RESUMO
DNA methylation is an epigenetic modification that can alter gene expression, and the incidence can vary across developmental stages, inflammatory conditions, and sexes. The effects of viral maternal viral infection and sex on the DNA methylation patterns were studied in the hypothalamus of a pig model of immune activation during development. DNA methylation at single-base resolution in regions of high CpG density was measured on 24 individual hypothalamus samples using reduced representation bisulfite sequencing. Differential over- and under-methylated sites were identified and annotated to proximal genes and corresponding biological processes. A total of 120 sites were differentially methylated (FDR-adjusted p-value < 0.05) between maternal infection or sex groups. Among the 66 sites differentially methylated between groups exposed to inflammatory signals and control, most sites were over-methylated in the challenged group and included sites in the promoter regions of genes SIRT3 and NRBP1. Among the 54 differentially methylated sites between females and males, most sites were over-methylated in females and included sites in the promoter region of genes TNC and EIF4G1. The analysis of the genes proximal to the differentially methylated sites suggested that biological processes potentially impacted include immune response, neuron migration and ensheathment, peptide signaling, adaptive thermogenesis, and tissue development. These results suggest that translational studies should consider that the prolonged effect of maternal infection during gestation may be enacted through epigenetic regulatory mechanisms that may differ between sexes.
Assuntos
Metilação de DNA , Epigênese Genética , Masculino , Feminino , Animais , Suínos , Ilhas de CpG , Epigenômica/métodos , Hipotálamo/metabolismoRESUMO
The combination of multiple omics approaches has emerged as an innovative holistic scope to provide a more comprehensive view of the molecular and physiological events underlying human diseases (including obesity, dyslipidemias, fatty liver, insulin resistance, and inflammation), as well as for elucidating unique and specific metabolic phenotypes. These omics technologies include genomics (polymorphisms and other structural genetic variants), epigenomics (DNA methylation, histone modifications, long non-coding RNA, telomere length), metagenomics (gut microbiota composition, enterotypes), transcriptomics (RNA expression patterns), proteomics (protein quantities), and metabolomics (metabolite profiles), as well as interactions with dietary/nutritional factors. Although more evidence is still necessary, it is expected that the incorporation of integrative omics could be useful not only for risk prediction and early diagnosis but also for guiding tailored dietary treatments and prognosis schemes. Some challenges include ethical and regulatory issues, the lack of robust and reproducible results due to methodological aspects, the high cost of omics methodologies, and high-dimensional data analyses and interpretation. In this review, we provide examples of system biology studies using multi-omics methodologies to unravel novel insights into the mechanisms and pathways connecting the genotype to clinically relevant traits and therapy outcomes for precision nutrition applications in health and disease.
Assuntos
RNA Longo não Codificante , Epigenômica/métodos , Genômica/métodos , Humanos , Metabolômica/métodos , Proteômica/métodosRESUMO
DNA methylation is the most studied epigenetic mark in both plants and animals. The gold standard for assaying genome-wide DNA methylation at single-base resolution is whole-genome bisulfite sequencing (WGBS). Here, we describe an improved procedure for WGBS and original bioinformatic workflows applied to unravel tissue-specific variations of the methylome in relation to gene expression and accumulation of secondary metabolites in the medicinal plant Catharanthus roseus.
Assuntos
Epigenoma , Sequenciamento de Nucleotídeos em Larga Escala , Animais , DNA/genética , Metilação de DNA , Epigenômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Especificidade de Órgãos/genética , Análise de Sequência de DNA/métodos , SulfitosRESUMO
BACKGROUNDTargeted arterial infusion of verapamil combined with chemotherapy (TVCC) is an effective clinical interventional therapy for esophageal squamous cell carcinoma (ESCC), but multidrug resistance (MDR) remains the major cause of relapse or poor prognosis, and the underlying molecular mechanisms of MDR, temporal intratumoral heterogeneity, and clonal evolutionary processes of resistance have not been determined.METHODSTo elucidate the roles of genetic and epigenetic alterations in the evolution of acquired resistance during therapies, we performed whole-exome sequencing on 16 serial specimens from 7 patients with ESCC at every cycle of therapeutic intervention from 3 groups, complete response, partial response, and progressive disease, and we performed whole-genome bisulfite sequencing for 3 of these 7 patients, 1 patient from each group.RESULTSPatients with progressive disease exhibited a substantially higher genomic and epigenomic temporal heterogeneity. Subclonal expansions driven by the beneficial new mutations were observed during combined therapies, which explained the emergence of MDR. Notably, SLC7A8 was identified as a potentially novel MDR gene, and functional assays demonstrated that mutant SLC7A8 promoted the resistance phenotypes of ESCC cell lines. Promoter methylation dynamics during treatments revealed 8 drug resistance protein-coding genes characterized by hypomethylation in promoter regions. Intriguingly, promoter hypomethylation of SLC8A3 and mutant SLC7A8 were enriched in an identical pathway, protein digestion and absorption, indicating a potentially novel MDR mechanism during treatments.CONCLUSIONOur integrated multiomics investigations revealed the dynamics of temporal genetic and epigenetic inter- and intratumoral heterogeneity, clonal evolutionary processes, and epigenomic changes, providing potential MDR therapeutic targets in treatment-resistant patients with ESCC during combined therapies.FUNDINGNational Natural Science Foundation of China, Science Foundation of Peking University Cancer Hospital, CAMS Innovation Fund for Medical Sciences, Major Program of Shenzhen Bay Laboratory, Guangdong Basic and Applied Basic Research Foundation, and the third round of public welfare development and reform pilot projects of Beijing Municipal Medical Research Institutes.
Assuntos
Sistema y+ de Transporte de Aminoácidos/genética , Antineoplásicos/uso terapêutico , Resistencia a Medicamentos Antineoplásicos/genética , Epigenômica/métodos , Neoplasias Esofágicas/genética , Carcinoma de Células Escamosas do Esôfago/genética , Cadeias Leves da Proteína-1 Reguladora de Fusão/genética , Mutação , Sistema y+ de Transporte de Aminoácidos/metabolismo , Terapia Combinada , Metilação de DNA , DNA de Neoplasias/genética , Neoplasias Esofágicas/patologia , Neoplasias Esofágicas/terapia , Carcinoma de Células Escamosas do Esôfago/patologia , Carcinoma de Células Escamosas do Esôfago/terapia , Feminino , Cadeias Leves da Proteína-1 Reguladora de Fusão/metabolismo , Humanos , Masculino , Sequenciamento do ExomaRESUMO
DNA methylation serves to mark DNA as either a directed epigenetic signaling modification or in response to DNA lesions. Methods for detecting DNA methylation have become increasingly more specific and sensitive over time. Conventional methods for detecting DNA methylation, ranging from paper chromatography to differential restriction enzyme digestion preference to dot blots, have more recently been supplemented by ultrahigh performance liquid chromatography coupled with mass spectrometry (UHPLC-MS/MS) to accurately quantify specific DNA methylation. Methylated DNA can also be sequenced by either methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) or single-molecule real-time sequencing (SMRTseq) for identifying genomic locations of DNA methylation. Here we describe a protocol for the detection and quantification of epigenetic signaling DNA methylation modifications including, N6-methyladenine (6mA), N4-methylcytosine (4mC) and C5-methylcytosine (5mC) in genomic DNA by triple quadrupole liquid chromatography coupled with tandem mass spectrometry (QQQ-LC-MS/MS). The high sensitivity of the UHPLC-MS/MS methodology and the use of calibration standards of pure nucleosides allow for the accurate quantification of DNA methylation.
Assuntos
Cromatografia Líquida de Alta Pressão , Metilação de DNA , Epigênese Genética , Epigenômica , Genoma , Espectrometria de Massas em Tandem , Adenina , Epigenômica/métodos , Epigenômica/normas , Reprodutibilidade dos TestesRESUMO
Here, we provide a detailed protocol for our previously published technique, APOBEC-Coupled Epigenetic Sequencing (ACE-Seq), which localizes 5-hydroxymethylcytosine at single nucleotide resolution using nanogram quantities of input genomic DNA. In addition to describing suggested troubleshooting workflows, these methods include four important updates which should facilitate widespread implementation of the technique: (1) additionally optimized reaction conditions; (2) redesigned quality controls which can be performed prior to resource-consumptive deep sequencing; (3) confirmation that the less active, uncleaved APOBEC3A (A3A) fusion protein, which is easier to purify, can be used to perform ACE-Seq ; and (4) an example bioinformatic pipeline with suggested filtering strategies. Finally, we have provided a supplementary video which gives a narrated overview of the entire method and focuses on how best to perform the snap cool and A3A deamination steps central to successful execution of the method.
Assuntos
5-Metilcitosina/análogos & derivados , Epigenômica/métodos , Análise de Sequência de DNA/métodos , 5-Metilcitosina/análise , Animais , Biologia Computacional , Citidina Desaminase/metabolismo , Citosina/análise , Citosina/metabolismo , DNA/genética , Metilação de DNA/genética , Humanos , Proteínas/metabolismo , Imagem Individual de Molécula/métodos , Sulfitos/químicaRESUMO
Acupuncture has been widely used for treating diseases since the ancient days in China, but the mechanism by which acupuncture exerts such powerful roles is unclear. Epigenetics, including DNA methylation, histone modification, and post-transcriptional regulation of miRNAs, is the study of heritable changes in gene expression that do not include DNA sequence alterations. Epigenetics has become a new strategy for the basic and clinical research of acupuncture in the last decade. Some investigators have been trying to illustrate the mechanism of acupuncture from an epigenetics perspective, which has shed new lights on the mechanisms and applications of acupuncture. Moreover, the introduction of epigenetics into the regulatory mechanism in acupuncture treatment has provided more objective and scientific support for acupuncture theories and brought new opportunities for the improvement of acupuncture studies. In this paper, we reviewed the literatures that has demonstrated that acupuncture could directly or indirectly affect epigenetics, in order to highlight the progress of acupuncture studies correlated to epigenetic regulations. We do have to disclose that the current evidence in this review is not enough to cover all the complex interactions between multiple epigenetic modifications and their regulations. However, the up-to-date results can help us to better understand acupuncture's clinical applications and laboratory research.
Assuntos
Terapia por Acupuntura , Epigenômica/métodos , Montagem e Desmontagem da Cromatina/fisiologia , Metilação de DNA/fisiologia , Código das Histonas/fisiologia , Humanos , MicroRNAs/fisiologiaRESUMO
BACKGROUND: DNA methylation (DNAm) age constitutes a powerful tool to assess the molecular age and overall health status of biological samples. Recently, it has been shown that tissue-specific DNAm age predictors may present superior performance compared to the pan- or multi-tissue counterparts. The skin is the largest organ in the body and bears important roles, such as body temperature control, barrier function, and protection from external insults. As a consequence of the constant and intimate interaction between the skin and the environment, current DNAm estimators, routinely trained using internal tissues which are influenced by other stimuli, are mostly inadequate to accurately predict skin DNAm age. RESULTS: In the present study, we developed a highly accurate skin-specific DNAm age predictor, using DNAm data obtained from 508 human skin samples. Based on the analysis of 2,266 CpG sites, we accurately calculated the DNAm age of cultured skin cells and human skin biopsies. Age estimation was sensitive to the biological age of the donor, cell passage, skin disease status, as well as treatment with senotherapeutic drugs. CONCLUSIONS: This highly accurate skin-specific DNAm age predictor constitutes a holistic tool that will be of great use in the analysis of human skin health status/molecular aging, as well as in the analysis of the potential of established and novel compounds to alter DNAm age.
Assuntos
Metilação de DNA/genética , Epigenoma/genética , Envelhecimento Saudável/genética , Pele/metabolismo , Adulto , Idoso , Idoso de 80 Anos ou mais , Envelhecimento/genética , Algoritmos , Ilhas de CpG/genética , Epigenômica/métodos , Feminino , Fibroblastos/metabolismo , Fibroblastos/patologia , Nível de Saúde , Humanos , Aprendizado de Máquina , Masculino , Pessoa de Meia-Idade , Pele/patologiaRESUMO
BACKGROUND: IGF1 is a key molecule in the regulation of growth and metabolism. Low IGF1 secretion is known to cause growth restriction in childhood, as well as deregulated lipid metabolism, cardiovascular disease, and diabetes in adulthood. The IGF1 gene P2 promoter is highly methylated, resulting in low secretion of IGF1 in small infants and children. However, it is unknown when this methylation occurs. The aim of study was to clarify the point when this epigenetic program occurs during intrauterine development. We analyzed 56 preterm infants born before 32 weeks of gestation, including 19 intrauterine growth restriction (IUGR) infants whose birth weights were lower than - 2SD calculated by the Japanese datasets. We extracted genomic DNA from whole blood at birth; methylation of the six CpG sites in the IGF1 P2 promoter was analyzed by the bisulfite amplicon method using the MiSeq platform. RESULTS: In contrast to term infants and children, the methylation of all six CpG sites positively correlated with body weight and body length at birth. IGF1 P2 promoter methylation levels were significantly reduced in all six CpG sites in infants with IUGR. CONCLUSIONS: These findings indicated that the IGF1 gene is epigenetically activated before 32 weeks of gestation in infants with IUGR and that the activated gene may become suppressed after this time point. This study may provide new insights to prevent the onset of adult diseases and to aid in nutritional management for preterm birth infants in neonatal intensive care units.
Assuntos
Epigenômica/métodos , Retardo do Crescimento Fetal/genética , Fator de Crescimento Insulin-Like I/genética , Adulto , Doenças Cardiovasculares/genética , Estudos de Casos e Controles , Criança , Ilhas de CpG/genética , Metilação de DNA/genética , Diabetes Mellitus/genética , Feminino , Idade Gestacional , Humanos , Recém-Nascido , Recém-Nascido Prematuro , Recém-Nascido Pequeno para a Idade Gestacional/sangue , Unidades de Terapia Intensiva Neonatal/normas , Transtornos do Metabolismo dos Lipídeos/genética , Terapia Nutricional/métodos , Gravidez , Nascimento Prematuro/genética , Regiões Promotoras GenéticasRESUMO
Multi-omics approach nowadays increasingly applied to molecular research in many fields of life sciences. Biogerontology is not an exception; multi-omics gives possibility to evaluate complex biomarkers (or panels) which consist of quantitative as well as phenotypic ones. It is especially important because of weak understanding of the nature of aging. The difficulty now is distinguishing between causes and effects of aging. The application of the whole set of metabolome, methylome, transcriptome, proteome or metagenome data in aging biomarker design becomes the only way to create a holistic view of aging landscape without missing undiscovered mechanisms and levels of organization. We found patents, up-to-date multi-omics datasets and studies, which include bioinformatics innovations to predict biological age in humans. We hope that the review will be also useful for clinicians, because it follows majorly translational purposes.
Assuntos
Envelhecimento/fisiologia , Epigenômica/métodos , Genômica/métodos , Metabolômica/métodos , Biomarcadores , Geriatria/tendências , Humanos , Pesquisa Translacional BiomédicaRESUMO
The evolution of human diets led to preferences toward polyunsaturated fatty acid (PUFA) content with 'Western' diets enriched in ω-6 PUFAs. Mounting evidence points to ω-6 PUFA excess limiting metabolic and cognitive processes that define longevity in humans. When chosen during pregnancy, ω-6 PUFA-enriched 'Western' diets can reprogram maternal bodily metabolism with maternal nutrient supply precipitating the body-wide imprinting of molecular and cellular adaptations at the level of long-range intercellular signaling networks in the unborn fetus. Even though unfavorable neurological outcomes are amongst the most common complications of intrauterine ω-6 PUFA excess, cellular underpinnings of life-long modifications to brain architecture remain unknown. Here, we show that nutritional ω-6 PUFA-derived endocannabinoids desensitize CB1 cannabinoid receptors, thus inducing epigenetic repression of transcriptional regulatory networks controlling neuronal differentiation. We found that cortical neurons lose their positional identity and axonal selectivity when mouse fetuses are exposed to excess ω-6 PUFAs in utero. Conversion of ω-6 PUFAs into endocannabinoids disrupted the temporal precision of signaling at neuronal CB1 cannabinoid receptors, chiefly deregulating Stat3-dependent transcriptional cascades otherwise required to execute neuronal differentiation programs. Global proteomics identified the immunoglobulin family of cell adhesion molecules (IgCAMs) as direct substrates, with DNA methylation and chromatin accessibility profiling uncovering epigenetic reprogramming at >1400 sites in neurons after prolonged cannabinoid exposure. We found anxiety and depression-like behavioral traits to manifest in adult offspring, which is consistent with genetic models of reduced IgCAM expression, to suggest causality for cortical wiring defects. Overall, our data uncover a regulatory mechanism whose disruption by maternal food choices could limit an offspring's brain function for life.
Assuntos
Encéfalo/efeitos dos fármacos , Dieta Ocidental/efeitos adversos , Epigênese Genética/efeitos dos fármacos , Animais , Ansiedade , Encéfalo/metabolismo , Metilação de DNA/efeitos dos fármacos , Depressão , Dieta , Suplementos Nutricionais , Endocanabinoides/metabolismo , Epigênese Genética/genética , Epigenômica/métodos , Ácidos Graxos Ômega-3/metabolismo , Ácidos Graxos Ômega-6/metabolismo , Ácidos Graxos Insaturados/metabolismo , Feminino , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Neurônios/metabolismo , Gravidez , Receptor CB1 de Canabinoide/efeitos dos fármacosRESUMO
Transcriptional regulation is pivotal to the specification of distinct cell types during embryonic development. However, it still lacks a systematic way to identify key transcription factors (TFs) orchestrating the temporal and tissue specificity of gene expression. Here, we integrated epigenomic and transcriptomic data to reveal key regulators from two cells to postnatal day 0 in mouse embryogenesis. We predicted three-dimensional chromatin interactions in 12 tissues across eight developmental stages, which facilitates linking TFs to their target genes for constructing transcriptional regulatory networks. To identify driver TFs, we developed a new algorithm, dubbed Taiji, to assess the global influence of each TF and systematically uncovered TFs critical for lineage-specific and stage-dependent tissue specification. We have also identified TF combinations that function in spatiotemporal order to form transcriptional waves regulating developmental progress. Furthermore, lacking stage-specific TF combinations suggests a distributed timing strategy to orchestrate the coordination between tissues during embryonic development.
Assuntos
Algoritmos , Desenvolvimento Embrionário/genética , Regulação da Expressão Gênica no Desenvolvimento , Redes Reguladoras de Genes , Fatores de Transcrição/genética , Animais , Epigenômica/métodos , Perfilação da Expressão Gênica/métodos , Camundongos , Especificidade de Órgãos/genética , Fatores de Transcrição/classificaçãoRESUMO
Cleft lip with or without cleft palate (CL/P) is a common human birth defect whose etiologies remain largely unknown. Several studies have demonstrated that periconceptional supplementation of folic acid can reduce risk of CL/P in offspring. In this study, we tested the hypothesis that the preventive effect of folic acid is manifested through epigenetic modifications by determining whether DNA methylation changes are associated with CL/P. To more readily observe the potential effects of maternal folate on the offspring epigenome, we focused on births prior to mandatory dietary folate fortification in the United States (i.e. birth year 1997 or earlier). Genomic DNA methylation levels were assessed from archived newborn bloodspots in a 182-member case-control study using the Illumina® Human Beadchip 450K array. CL/P cases displayed striking epigenome-wide hypomethylation relative to controls: 63% of CpGs interrogated had lower methylation levels in case newborns, a trend which held up in racially stratified sub-groups. 28 CpG sites reached epigenome-wide significance and all were case-hypomethylated. The most significant CL/P-associated differentially methylated region encompassed the VTRNA2-1 gene, which was also hypomethylated in cases (FWER p = 0.014). This region has been previously characterized as a nutritionally-responsive, metastable epiallele and CL/P-associated methylation changes, in general, were greater at or near putative metastable epiallelic regions. Gene Set Enrichment Analysis of CL/P-associated DMRs showed an over-representation of genes involved in palate development such as WNT9B, MIR140 and LHX8. CL/P-associated DNA methylation changes may partly explain the mechanism by which orofacial clefts are responsive to maternal folate levels.
Assuntos
Fenda Labial/genética , Metilação de DNA , Epigenômica/métodos , Ácido Fólico/administração & dosagem , Estudos de Casos e Controles , Fenda Labial/prevenção & controle , Suscetibilidade a Doenças , Epigênese Genética , Feminino , Humanos , Recém-Nascido , Proteínas com Homeodomínio LIM/genética , Masculino , Exposição Materna , MicroRNAs/genética , Fatores de Transcrição/genética , Proteínas Wnt/genéticaRESUMO
The Bruton tyrosine kinase (BTK) inhibitor ibrutinib has substantially improved therapeutic options for chronic lymphocytic leukemia (CLL). Although ibrutinib is not curative, it has a profound effect on CLL cells and may create new pharmacologically exploitable vulnerabilities. To identify such vulnerabilities, we developed a systematic approach that combines epigenome profiling (charting the gene-regulatory basis of cell state) with single-cell chemosensitivity profiling (quantifying cell-type-specific drug response) and bioinformatic data integration. By applying our method to a cohort of matched patient samples collected before and during ibrutinib therapy, we identified characteristic ibrutinib-induced changes that provide a starting point for the rational design of ibrutinib combination therapies. Specifically, we observed and validated preferential sensitivity to proteasome, PLK1, and mTOR inhibitors during ibrutinib treatment. More generally, our study establishes a broadly applicable method for investigating treatment-specific vulnerabilities by integrating the complementary perspectives of epigenetic cell states and phenotypic drug responses in primary patient samples.
Assuntos
Tirosina Quinase da Agamaglobulinemia/metabolismo , Leucemia Linfocítica Crônica de Células B/tratamento farmacológico , Adenina/análogos & derivados , Tirosina Quinase da Agamaglobulinemia/antagonistas & inibidores , Proteínas de Ciclo Celular/metabolismo , Cromatina/fisiologia , Combinação de Medicamentos , Resistencia a Medicamentos Antineoplásicos/genética , Epigênese Genética/genética , Epigenômica/métodos , Humanos , Leucemia Linfocítica Crônica de Células B/genética , Piperidinas , Inibidores de Proteínas Quinases , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas Tirosina Quinases/metabolismo , Proteínas Tirosina Quinases/fisiologia , Proteínas Proto-Oncogênicas/metabolismo , Pirazóis/farmacologia , Pirimidinas/farmacologia , Transdução de Sinais , Análise de Célula Única/métodos , Serina-Treonina Quinases TOR/metabolismo , Quinase 1 Polo-LikeRESUMO
Much progress has happened in understanding developmental vulnerability to preventable environmental hazards. Along with the improved insight, the perspective has widened, and developmental toxicity now involves latent effects that can result in delayed adverse effects in adults or at old age and additional effects that can be transgenerationally transferred to future generations. Although epidemiology and toxicology to an increasing degree are exploring the adverse effects from developmental exposures in human beings, the improved documentation has resulted in little progress in protection, and few environmental chemicals are currently regulated to protect against developmental toxicity, whether it be neurotoxicity, endocrine disruption or other adverse outcome. The desire to obtain a high degree of certainty and verification of the evidence used for decision-making must be weighed against the costs and necessary duration of research, as well as the long-term costs to human health because of delayed protection of vulnerable early-life stages of human development and, possibly, future generations. Although two-generation toxicology tests may be useful for initial test purposes, other rapidly emerging tools need to be seriously considered from computational chemistry and metabolomics to CLARITY-BPA-type designs, big data and population record linkage approaches that will allow efficient generation of new insight; epigenetic mechanisms may necessitate a set of additional regulatory tests to reveal such effects. As reflected by the Prenatal Programming and Toxicity (PPTOX) VI conference, the current scientific understanding and the timescales involved require an intensified approach to protect against preventable adverse health effects that can harm the next generation and generations to come. While further research is needed, the main emphasis should be on research translation and timely public health intervention to avoid serious, irreversible and perhaps transgenerational harm.
Assuntos
Ecotoxicologia/métodos , Disruptores Endócrinos/efeitos adversos , Exposição Ambiental/efeitos adversos , Medicina Ambiental/métodos , Efeitos Tardios da Exposição Pré-Natal/diagnóstico , Animais , Big Data , Química Computacional/métodos , Congressos como Assunto , Modelos Animais de Doenças , Epigênese Genética/efeitos dos fármacos , Epigenômica/métodos , Feminino , Desenvolvimento Fetal/efeitos dos fármacos , Desenvolvimento Fetal/genética , Humanos , Metabolômica/métodos , Gravidez , Efeitos Tardios da Exposição Pré-Natal/etiologia , Efeitos Tardios da Exposição Pré-Natal/prevenção & controle , Projetos de Pesquisa , Medição de Risco/métodos , Fatores de TempoRESUMO
Contents Summary 738 I. Introduction 738 II. RRBS loci as genome-wide epigenetic markers 739 III. Exploiting functional annotation of RRBS loci 739 IV. Limitations of RRBS methods for nonmodel species 740 V. Maximising the impact of RRBS in plants 741 VI. Conclusions 741 Acknowledgements 741 SUMMARY: Investigating the features and implications of epigenetic mechanisms across the breadth of organisms and ecosystems is important for understanding the ecological relevance of epigenetics. Several cost-effective reduced representation bisulfite sequencing approaches (RRBS) have been recently developed and applied to different organisms that lack a well annotated reference genome. These new approaches improve the assessment of epigenetic diversity in ecological settings and may provide functional insights. We assess here the opportunities and limitations of RRBS in nonmodel plant species. Well thought out experimental designs that include complementary gene expression studies, and the improvement of genomics resources for the target group, promise to maximize the effect of future RRBS studies.
Assuntos
Fenômenos Ecológicos e Ambientais , Epigenômica/métodos , Plantas/genética , Análise de Sequência de DNA/métodos , Sulfitos/química , Anotação de Sequência MolecularRESUMO
INTRODUCTION: Chronic hepatitis B is a serious disease causing serious harm to the human health. Chinese medicine has its unique advantages in the clinical prevention and treatment, while the syndrome of Chinese medicine lacks the understanding at the micro level. There are some theoretical commonalities between the epigenetics and traditional Chinese medicine (TCM) syndromes. The biological basis of chronic hepatitis B (CHB) syndrome differentiation from the perspective of epigenetics is of great significance to diagnose and prevent the diseases. METHODS: This protocol is a case-control, noninterventional, observational clinical study. Patients with CHB for spleen-stomach damp heat and liver depression and spleen deficiency, with 12 each and 11 healthy volunteers were recruited. Peripheral venous blood was collected from the participants. DNA methylated transferase, genomic DNA methylated spectrum, methylated DNA binding protein MeCP2, chronic infection of hepatitis B virus with methylated related proteins, and miRNA target genes were analyzed. OBJECTIVES: From the perspective of DNA methylation epigenetics, "DNA methylation-miRNA-Target gene" is the main line, which further reveals the essence of TCM syndrome. To improve the level of TCM clinical syndrome differentiation and the clinical efficacy of TCM, especially in the study of TCM syndromes of CHB, discovering its underlying biological signature is necessary. TRIAL REGISTRATION: Clinical Trials Registration: ChiCTR1800017365, registered 26 July 2018.
Assuntos
Epigenômica/métodos , Vírus da Hepatite B/genética , Hepatite B Crônica/genética , Medicina Tradicional Chinesa/efeitos adversos , Adolescente , Adulto , Estudos de Casos e Controles , China/epidemiologia , Metilação de DNA/genética , Feminino , Hepatite B Crônica/sangue , Hepatite B Crônica/tratamento farmacológico , Humanos , Masculino , Medicina Tradicional Chinesa/métodos , MicroRNAs/genética , Pessoa de Meia-Idade , Síndrome , Adulto JovemRESUMO
Gene-nutrient interactions are important contributors to health management and disease prevention. Nutrition can alter gene expression, as well as the susceptibility to disease, including cancer, through epigenetic changes. Nutrients can influence the epigenetic status through several mechanisms, such as DNA methylation, histone modifications, and miRNA-dependent gene silencing. These alterations were associated with either increased or decreased risk for cancer development. There is convincing evidence indicating that several foods have protective roles in cancer prevention, by inhibiting tumor progression directly or through modifying tumor's microenvironment that leads to hostile conditions favorable to tumor initiation or growth. While nutritional intakes from foods cannot be adequately controlled for dosage, the role of nutrients in the epigenetics of cancer has led to more research aimed at developing nutriceuticals and drugs as cancer therapies. Clinical studies are needed to evaluate the optimum doses of dietary compounds, the safety profile of dosages, to establish the most efficient way of administration, and bioavailability, in order to maximize the beneficial effects already discovered, and to ensure replicability. Thus, nutrition represents a promising tool to be used not only in cancer prevention, but hopefully also in cancer treatment.
Assuntos
Suplementos Nutricionais , Epigênese Genética , Regulação Neoplásica da Expressão Gênica , Neoplasias/genética , Nutrientes , Dieta , Epigenômica/métodos , Alimentos , Contaminação de Alimentos , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Histonas/metabolismo , Humanos , Neoplasias/metabolismo , Neoplasias/terapia , Nutrientes/metabolismo , Nutrientes/farmacologia , Terapia Nutricional , Estado Nutricional , Substâncias ProtetorasRESUMO
There is an urgent need to develop more effective therapies for hepatocellular carcinoma (HCC) because of its aggressiveness. Guadecitabine (SGI-110) is a second-generation DNA methyltransferase inhibitor (DNMTi), which is currently in clinical trials for HCC and shows greater stability and performance over first-generation DNMTis. In order to identify potential therapeutic targets of SGI-110 for clinical trials, HCC cell lines (SNU398, HepG2, and SNU475) were used to evaluate the effects of transient SGI-110 treatment by an integrative analysis of DNA methylation, nucleosome accessibility, gene expression profiles, and its clinical relevance by comparison to The Cancer Genome Atlas (TCGA) HCC clinical data. Each HCC cell line represents a different DNA methylation subtype of primary HCC tumors based on TCGA data. After SGI-110 treatment, all cell lines were sensitive to SGI-110 with prolonged antiproliferation effects. Expression of up-regulated genes, including tumor suppressors, was positively correlated with nucleosome accessibility and negatively correlated with gene promoter DNA methylation. Alternatively, expression of down-regulated genes, such as oncogenes, was negatively correlated with nucleosome accessibility and positively correlated with gene body DNA methylation. SGI-110 can also act as a dual inhibitor to down-regulate polycomb repressive complex 2 (PRC2) genes by demethylating their gene bodies, resulting in reactivation of PRC2 repressed genes without involvement of DNA methylation. Furthermore, it can up-regulate endogenous retroviruses to reactivate immune pathways. Finally, about 48% of frequently altered genes in primary HCC tumors can be reversed by SGI-110 treatment. CONCLUSION: Our integrative analysis has successfully linked the antitumor effects of SGI-110 to detailed epigenetic alterations in HCC cells, identified potential therapeutic targets, and provided a rationale for combination treatments of SGI-110 with immune checkpoint therapies.
Assuntos
Azacitidina/análogos & derivados , Carcinoma Hepatocelular/tratamento farmacológico , Regulação Neoplásica da Expressão Gênica , Neoplasias Hepáticas/tratamento farmacológico , Metiltransferases/genética , Azacitidina/farmacologia , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/patologia , Linhagem Celular Tumoral/efeitos dos fármacos , Metilação de DNA , Inibidores Enzimáticos/farmacologia , Epigenômica/métodos , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Humanos , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/patologia , Terapia de Alvo Molecular , Sensibilidade e EspecificidadeRESUMO
Motivation: The rapid development of next-generation sequencing technology provides an opportunity to study genome-wide DNA methylation at single-base resolution. However, depletion of unmethylated cytosines brings challenges for aligning bisulfite-converted sequencing reads to a large reference. Software tools for aligning methylation reads have not yet been comprehensively evaluated, especially for the widely used reduced representation bisulfite sequencing (RRBS) that involves enrichment for CpG islands (CGIs). Results: We specially developed a simulator, RRBSsim, for benchmarking analysis of RRBS data. We performed extensive comparison of seven mapping algorithms for methylation analysis in both real and simulated RRBS data. Eighteen lung tumors and matched adjacent tissues were sequenced by the RRBS protocols. Our empirical evaluation found that methylation results were less consistent between software tools for CpG sites with low sequencing depth, medium methylation level, on CGI shores or gene body. These observations were further confirmed by simulations that indicated software tools generally had lower recall of detecting these vulnerable CpG sites and lower precision of estimating methylation levels in these CpG sites. Among the software tools tested, bwa-meth and BS-Seeker2 (bowtie2) are currently our preferred aligners for RRBS data in terms of recall, precision and speed. Existing aligners cannot efficiently handle moderately methylated CpG sites and those CpG sites on CGI shores or gene body. Interpretation of methylation results from these vulnerable CpG sites should be treated with caution. Our study reveals several important features inherent in methylation data, and RRBSsim provides guidance to advance sequence-based methylation data analysis and methodological development. Availability and implementation: RRBSsim is a simulator for benchmarking analysis of RRBS data and its source code is available at https://github.com/xwBio/RRBSsim or https://github.com/xwBio/Docker-RRBSsim. Supplementary information: Supplementary data are available at Bioinformatics online.