical relevance was also verified in 152 independent cohorts. RESULTS: Using genome-wide methylation array, Zinc finger protein 278 (ZNF278), Family with sequence similarity 155 member A (FAM155A) and Dipeptidyl peptidase 6 (DPP6) were selected for tumor-specific hypermethylated genes in primary ccRCC. The promoter methylation of these genes occurred more frequently in ccRCC than normal kidney in independent validation cohort. The hypermethylation of three genes were associated with advanced tumor stage and high grade tumor in ccRCC. During median follow-up of 39.2 (interquartile range, 15.4–79.1) months, 22 (14.5%) patients experienced distant metastasis. Multivariate analysis identified the methylation status of these three genes, either alone, or in a combined risk score as an independent predictor of distant metastasis. CONCLUSION: The promoter methylation of ZNF278, FAM155A and DPP6 genes are associated with aggressive tumor phenotype and early development of distant metastasis in patients with surgically treated ccRCC. These potential methylation markers, either alone, or in combination, could provide novel targets for development of individualized therapeutic and prevention regimens.


Subject(s)
Carcinoma, Renal Cell , Cohort Studies , Disease-Free Survival , Epigenomics , Follow-Up Studies , Humans , Kidney , Methylation , Multivariate Analysis , Neoplasm Metastasis , Phenotype , Zinc Fingers
20.
Article in English | WPRIM | ID: wpr-762171

ABSTRACT

Nonsteroidal anti-inflammatory drug (NSAID)-exacerbated respiratory disease (NERD) has attracted a great deal of attention because of its association with severe asthma. However, it remains widely underdiagnosed in asthmatics as well as the general population. Upon pharmacological inhibition of cyclooxygenase 1 by NSAIDs, production of anti-inflammatory prostaglandin E2 and lipoxins ceases, while release of proinflammatory cysteinyl leukotrienes increases. To determine the underlying mechanisms, many studies have attempted to elucidate the genetic variants, such as single nucleotide polymorphisms, responsible for alterations of prostaglandins and leukotrienes, but the results of these genetic studies could not explain the whole genetic pathogenesis of NERD. Accordingly, the field of epigenetics has been introduced as an additional contributor to genomic alteration underlying the development of NERD. Recently, changes in CpG methylation, as one of the epigenetic components, have been identified in target tissues of NERD. This review discusses in silico analyses of both genetic and epigenetic components to gain a better understanding of their complementary roles in the development of NERD. Although the molecular mechanisms underlying NERD pathogenesis remain poorly understood, genetic and epigenetic variations play significant roles. Our results enhance the understanding of the genetic and epigenetic mechanisms involved in the development of NERD and suggest new approaches toward better diagnosis and management.


Subject(s)
Anti-Inflammatory Agents, Non-Steroidal , Asthma , Computer Simulation , Cyclooxygenase 1 , Diagnosis , Dinoprostone , Epigenomics , Genetics , Leukotrienes , Lipoxins , Methylation , Polymorphism, Single Nucleotide , Prostaglandins
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