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DNA methylation miRNA

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https://www.readbyqxmd.com/read/29440175/pan-cancer-molecular-classes-transcending-tumor-lineage-across-32-cancer-types-multiple-data-platforms-and-over-10-000-cases
#1
Chad J Creighton, Fengju Chen, Yiqun Zhang, Don L Gibbons, Benjamin Deneen, David Kwiatkowski, Michael Ittmann
PURPOSE: The Cancer Genome Atlas data resources represent an opportunity to explore commonalities across cancer types involving multiple molecular levels, but tumor lineage and histology can represent a barrier in moving beyond differences related to cancer type. EXPERIMENTAL DESIGN: On the basis of gene expression data, we classified 10224 cancers, representing 32 major types, into ten molecular-based "classes."  Molecular patterns representing tissue or histologic dominant effects were first removed computationally, with the resulting classes representing emergent themes across tumor lineages...
February 9, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29435941/the-mir-302-mediated-induction-of-pluripotent-stem-cells-ipsc-multiple-synergistic-reprogramming-mechanisms
#2
Shao-Yao Ying, William Fang, Shi-Lung Lin
Pluripotency represents a unique feature of embryonic stem cells (ESCs). To generate ESC-like-induced pluripotent stem cells (iPSCs) derived from somatic cells, the cell genome needs to be reset and reprogrammed to express the ESC-specific transcriptome. Numerous studies have shown that genomic DNA demethylation is required for epigenetic reprogramming of somatic cell nuclei to form iPSCs; yet, the mechanism remains largely unclear. In ESCs, the reprogramming process goes through two critical stages: germline and zygotic demethylation, both of which erase genomic DNA methylation sites and hence allow for different gene expression patterns to be reset into a pluripotent state...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29435111/impact-of-dlk1-dio3-imprinted-cluster-hypomethylation-in-smoker-patients-with-lung-cancer
#3
Sonia Molina-Pinelo, Ana Salinas, Nicolás Moreno-Mata, Irene Ferrer, Rocío Suarez, Eduardo Andrés-León, Manuel Rodríguez-Paredes, Julian Gutekunst, Eloisa Jantus-Lewintre, Carlos Camps, Amancio Carnero, Luis Paz-Ares
DNA methylation is important for gene expression and genome stability, and its disruption is thought to play a key role in the initiation and progression of cancer and other diseases. The DLK1-DIO3 cluster has been shown to be imprinted in humans, and some of its components are relevant to diverse pathological processes. The purpose of this study was to assess the methylation patterns of the DLK1-DIO3 cluster in patients with lung cancer to study its relevance in the pathogenesis of this disease. We found a characteristic methylation pattern of this cluster in smoking associated lung cancer, as compared to normal lung tissue...
January 12, 2018: Oncotarget
https://www.readbyqxmd.com/read/29434904/epigenetic-actions-of-environmental-factors-and-promising-drugs-for-cancer-therapy
#4
Zhong-Tian Bai, Bing Bai, Jun Zhu, Cui-Xia Di, Xun Li, Wen-Ce Zhou
Carcinogenesis is known to be primarily associated with gene mutations. Recently, increasing evidence has suggested that epigenetic events also serve crucial roles in tumor etiology. Environmental factors, including nutrition, toxicants and ethanol, are involved in carcinogenesis through inducing epigenetic modifications, such as DNA methylation, histone deacetylase and miRNA regulation. Studying epigenetic mechanisms has facilitated the development of early diagnostic strategies and potential therapeutic avenues...
February 2018: Oncology Letters
https://www.readbyqxmd.com/read/29402726/high-expression-of-tet1-predicts-poor-survival-in-cytogenetically-normal-acute-myeloid-leukemia-from-two-cohorts
#5
Jinghan Wang, Fenglin Li, Zhixin Ma, Mengxia Yu, Qi Guo, Jiansong Huang, Wenjuan Yu, Yungui Wang, Jie Jin
Ten-Eleven-Translocation 1 (TET1) plays a role in the DNA methylation process and gene activation. Recent reports suggest TET1 acts as an oncogene in leukemia development. However, the clinical relevance and biological insight of TET1 expression in cytogenetically normal acute myeloid leukemia (CN-AML) is unknown. In this study, quantification of TET1 transcript by real-time quantitative PCR in bone marrow blasts was performed in 360 CN-AML patients. As a result, high TET1 expression was more common in M0/M1 morphology and genes of NPM1 mutations, and underrepresented in CEBPA double allele mutations in our AML patients...
January 31, 2018: EBioMedicine
https://www.readbyqxmd.com/read/29385306/di-2-ethylhexyl-phthalate-dehp-influences-follicular-development-in-mice-between-the-weaning-period-and-maturity-by-interfering-with-ovarian-development-factors-and-micrornas
#6
Jin Liu, Wenxiang Wang, Jianlin Zhu, Yuchen Li, Lingfeng Luo, Yuanyuan Huang, Wenchang Zhang
Although studies have shown that di(2-ethylhexyl) phthalate (DEHP) can disrupt ovarian function, few reports have focused on follicular development in mice between the weaning period and maturity, especially with respect to microRNA (miRNA) expression. In this study, 21-day-old ICR mice were administered DEHP at doses of 0, 100, 400, and 1600 mg/(kg d) for 6 weeks by gavage. After DEHP administration, a significant decrease in the expression of follicle development-related factors (including c-kit, kitl, gdf9, and atm) was observed by quantitative real-time PCR (RT-PCR), but no significant difference in the proteins encoded by these genes was observed by Western blot...
January 31, 2018: Environmental Toxicology
https://www.readbyqxmd.com/read/29384211/the-importance-of-mirnas-and-epigenetics-in-acute-lymphoblastic-leukemia-prognosis
#7
REVIEW
Reza Ranjbar, Ansar Karimian, Masoud Aghai, Mehdi Tourani, Seyed Mostafa Mir, Javid Sabour, Farhad Jadidi, Bahman Yousefi
Acute lymphoblastic leukemia (ALL), one of the most common malignant human disorders, originates in different important genetic lesions in T-cell or B-cell progenitors. ALL is a malignant lymphoid progenitor with peak prevalence in children (2-5 years). The rate of survival when one is suffering from ALL depends on various agents including the age of the patient, responses to anti-leukemic therapy, and cell biology. miRNAs and epigenetics are important regulatory factors in the expression of genes. miRNAs are noncoding RNA with inhibitory effectors on specific mRNA...
January 31, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29382514/-epigenetic-alterations-in-acute-lymphoblastic-leukemia
#8
REVIEW
María Del Pilar Navarrete-Meneses, Patricia Pérez-Vera
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. It is well-known that genetic alterations constitute the basis for the etiology of ALL. However, genetic abnormalities are not enough for the complete development of the disease, and additional alterations such as epigenetic modifications are required. Such alterations, like DNA methylation, histone modifications, and noncoding RNA regulation have been identified in ALL. DNA hypermethylation in promoter regions is one of the most frequent epigenetic modifications observed in ALL...
July 2017: Boletín Médico del Hospital Infantil de México
https://www.readbyqxmd.com/read/29381081/epigenetic-mechanisms-in-the-placenta-related-to-infant-neurodevelopment
#9
Barry M Lester, Carmen J Marsit
As the 'third brain' the placenta links the developing fetal brain and the maternal brain enabling study of epigenetic process in placental genes that affect infant neurodevelopment. We described the characteristics and findings of the 17 studies on epigenetic processes in placental genes and human infant neurobehavior. Studies showed consistent findings in the same cohort of term healthy infants across epigenetic processes (DNA methylation, genome wide, gene and miRNA expression) genomic region (single and multiple genes, imprinted genes and miRNAs) using candidate gene and genome wide approaches and across biobehavioral systems (neurobehavior, cry acoustics and neuroendocrine)...
January 30, 2018: Epigenomics
https://www.readbyqxmd.com/read/29366539/epigenetic-mechanisms-in-coronary-artery-disease-the-current-state-and-prospects
#10
REVIEW
Lian Duan, Chao Liu, Junyuan Hu, Yongmei Liu, Jie Wang, Guang Chen, Zhaoling Li, Hengwen Chen
Coronary artery disease (CAD) is the leading cause of morbidity and mortality. CAD has both genetic and environmental causes. In the past two decades, the understanding of epigenetics has advanced swiftly and vigorously. It has been demonstrated that epigenetic modifications are associated with the onset and progression of CAD. This review aims to improve the understanding of the epigenetic mechanisms closely related to CAD and to provide a novel perspective on the onset and development of CAD. Epigenetic changes include DNA methylation, histone modification, microRNA and lncRNA, which are interrelated with critical genes and influence the expression of those genes...
December 30, 2017: Trends in Cardiovascular Medicine
https://www.readbyqxmd.com/read/29343074/understanding-the-influence-of-antipsychotic-drugs-on-global-methylation-events-and-its-relevance-in-treatment-response
#11
Babu Swathy, Koramannil R Saradalekshmi, Indu V Nair, Chandrasekharan Nair, Moinak Banerjee
AIM: The present study intends to evaluate whether antipsychotic drugs can modulate the host epigenome and if so whether drug-induced epigenetic modulation can explain the heterogeneity in drug response. METHODS: Present study was conducted in in vitro cells and significance of these in vitro observations was further evaluated in a clinical setting, between drug responsive and nonresponsive schizophrenia patients. A number of DNA modifications were assessed at global level using 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine followed by evaluating the expression of epigenetic modifier genes and their crosstalk with miRNAs...
January 18, 2018: Epigenomics
https://www.readbyqxmd.com/read/29330288/epigenetically-regulated-chromosome-14q32-mirna-cluster-induces-metastasis-and-predicts-poor-prognosis-in-lung-adenocarcinoma-patients
#12
Margarita Gonzalez-Vallinas, Manuel Rodriguez-Paredes, Marco Albrecht, Carsten Sticht, Damian Stichel, Julian Gutekunst, Adriana Pitea, Steffen Sass, Francisco J Sánchez-Rivera, Justo L Bermejo, Jennifer Schmitt, Carolina De La Torre, Arne Warth, Fabian Theis, Nikola Mueller, Norbert Gretz, Thomas Muley, Michael Meister, Darjus F Tschaharganeh, Peter Schirmacher, Franziska Matthäus, Kai Breuhahn
Most lung cancer deaths are related to metastases, which indicates the necessity of detecting and inhibiting tumor cell dissemination. Here, we aimed to identify microRNAs (miRNAs) involved in metastasis of lung adenocarcinoma as prognostic biomarkers and therapeutic targets. To that end, lymph node metastasis-associated miRNAs were identified in The Cancer Genome Atlas (TCGA) lung adenocarcinoma patient cohort (sequencing data; n=449) and subsequently validated by RT-qPCR in an independent clinical cohort (n=108)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330124/manipulating-the-epigenome-for-the-treatment-of-disorders-with-thrombotic-complications
#13
REVIEW
Faith A A Kwa, Denise E Jackson
The haemostatic system is tightly regulated to maintain homeostasis to avoid unwanted bleeding or thrombotic complications. Recent research has highlighted the importance of epigenetic changes, such as DNA methylation, histone modifications, and miRNA-based mechanisms, that alter gene expression. This can give rise to dysregulated haemostatic or vascular expressed molecules contributing to the development of thrombotic complications. Targeting these epigenetic changes could provide a new avenue for the treatment of pathological blood clots...
January 9, 2018: Drug Discovery Today
https://www.readbyqxmd.com/read/29324665/genome-wide-methylation-patterns-in-androgen-independent-prostate-cancer-cells-a-comprehensive-analysis-combining-medip-bisulfite-rna-and-microrna-sequencing-data
#14
Yumin Wang, Tingting Qin, Wangqiang Hu, Binghua Chen, Meijie Dai, Gang Xu
This study aimed to investigate the mechanisms underlying the development of the androgen-independent phenotype in prostate cancer. Methylation patterns were detected in androgen-independent and androgen-dependent lymph node carcinoma of the prostate (LNCaP) prostate carcinoma cells based on methylated DNA immunoprecipitation-bisulfite sequencing data and differentially methylated regions (DMRs) were identified. Differentially expressed genes (DEGs) and micro RNAs (miRNAs) with DMRs (named MDEGs and MDEmiRNAs) were identified by combining transcriptome and methylation data, and transcription factor (TF)-DEGs with DMRs in promoter (PMDEGs) and MDEmiRNA-MDEGs networks were constructed...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29322932/identification-of-prognostic-signature-in-cancer-based-on-dna-methylation-interaction-network
#15
Wei-Lin Hu, Xiong-Hui Zhou
BACKGROUND: The identification of prognostic biomarkers for cancer patients is essential for cancer research. These days, DNA methylation has been proved to be associated with cancer prognosis. However, there are few methods which identify the prognostic markers based on DNA methylation data systematically, especially considering the interaction among DNA methylation sites. METHODS: In this paper, we first evaluated the stabilities of microRNA, mRNA, and DNA methylation data in prognosis of cancer...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29322925/subtype-identification-from-heterogeneous-tcga-datasets-on-a-genomic-scale-by-multi-view-clustering-with-enhanced-consensus
#16
Menglan Cai, Limin Li
BACKGROUND: The Cancer Genome Atlas (TCGA) has collected transcriptome, genome and epigenome information for over 20 cancers from thousands of patients. The availability of these diverse data types makes it necessary to combine these data to capture the heterogeneity of biological processes and phenotypes and further identify homogeneous subtypes for cancers such as breast cancer. Many multi-view clustering approaches are proposed to discover clusters across different data types. The problem is challenging when different data types show poor agreement of clustering structure...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29322795/analysis-of-dna-methylation-and-microrna-expression-in-nut-nuclear-protein-in-testis-midline-carcinoma-of-the-sinonasal-tract-a-clinicopathological-immunohistochemical-and-molecular-genetic-study
#17
J Laco, H Kovarikova, M Chmelarova, H Vosmikova, K Sieglova, I Bubancova, P Dundr, K Nemejcova, J Michalek, P Celakovsky, R Mottl, I Sirak, M Vosmik, I Marek, T Geryk, J Mejzlik, J Satankova, A Ryska
The aim of this study was a detailed clinicopathological investigation of sinonasal NUT midline carcinoma (NMC), including analysis of DNA methylation and microRNA (miRNA) expression. Three (5%) cases of NMC were detected among 56 sinonasal carcinomas using immunohistochemical screening and confirmed by fluorescence in situ hybridization. The series comprised 2 males and 1 female, aged 46, 60, and 65 years. Two tumors arose in the nasal cavity and one in the maxillary sinus. The neoplasms were staged pT1, pT3, and pT4a (all cN0M0)...
2018: Neoplasma
https://www.readbyqxmd.com/read/29290818/methylation-associated-silencing-of-mir-193a-3p-promotes-ovarian-cancer-aggressiveness-by-targeting-grb7-and-mapk-erk-pathways
#18
Kangmei Chen, Michelle Xin Liu, Celia Sze-Ling Mak, Mingo Ming-Ho Yung, Thomas Ho-Yin Leung, Dakang Xu, Siew-Fei Ngu, Karen Kar-Loen Chan, Huijuan Yang, Hextan Yuen-Sheung Ngan, David Wai Chan
Human growth factor receptor-bound protein-7 (GRB7) is a pivotal mediator involved in receptor tyrosine kinase signaling and governing diverse cellular processes. Aberrant upregulation of GRB7 is frequently associated with the progression of human cancers. However, the molecular mechanisms leading to the upregulation of GRB7 remain largely unknown. Here, we propose that the epigenetic modification of GRB7 at the post-transcriptional level may be a crucial factor leading to GRB7 upregulation in ovarian cancers...
2018: Theranostics
https://www.readbyqxmd.com/read/29285183/targeting-microrna-uhrf1-pathways-as-a-novel-strategy-for-cancer-therapy
#19
Hani Choudhry, Mazin A Zamzami, Ziad Omran, Wei Wu, Marc Mousli, Christian Bronner, Mahmoud Alhosin
Ubiquitin-like containing plant homeodomain and RING finger domains 1 (UHRF1) is an anti-apoptotic protein involved in the silencing of several tumor suppressor genes (TSGs) through epigenetic modifications including DNA methylation and histone post-translational alterations, and also epigenetic-independent mechanisms. UHRF1 overexpression is observed in a number of solid tumors and hematological malignancies, and is considered a primary mechanism in inhibiting apoptosis. UHRF1 exerts its inhibitory activity on TSGs by binding to functional domains and therefore influences several epigenetic actors including DNA methyltransferase, histone deacetylase 1, histone acetyltransferase Tat-interacting protein 60 and histone methyltransferases G9a and Suv39H1...
January 2018: Oncology Letters
https://www.readbyqxmd.com/read/29279257/epigenetic-changes-in-headache
#20
M S Cámara, M Martín Bujanda, M Mendioroz Iriarte
INTRODUCTION: Multiple factors, including both genetic and environmental mechanisms, appear to play a role in the aetiology of headache. An interesting area of study is the possible involvement of epigenetic mechanisms in headache development and the transformation to chronic headache, and the potential role of these factors as a therapeutic target. METHODS: We performed a literature review of the involvement of different epigenetic mechanisms in headache, mainly using the Medline/PubMed database...
December 23, 2017: Neurología: Publicación Oficial de la Sociedad Española de Neurología
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