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1.
Anticancer Res ; 39(10): 5381-5391, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31570433

RESUMO

BACKGROUND/AIM: Long noncoding RNAs (lncRNAs) are noncoding transcripts that are >200 nucleotides in length. However, the biological functions and regulation mechanisms of lncRNAs in gastric carcinogenesis remain unknown. MATERIALS AND METHODS: The expression levels of Linc00472 were analyzed by real-time PCR. The DNA methylation status was assessed using Combined Bisulfite Restriction Analysis (COBRA). The biological role of Linc00472 was assessed in AGS cells with Linc00472 overexpression. RESULTS: Using the next-generation sequencing approach, we identified DNA methylation-associated lncRNAs in gastric cancer cells. Among them, the expression level of Linc00472 significantly decreased in gastric cancer tissues compared to adjacent normal tissues. Furthermore, we observed a more frequent hypermethylation of CpG islands upstream of Linc00472 in gastric cancer tissues. Ectopic Linc00472 expression could significantly inhibit gastric cancer cell growth and migration. CONCLUSION: Epigenetically regulated Linc00472 expression plays a crucial role in modulating gastric cancer cell growth and motility.


Assuntos
Metilação de DNA/genética , RNA Longo não Codificante/genética , Neoplasias Gástricas/genética , Carcinogênese/genética , Linhagem Celular Tumoral , Movimento Celular/genética , Proliferação de Células/genética , Ilhas de CpG/genética , Regulação Neoplásica da Expressão Gênica/genética , Humanos
2.
Zhongguo Shi Yan Xue Ye Xue Za Zhi ; 27(5): 1540-1547, 2019 Oct.
Artigo em Chinês | MEDLINE | ID: mdl-31607309

RESUMO

OBJECTIVE: To investigate the expression, mechanism and methylation level of miR-28-5p in multiple myeloma (MM), so as to provide the expirement basis for searching new targeted therapy. METHODS: RT-PCR was used to detect the expression levels of miR-28-5p and potential target CCND1 in CD138+ cells of the patients with MM and bone marrow mononuclear cells of patients with iron defficiency anemia(IDA) as control, Methylation-specific PCR(MSP) was used to detect methylation levels of CpG island in LPP/miR-28-5p promoter region and the correlation with other clinical indicators was analyzed. The 5-aza-2'-deoxycytidine (5-Aza-dC,DAC) was used to treat MM cell line U266; after drug treatment,MSP was used to analyze the methylation status of the CpG islands in LPP/miR-28-5p promoter; the qPCR was used to detect the expression levels of miR-28-5p,and the regulatory mechanism of miR-28-5p expression was explored furtherly. RESULTS: The methylation level of CpG island in LPP/miR-28-5p promoter region of MM patients was significantly higher than that of IDA patients. The relative expression level of miR-28-5p in MM patients was significantly lower than that of IDA patients. The relative expression level of miR-28-5p in newly diagnosed MM patients was higher than that in relapsed/progressive patients. The miR-28-5p target CCND1 was expressed at high levels in MM patients with LPP / miR-28-5p methylation, the expression level of miR-28-5p in MM patients correlated with ß2-MG concentration. 5-aza-dc could significantly inhibit the growth of U266 cell line, arrest the cell cycle in G1 phase, inhibit the biosynthesis of cellular RNA and protein and promote cell apoptosis. At the same time, up-regulation of miR-28-5p expression was found. CONCLUSION: The expression of miR-28-5p in MM patients is regulated by methylation of CpG islands in the promoter region of the genome.miR-28-5p may act as a tumor suppressor gene, and its low expression may be involved in the occurrence and development of MM, suggesting that miR-28-5p may become a new target for the treatment of MM.


Assuntos
MicroRNAs/genética , Mieloma Múltiplo , Linhagem Celular Tumoral , Ilhas de CpG , Metilação de DNA , Epigênese Genética , Regulação Neoplásica da Expressão Gênica , Humanos , Mieloma Múltiplo/genética
3.
Medicine (Baltimore) ; 98(43): e17578, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31651862

RESUMO

BACKGROUND: To evaluate the methylation levels of human telomerase reverse transcriptase (hTERT) promoter three CpG island (CGIs) regions and its prognostic impact in Chinese patients with acral and mucosal melanoma. METHODS: Bioinformatics software was used to analyze hTERT gene promoter. Fresh frozen tissues were taken from 14 patients with melanoma (6 acral melanoma and 8 mucosal melanoma) and 14 pigmented nevus as control subjects (14 acral pigmented nevus). Bisulfite sequencing PCR (BSP) combined TA clone sequencing was used to assess the methylation levels of hTERT promoter CGIs regions. The relative expression level of hTERT mRNA was measured by quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS: CGIs-1 (-1392--1098 bp), CGIs-2 (-945--669 bp), and CGIs-3 (-445--48 bp) were selected for our study. Our results indicated that the methylation levels of hTERT promotor CGIs regions in melanoma were greater than pigmented nevus (CGIs-1: 69.3 ±â€Š18.7% vs 46.8 ±â€Š20.4%, t = 3.048 P = .005; CGIs-2: 73.8 ±â€Š14.7% vs 55.6 ±â€Š16.0%, t = 3.120 P = .004; CGIs-3: 5.8 ±â€Š2.2% vs 2.2 ±â€Š1.3%, t = 5.164 P < .001). The relative expression level of hTERT in melanoma was greater than in pigmented nevus (50.39 ±â€Š9.16 vs 26.10 ±â€Š7.25, t = 7.778, P < .001). Linear regression analysis showed that the methylation level of CGIs-2 in melanoma was positively correlated with the relative expression level of hTERT mRNA (R = .490, F = 13.478, P = .003). Combined with the analysis of clinicopathological features, the methylation level of CGIs-2 in melanoma with lymph node metastasis was greater than in melanoma without lymph node metastasis, and the methylation level of CGIs-2 increased with TNM staging. CONCLUSION: CGIs-2 methylation level was associated with the relative expression level of hTERT mRNA, lymph node metastasis and TNM staging, suggesting that CGIs-2 hypermethylation might be used to evaluate the prognosis in Chinese patients with acral and mucosal melanoma.


Assuntos
Ilhas de CpG/genética , Metilação de DNA/genética , Melanoma/genética , Proteína 2 de Ligação a Metil-CpG/metabolismo , Telomerase/metabolismo , Idoso , Grupo com Ancestrais do Continente Asiático/genética , China , Biologia Computacional , Feminino , Humanos , Modelos Lineares , Metástase Linfática , Masculino , Melanoma/mortalidade , Melanoma/patologia , Pessoa de Meia-Idade , Estadiamento de Neoplasias , Reação em Cadeia da Polimerase , Prognóstico , RNA Mensageiro/metabolismo
4.
BMC Bioinformatics ; 20(1): 510, 2019 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-31640538

RESUMO

BACKGROUND: In human genetic association studies with high-dimensional gene expression data, it has been well known that statistical selection methods utilizing prior biological network knowledge such as genetic pathways and signaling pathways can outperform other methods that ignore genetic network structures in terms of true positive selection. In recent epigenetic research on case-control association studies, relatively many statistical methods have been proposed to identify cancer-related CpG sites and their corresponding genes from high-dimensional DNA methylation array data. However, most of existing methods are not designed to utilize genetic network information although methylation levels between linked genes in the genetic networks tend to be highly correlated with each other. RESULTS: We propose new approach that combines data dimension reduction techniques with network-based regularization to identify outcome-related genes for analysis of high-dimensional DNA methylation data. In simulation studies, we demonstrated that the proposed approach overwhelms other statistical methods that do not utilize genetic network information in terms of true positive selection. We also applied it to the 450K DNA methylation array data of the four breast invasive carcinoma cancer subtypes from The Cancer Genome Atlas (TCGA) project. CONCLUSIONS: The proposed variable selection approach can utilize prior biological network information for analysis of high-dimensional DNA methylation array data. It first captures gene level signals from multiple CpG sites using data a dimension reduction technique and then performs network-based regularization based on biological network graph information. It can select potentially cancer-related genes and genetic pathways that were missed by the existing methods.


Assuntos
Metilação de DNA , Epigenômica , Redes Reguladoras de Genes , Estudos de Associação Genética , Neoplasias da Mama/genética , Estudos de Casos e Controles , Simulação por Computador , Ilhas de CpG , Feminino , Humanos , Análise de Sequência com Séries de Oligonucleotídeos
5.
Genome Biol ; 20(1): 196, 2019 09 26.
Artigo em Inglês | MEDLINE | ID: mdl-31554518

RESUMO

BACKGROUND: DNA methylation (DNAm) is a critical regulator of both development and cellular identity and shows unique patterns in neurons. To better characterize maturational changes in DNAm patterns in these cells, we profile the DNAm landscape at single-base resolution across the first two decades of human neocortical development in NeuN+ neurons using whole-genome bisulfite sequencing and compare them to non-neurons (primarily glia) and prenatal homogenate cortex. RESULTS: We show that DNAm changes more dramatically during the first 5 years of postnatal life than during the entire remaining period. We further refine global patterns of increasingly divergent neuronal CpG and CpH methylation (mCpG and mCpH) into six developmental trajectories and find that in contrast to genome-wide patterns, neighboring mCpG and mCpH levels within these regions are highly correlated. We integrate paired RNA-seq data and identify putative regulation of hundreds of transcripts and their splicing events exclusively by mCpH levels, independently from mCpG levels, across this period. We finally explore the relationship between DNAm patterns and development of brain-related phenotypes and find enriched heritability for many phenotypes within identified DNAm features. CONCLUSIONS: By profiling DNAm changes in NeuN-sorted neurons over the span of human cortical development, we identify novel, dynamic regions of DNAm that would be masked in homogenate DNAm data; expand on the relationship between CpG methylation, CpH methylation, and gene expression; and find enrichment particularly for neuropsychiatric diseases in genomic regions with cell type-specific, developmentally dynamic DNAm patterns.


Assuntos
Encéfalo/crescimento & desenvolvimento , Metilação de DNA , Neurônios/metabolismo , Adolescente , Encéfalo/embriologia , Encéfalo/metabolismo , Encéfalo/fisiologia , Criança , Pré-Escolar , Ilhas de CpG , Expressão Gênica , Genômica , Humanos , Lactente , Recém-Nascido , Plasticidade Neuronal , Isoformas de RNA/química , Isoformas de RNA/metabolismo , Processamento de RNA , Adulto Jovem
6.
Adv Exp Med Biol ; 1178: 175-206, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31493228

RESUMO

A global DNA hypomethylation and local changes in the methylation levels of specific DNA loci occur during aging in mammals. Global hypomethylation mainly affects highly methylated repeat sequences, such as transposable elements; it is an essentially stochastic process usually referred to as "epigenetic drift." Specific changes in DNA methylation affect various genome sequences and could be either hypomethylation or hypermethylation, but the prevailing tendencies are hypermethylation of promoter sequences associated with CpG islands and hypomethylation of CpG poor genes. Methylation levels of multiple CpG sites display a strong correlation to age common between individuals of the same species. Collectively, methylation of such CpG sites could be used as "epigenetic clocks" to predict biological age. Furthermore, the discrepancy between epigenetic and chronological ages could be predictive of all-cause mortality and multiple age-associated diseases. Random changes in DNA methylation (epigenetic drift) could also affect the aging phenotype, causing accidental changes in gene expression and increasing the transcriptional noise between cells of the same tissue. Both effects could become detrimental to tissue functioning and cause a gradual decline in organ function during aging. Strong evidence shows that epigenetic systems contribute to lifespan control in various organisms. Similar to other cell systems, the epigenome is prone to gradual degradation due to the genome damage, stressful agents and other aging factors. However, unlike mutations and many other hallmarks of aging, age-related epigenetic changes could be fully or partially reversed to a "young" state.


Assuntos
Envelhecimento , Epigênese Genética , Marcadores Genéticos , Envelhecimento/genética , Animais , Ilhas de CpG/genética , Metilação de DNA , Epigenômica , Marcadores Genéticos/genética , Longevidade
7.
BMC Infect Dis ; 19(1): 802, 2019 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-31510934

RESUMO

BACKGROUND: Chronic infection with hepatitis B virus (HBV) is a serious global health problem. Persistence of the virus occurs as a result of stability of the replication intermediate comprising covalently closed circular DNA (cccDNA). Development of drugs that are capable of disabling this cccDNA is vital. METHODS: To investigate an epigenetic approach to inactivating viral DNA, we engineered transcriptional repressors that comprise an HBV DNA-binding domain of transcription activator like effectors (TALEs) and a fused Krüppel Associated Box (KRAB). These repressor TALEs (rTALEs) targeted the viral surface open reading frame and were placed under transcription control of constitutively active or liver-specific promoters. RESULTS: Evaluation in cultured cells and following hydrodynamic injection of mice revealed that the rTALEs significantly inhibited production of markers of HBV replication without evidence of hepatotoxicity. Increased methylation of HBV DNA at CpG island II showed that the rTALEs caused intended epigenetic modification. CONCLUSIONS: Epigenetic modification of HBV DNA is a new and effective means of inactivating the virus in vivo. The approach has therapeutic potential and avoids potentially problematic unintended mutagenesis of gene editing.


Assuntos
DNA Viral/genética , Vírus da Hepatite B/crescimento & desenvolvimento , Vírus da Hepatite B/genética , Hepatite B/terapia , Hepatite B/virologia , Proteínas Repressoras/metabolismo , Replicação Viral/genética , Animais , Linhagem Celular , Ilhas de CpG , Metilação de DNA , DNA Circular/genética , DNA Viral/biossíntese , Epigênese Genética , Feminino , Fígado/metabolismo , Fígado/virologia , Camundongos , Fases de Leitura Aberta/genética , Regiões Promotoras Genéticas/genética , Proteínas Repressoras/genética
8.
J Cancer Res Clin Oncol ; 145(11): 2835-2843, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31506740

RESUMO

PURPOSE: Molecular mechanisms of response to hypomethylating agents in patients with myelodysplastic syndromes (MDS) and chronic myelomonocytic leukemia (CMML) still remain largely unknown. Therefore, the effects of 5-Azacytidine (Aza) on clonal architecture and DNA methylation were investigated in this study. METHODS: Using next-generation sequencing (NGS), 30 myeloid leukemia-associated genes were analyzed in 15 MDS/CMML patients with excellent response to Aza. Effects on methylation levels were analyzed by quantitative methylation analysis using pyrosequencing for the global methylation marker LINE-1 in patients and myeloid cell lines. Various myeloid cell lines and a healthy cohort were screened for methylation levels in 23 genes. Selected targets were verified on the MDS/CMML cohort. RESULTS: The study presented here showed a stable variant allele frequency and stable global methylation levels in responding patients. A significant demethylation of EZH2 and NOTCH1 was revealed in patients with Aza response. CONCLUSIONS: A response to Aza is not associated with eradication of malignant clones, but rather with a stabilization of the clonal architecture. We suggest changes in CpG methylation levels of EZH2 and NOTCH1 as potential targets of epigenetic response to Aza treatment which may also serve as useful biomarkers after clinical evaluation.


Assuntos
Azacitidina/farmacologia , Biomarcadores Tumorais/genética , Proteína Potenciadora do Homólogo 2 de Zeste/genética , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Leucemia Mielomonocítica Crônica/genética , Síndromes Mielodisplásicas/genética , Receptor Notch1/genética , Idoso , Antimetabólitos Antineoplásicos/farmacologia , Estudos de Casos e Controles , Ilhas de CpG , Metilação de DNA , Proteína Potenciadora do Homólogo 2 de Zeste/metabolismo , Feminino , Seguimentos , Perfilação da Expressão Gênica , Humanos , Leucemia Mielomonocítica Crônica/tratamento farmacológico , Leucemia Mielomonocítica Crônica/patologia , Masculino , Pessoa de Meia-Idade , Síndromes Mielodisplásicas/tratamento farmacológico , Síndromes Mielodisplásicas/patologia , Prognóstico , Receptor Notch1/metabolismo , Células Tumorais Cultivadas
9.
Gene ; 721: 144107, 2019 Dec 30.
Artigo em Inglês | MEDLINE | ID: mdl-31499127

RESUMO

BACKGROUND: Gene environment interactions leading to epigenetic alterations play pivotal role in the pathogenesis of Coronary Artery Disease (CAD). Altered DNA methylation is one such epigenetic factor that could lead to altered disease etiology. In this study, we comprehensively identified methylation sites in several genes that have been previously associated with young CAD patients. METHODS: The study population consisted of 42 healthy controls and 33 young CAD patients (age group <50 years). We performed targeted bisulfite sequencing of promoter as well as gene body regions of several genes in various pathways like cholesterol synthesis and metabolism, endothelial dysfunction, apoptosis, which are implicated in the development of CAD. RESULTS: We observed that the genes like GALNT2, HMGCR were hypermethylated in the promoter whereas LDLR gene promoter was hypomethylated indicating that intracellular LDL uptake was higher in CAD patients. Although APOA1 did not show significant change in methylation but APOC3 and APOA5 showed variation in methylation in promoter and exonic regions. Glucokinase (GCK) and endothelial nitric oxide synthase 3 (NOS3) were hyper methylated in the promoter. Genes involved in apoptosis (BAX/BCL2/AKT2) and inflammation (PHACTR1/LCK) also showed differential methylation between controls and CAD patients. A combined analysis of the methylated CpG sites using machine learning tool revealed 14 CpGs in 11 genes that could discriminate CAD cases from controls with over 93% accuracy. CONCLUSIONS: This study is unique because it highlights important gene methylation alterations which might predict the risk of young CAD in Indian population. Large scale studies in different populations would be important for validating our findings and understanding the epigenetic events associated with CAD.


Assuntos
Doença da Artéria Coronariana/metabolismo , Ilhas de CpG , Metilação de DNA , Análise de Sequência de DNA , Adulto , Apolipoproteínas/genética , Proteínas Reguladoras de Apoptose/genética , Proteínas Reguladoras de Apoptose/metabolismo , Doença da Artéria Coronariana/genética , Doença da Artéria Coronariana/patologia , Feminino , Humanos , Inflamação/genética , Inflamação/metabolismo , Inflamação/patologia , Masculino , Pessoa de Meia-Idade , Sulfitos/química
10.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 36(8): 769-772, 2019 Aug 10.
Artigo em Chinês | MEDLINE | ID: mdl-31400124

RESUMO

OBJECTIVE: To explore the characteristics of differentially methylated genes and gene ontology associated with neural tube defects (NTDs). METHODS: Twelve subjects from 3 NTDs pedigrees were enrolled. Patients with NTDs have served as the case group, while their family members with normal phenotypes have served as the control group. Genomic DNA was extracted from peripheral venous blood samples of the families and used for DNA methylation analysis. Pairwise comparison was carried out primarily for patient-offspring pairs, and co-segregation of methylation pattern with NTDs was analyzed. Pathway related to differentially methylated genes was predicted with DAVID software. RESULTS: Pairwise comparison indicated that VTRNA2-1 was the only gene in which all CpG sites were methylated. Co-segregation of VTRNA2-1 gene methylation with NTDs was found in all pedigrees. Pathways of hypermethylated genes included plasma membrane component, regulation of cellular protein metabolic process, and regulation of actin cytoskeleton organization, while the pathways of hypomethylated genes have included transcription regulator activity, cell adhesion, and neuronal differentiation. CONCLUSION: Methylation of the VTRNA2-1 gene has co-segregated with NTDs in the studied pedigrees. The pathways of differentially methylated genes has involved with mechanism of neural tube development.


Assuntos
Metilação de DNA , MicroRNAs/genética , Defeitos do Tubo Neural/genética , Ilhas de CpG , Ontologia Genética , Humanos , Linhagem
11.
Bioelectrochemistry ; 130: 107343, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31401517

RESUMO

Skin is a very suitable target for gene therapy and DNA vaccination due to its accessibility, its surface and its ability to produce transgenes. Gene electrotransfer (GET) to the skin is under development for clinical applications for DNA vaccine or local treatment such as wound healing. Local treatments are effective if the expression of the plasmid affects only the local environment (skin) by inducing an efficient concentration over a prolonged period. In this study, we evaluate the control of expression in the skin of a plasmid coding a fluorescent protein by its CpG (cytosine-phosphate-guanine motif) content. Two fluorescent reporter genes are evaluated: tdTomato and GFP. The expression is followed on the long term by in vivo fluorescence imaging. Our results show that GET mediated expression in the skin can be controlled by the CpG content of the plasmid. Long term expression (>120 days) can be obtained at high level with CpG-free constructs associated with a proper design of the electrodes where the field distribution mediating the gene electrotransfer is present deep in the skin.


Assuntos
DNA/administração & dosagem , Técnicas de Transferência de Genes , Plasmídeos/administração & dosagem , Pele/metabolismo , Animais , Ilhas de CpG , DNA/genética , Eletrodos , Eletroporação/métodos , Feminino , Genes Reporter , Camundongos Endogâmicos C57BL , Plasmídeos/genética
12.
BMC Bioinformatics ; 20(1): 431, 2019 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-31426747

RESUMO

BACKGROUND: Protein pulldown using Methyl-CpG binding domain (MBD) proteins followed by high-throughput sequencing is a common method to determine DNA methylation. Algorithms have been developed to estimate absolute methylation level from read coverage generated by affinity enrichment-based techniques, but the most accurate one for MBD-seq data requires additional data from an SssI-treated Control experiment. RESULTS: Using our previous characterizations of Methyl-CpG/MBD2 binding in the context of an MBD pulldown experiment, we build a model of expected MBD pulldown reads as drawn from SssI-treated DNA. We use the program BayMeth to evaluate the effectiveness of this model by substituting calculated SssI Control data for the observed SssI Control data. By comparing methylation predictions against those from an RRBS data set, we find that BayMeth run with our modeled SssI Control data performs better than BayMeth run with observed SssI Control data, on both 100 bp and 10 bp windows. Adapting the model to an external data set solely by changing the average fragment length, our calculated data still informs the BayMeth program to a similar level as observed data in predicting methylation state on a pulldown data set with matching WGBS estimates. CONCLUSION: In both internal and external MBD pulldown data sets tested in this study, BayMeth used with our modeled pulldown coverage performs better than BayMeth run without the inclusion of any estimate of SssI Control pulldown, and is comparable to - and in some cases better than - using observed SssI Control data with the BayMeth program. Thus, our MBD pulldown alignment model can improve methylation predictions without the need to perform additional control experiments.


Assuntos
Biologia Computacional/métodos , Metilação de DNA/genética , DNA-Citosina Metilases/metabolismo , DNA/metabolismo , Modelos Biológicos , Alinhamento de Sequência , Algoritmos , Pareamento de Bases , Cromossomos Humanos Par 7/genética , Ilhas de CpG/genética , Genoma Humano , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Domínio de Ligação a CpG Metilada , Análise de Sequência de DNA/métodos
13.
Forensic Sci Int ; 302: 109926, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31444040

RESUMO

Missing, ineligible or delayed reference data to establish conventional dental or DNA identification are common scenarios in forensic practice. Therefore, it is worthwhile to explore new avenues that facilitate human identification. Due to the recent remarkable evolution in the prosthetic dental restorations based on dental implants and the emergence of novel DNA technologies utilized to infer the biological profile, the identification process has become easier than ever before. We report on a characteristic case, which highlights the particular importance of dental implants and DNA approaches in the prospective investigations for human identification. The aim of this publication is to focus on the possibility of identifying the batch numbers, even if they were not engraved in dental implants, making antemortem dental records of dental implants more easily accessible to establish a comparative dental identification. In addition, the reported case presents the supplementary data yielded through estimating the epigenetic age using DNA methylation as well as the biogeographical origin using Y-Haplotype and mitochondrial DNA analyses. Our results demonstrate that expanded oral implant investigations that also include implants extraction and comprehensive microscopic measurements can lead to identifying their batch numbers despite the numerous number of implants systems manufactured and distributed worldwide. Data saved by dental implant manufacturers can be very supportive and represent additional reference data for dental identification, when antemortem dental records are still missing. Furthermore, DNA methylation and mitochondrial DNA analyses can support the progress of investigation.


Assuntos
Impressões Digitais de DNA , Implantes Dentários , Repetições de Microssatélites , Idoso , Idoso de 80 Anos ou mais , Ilhas de CpG/genética , Metilação de DNA , Dente Suporte , Odontologia Legal , Genética Forense , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Radiografia Panorâmica
15.
Int J Sports Med ; 40(10): 670-677, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31342477

RESUMO

Apoptosis-associated, speck-like protein containing a caspase recruitment domain (ASC) plays an important role in inflammatory cytokine synthesis in peripheral blood mononuclear cells (PBMCs), and the expression of ASC is suppressed by increased methylation of its CpG sites. The current study investigated the longitudinal association of replacing sedentary time with light-intensity physical activity (LPA) or moderate to vigorous-intensity physical activity (MVPA) on the ASC methylation in middle-aged people. We investigated 1 238 individuals who participated in baseline and 5-year follow-up surveys of a population-based cohort study. Sedentary, LPA and MVPA time were objectively measured using accelerometers. ASC methylation in PBMCs was measured by pyrosequencing. Using a multiple linear regression and employing an isotemporal substitution model, the longitudinal associations of changes in the sedentary time, LPA and MVPA on the changes in the ASC methylation were analyzed after adjusting for potential confounders. Substituting 60 min per day of LPA for sedentary time was associated with 1.17 times (95% confidence interval 1.07, 1.27) higher ASC methylation levels (mean of 7 CpG sites, P<0.001). However, such effects were not seen for MVPA. These results suggest that substituting LPA for sedentary time may be linked with increased (favorable) ASC methylation as a potential biomarker of systemic inflammation.


Assuntos
Proteínas Adaptadoras de Sinalização CARD/química , Metilação de DNA , Exercício , Acelerometria , Idoso , Antropometria , Estudos de Coortes , Ilhas de CpG , Citocinas/sangue , Feminino , Monitores de Aptidão Física , Humanos , Leucócitos Mononucleares , Masculino , Pessoa de Meia-Idade , Comportamento Sedentário
16.
Medicine (Baltimore) ; 98(28): e16424, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31305461

RESUMO

Although the changes in DNA methylation are assumed to be due to the association between adverse intrauterine conditions and adult metabolic health, evidence from human studies is rare. Little is known about the changes in DNA methylation present at birth that affect metabolic profiles in childhood. Previous studies have shown that the melanocortin 4 receptor (MC4R) and hepatocyte nuclear factor 4 alpha (HNF4α) genes are associated with obesity and metabolic disorders. Thus, we investigated the associations of the DNA methylation statuses of MC4R and HNF4α in cord blood with metabolic profiles in childhood.We collected data from 90 children 7 to 9 years of age included in the Ewha Birth & Growth Cohort Study in Korea. DNA methylation was analyzed by pyrosequencing. The children were split into 2 groups according to the cutoff triglyceride (TG) levels (<110 and ≥110 mg/dL).The methylation statuses of MC4R and HNF4α at birth were significantly associated with the TG level in childhood (P < .05). It was interesting to note that the methylation statuses of MC4R and HNF4α in cord blood were significantly decreased, whereas childhood body mass index was significantly increased, in children with high TG levels compared with children with low TG levels (P < .05).Our findings show that the methylation statuses of MC4R and HNF4α at birth are associated with metabolic profiles in childhood. These epigenetic modifications occurring in early life may contribute to subsequent metabolic-related disorders. Thus, we suggest that DNA methylation status in cord blood may be predictive of the risk of developing metabolic syndrome.


Assuntos
Metilação de DNA , Fator 4 Nuclear de Hepatócito/genética , Regiões Promotoras Genéticas , Receptor Tipo 4 de Melanocortina/genética , Triglicerídeos/sangue , Índice de Massa Corporal , Criança , Desenvolvimento Infantil , Ilhas de CpG , Epigênese Genética , Feminino , Sangue Fetal/metabolismo , Seguimentos , Fator 4 Nuclear de Hepatócito/metabolismo , Humanos , Estudos Longitudinais , Masculino , Estudos Prospectivos , Receptor Tipo 4 de Melanocortina/metabolismo
17.
Nat Commun ; 10(1): 3095, 2019 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-31300640

RESUMO

The nasal cellular epigenome may serve as biomarker of airway disease and environmental response. Here we collect nasal swabs from the anterior nares of 547 children (mean-age 12.9 y), and measure DNA methylation (DNAm) with the Infinium MethylationEPIC BeadChip. We perform nasal Epigenome-Wide Association analyses (EWAS) of current asthma, allergen sensitization, allergic rhinitis, fractional exhaled nitric oxide (FeNO) and lung function. We find multiple differentially methylated CpGs (FDR < 0.05) and Regions (DMRs; ≥ 5-CpGs and FDR < 0.05) for asthma (285-CpGs), FeNO (8,372-CpGs; 191-DMRs), total IgE (3-CpGs; 3-DMRs), environment IgE (17-CpGs; 4-DMRs), allergic asthma (1,235-CpGs; 7-DMRs) and bronchodilator response (130-CpGs). Discovered DMRs annotated to genes implicated in allergic asthma, Th2 activation and eosinophilia (EPX, IL4, IL13) and genes previously associated with asthma and IgE in EWAS of blood (ACOT7, SLC25A25). Asthma, IgE and FeNO were associated with nasal epigenetic age acceleration. The nasal epigenome is a sensitive biomarker of asthma, allergy and airway inflammation.


Assuntos
Asma/diagnóstico , Metilação de DNA/imunologia , Inflamação/diagnóstico , Mucosa Nasal/imunologia , Adolescente , Asma/genética , Asma/imunologia , Asma/patologia , Biomarcadores/análise , Criança , Ilhas de CpG/genética , Ilhas de CpG/imunologia , Epigênese Genética/imunologia , Epigenômica/métodos , Feminino , Humanos , Inflamação/imunologia , Inflamação/patologia , Masculino , Mucosa Nasal/patologia
18.
Gene ; 712: 143954, 2019 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-31288058

RESUMO

BACKGROUND: Breast cancer (BC) is the highest cause of mortality among female cancer patients. In some cases, BC is due to Poly [ADP-ribose] polymerase 1 (PARP1) gene dysregulation, which has been involved in various important cellular processes. Among Iranian women, the association between PARP1 polymorphisms and BC was never studied before so in this case-control study, the genetic association of three SNPs (rs1136410, rs907187 and rs4653734) was analyzed with susceptibility to BC. METHODS: The study subjects were 386 Iranian females divided into 186 patients and 200 healthy controls. The genotypes of PARP1 variants were detected using ARMS and a combined ARMS-RFLP PCR method. RESULTS: The results showed that Carriers of CG and GG genotypes of the variant rs4653734 were at higher risk of BC compared with wild-type carriers (CC) and this variant was statistically significant under a recessive model of inheritance. Moreover, rs907187 was related to increased BC risk in the CC and GG genotypes under dominant and recessive models of inheritance. The G allele frequency of rs4653734 and rs907187 was higher in breast cancer patients than in normal subjects. No association was detected between rs1136410 and susceptibility to BC among studied groups. Furthermore, A-G-C haplotype was linked to an increased BC risk, whereas A-C-C and A-C-G haplotypes were related to a decreased risk of BC. In Silico predictions suggested that rs907187 affects E2F and E2F-4 transcription factors binding site. CONCLUSIONS: The current study suggests that rs907187 and rs4653734 have remarkable associations with BC risk among Iranian women.


Assuntos
Neoplasias da Mama/genética , Desequilíbrio de Ligação , Poli(ADP-Ribose) Polimerase-1/genética , Polimorfismo de Nucleotídeo Único , Adulto , Idoso , Alelos , Neoplasias da Mama/metabolismo , Estudos de Casos e Controles , Biologia Computacional , Ilhas de CpG , Feminino , Regulação Neoplásica da Expressão Gênica , Frequência do Gene , Predisposição Genética para Doença , Genótipo , Haplótipos , Humanos , Irã (Geográfico)/epidemiologia , Pessoa de Meia-Idade , Metástase Neoplásica , Polimorfismo de Fragmento de Restrição , Fatores de Risco , Fatores de Transcrição/metabolismo
19.
Methods Mol Biol ; 2018: 177-194, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31228157

RESUMO

Reduced representation bisulfite sequencing (RRBS) is an efficient approach for estimating cytosine methylation and hydroxymethylation at single nucleotide resolution with a focus on CpG sites located in CpG islands. Commonly used methods for multiplexing RRBS libraries involve a different indexed adapter, which is expensive to generate, for each library. Here, we describe a library preparation method that utilizes a universal adapter and labels samples with unique indexed PCR primers, significantly reducing the cost of multiplexed RRBS.


Assuntos
Primers do DNA/genética , Biblioteca Gênica , Análise de Sequência de DNA/veterinária , Sulfitos/química , 5-Metilcitosina/análogos & derivados , 5-Metilcitosina/química , Animais , Ilhas de CpG , Citosina/química , Metilação de DNA , Ratos
20.
J Dairy Sci ; 102(8): 7421-7434, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31178179

RESUMO

It is generally accepted that intracellular killing of microorganisms by production of reactive oxygen species (ROS) in the phagosome of the neutrophil is an important arm of innate defense. High-producing dairy cows are prone to periparturient metabolic and infectious diseases. Both myeloperoxidase (MPO) activity and ROS production decrease the day of parturition. Several studies have demonstrated changes in the expression of genes involved in, for example, metabolism and defense in the circulating neutrophil during peripartum. In this study, we wanted to further characterize the periparturient neutrophil in terms of its oxidative killing capacity by analyzing the oxidative burst at 3 levels. First, the ROS phenotype was evaluated using chemiluminescence. The cows (sampled within 24 h after parturition and at 135 d in milk) showed a significantly slower production of ROS at parturition. Both primiparous (n = 13) and multiparous (n = 12) cows were included in this study, but parity did not affect the kinetics of ROS production. Second, the expression of 11 genes involved in ROS production was measured in the same cows: cytochrome b-245 α and ß chain (CYBA, CYBB; coding for membrane-bound constituents of NADPH oxidase); neutrophil cytosolic factors 1, 2, and 4 (NCF1, NCF2, and NCF4); Rac family small GTPase 1 and 2 (RAC1 and RAC2; coding for regulatory proteins of NADPH oxidase); superoxide dismutase 2 (SOD2); catalase (CAT); myeloperoxidase (MPO; coding for enzymes involved in metabolizing downstream ROS); and spleen-associated tyrosine kinase (SYK; involved in signaling). During peripartum, a shift in expression in the oxidative killing pathway was observed, characterized by a downregulation of MPO and a simultaneous upregulation of the genes coding for NADPH oxidase. Third, as total DNA methylation is known to change during pregnancy, we investigated whether the observed differences were due to different methylation patterns. Promotor regions initiate transcription of particular genes; therefore, we analyzed the methylation status in annotated CpG islands of MPO and SOD2, 2 genes with a significant difference in expression between both lactation stages. The differences in methylation of these CpG islands were nonsignificant. High-throughput techniques may be necessary to obtain more detailed information on the total DNA methylation dynamics in bovine neutrophils and increase our understanding of how gene expression is controlled in neutrophils.


Assuntos
Bovinos/genética , Ilhas de CpG , Metilação de DNA , Regulação Enzimológica da Expressão Gênica , Neutrófilos/metabolismo , Peroxidase/genética , Superóxido Dismutase/genética , Animais , Feminino , Lactação , Leite/metabolismo , NADPH Oxidases/metabolismo , Paridade , Período Periparto , Peroxidase/metabolismo , Gravidez , Espécies Reativas de Oxigênio/metabolismo , Explosão Respiratória , Superóxido Dismutase/metabolismo
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