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https://www.readbyqxmd.com/read/29351612/a-mutational-signature-associated-with-alcohol-consumption-and-prognostically-significantly-mutated-driver-genes-in-esophageal-squamous-cell-carcinoma
#1
X C Li, M Y Wang, M Yang, H J Dai, B F Zhang, W Wang, X L Chu, X Wang, H Zheng, R F Niu, W Zhang, K X Chen
Background: Esophageal squamous cell carcinoma (ESCC) is often diagnosed at an advanced and incurable stage. Information on driver genes and prognosticators in ESCC remains incomplete. The objective was to elucidate significantly mutated genes (SMGs), mutational signatures, and prognosticators in ESCC. Patients and Methods: Three MutSig algorithms (i.e. MutSigCV, MutSigCL and MutSigFN) and "20/20+" ratio-metric were employed to identify SMGs. Nonnegative matrix factorization was used to decipher mutational signatures...
January 16, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29351579/lack-of-methyl-cpg-binding-protein-2-mecp2-affects-cell-fate-refinement-during-embryonic-cortical-development
#2
Clementina Cobolli Gigli, Linda Scaramuzza, Marco De Simone, Riccardo L Rossi, Davide Pozzi, Massimiliano Pagani, Nicoletta Landsberger, Francesco Bedogni
During differentiation, neurons progressively restrict their fate repressing the expression of specific genes. Here we describe the involvement in such developmental steps of the methyl-CpG binding protein 2 (MeCP2), an epigenetic factor that participates to chromatin folding and transcriptional regulation. We previously reported that, due to transcriptional impairments, the maturation of Mecp2 null neurons is delayed. To evaluate whether this could stem from altered progenitors proliferation and differentiation, we investigated whether lack of Mecp2 affects these features both in vitro and in vivo...
January 17, 2018: Cerebral Cortex
https://www.readbyqxmd.com/read/29350455/a-novel-prognostic-six-cpg-signature-in-glioblastomas
#3
An-An Yin, Nan Lu, Amandine Etcheverry, Marc Aubry, Jill Barnholtz-Sloan, Lu-Hua Zhang, Jean Mosser, Wei Zhang, Xiang Zhang, Yu-He Liu, Ya-Long He
AIMS: We aimed to identify a clinically useful biomarker using DNA methylation-based information to optimize individual treatment of patients with glioblastoma (GBM). METHODS: A six-CpG panel was identified by incorporating genome-wide DNA methylation data and clinical information of three distinct discovery sets and was combined using a risk-score model. Different validation sets of GBMs and lower-grade gliomas and different statistical methods were implemented for prognostic evaluation...
January 19, 2018: CNS Neuroscience & Therapeutics
https://www.readbyqxmd.com/read/29347875/universal-informative-cpg-sites-for-inferring-tumor-purity-from-dna-methylation-microarray-data
#4
Haixia Dou, Yun Fang, Xiaoqi Zheng
Tumor purity is an intrinsic property of tumor samples and potentially has severe impact on many types of data analysis. We have previously developed a statistical method, InfiniumPurify, which could infer purity of a tumor sample given its tumor type (available in TCGA) or a set of informative CpG (iDMC) sites. However, in many clinical practices, researchers may focus on a specific type of tumor samples that is not included in TCGA, and samples which are too few to identify reliable iDMCs. This greatly restricts the application of InfiniumPurify in cancer research...
December 28, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29345614/output-variability-across-animals-and-levels-in-a-motor-system
#5
Angela Wenning, Brian J Norris, Cengiz Günay, Daniel Kueh, Ronald L Calabrese
Rhythmic behaviors vary across individuals. We investigated the sources of this output variability across a motor system, from the central pattern generator (CPG) to the motor plant. In the bilaterally symmetric leech heartbeat system, the CPG orchestrates two coordinations in the bilateral hearts with different intersegmental phase relations (Δϕ) and periodic side-to-side switches. Population variability is large. We show that the system is precise within a coordination, that differences in repetitions of a coordination contribute little to population output variability, but that differences between bilaterally homologous cells may contribute to some of this variability...
January 18, 2018: ELife
https://www.readbyqxmd.com/read/29345269/tributyltin-induces-epigenetic-changes-and-decreases-the-expression-of-nuclear-respiratory-factor-1
#6
Saki Hanaoka, Keishi Ishida, Saki Tanaka, Shuichiro Sakamoto, Katsuhiro Okuda, Seigo Sanoh, Shigeru Ohta, Yaichiro Kotake
Tributyltin (TBT), a common organotin environmental pollutant, has been widely used as a component of marine antifouling paints. We previously reported that exposure to TBT inhibits the expression and DNA binding of nuclear respiratory factor-1 (NRF-1) and causes neurotoxicity. In the present study, we focused on the epigenetic effects of TBT and investigated whether TBT decreases NRF-1 expression via epigenetic modifications in SH-SY5Y human neuroblastoma cells. First, we found that exposure to 300 nM TBT decreases NRF-1 expression...
January 18, 2018: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/29344347/epigenetic-alterations-in-tramp-mice-epigenome-dna-methylation-profiling-using-medip-seq
#7
Wenji Li, Ying Huang, Davit Sargsyan, Tin Oo Khor, Yue Guo, Limin Shu, Anne Yuqing Yang, Chengyue Zhang, Ximena Paredes-Gonzalez, Michael Verzi, Ronald P Hart, Ah-Ng Kong
Purpose: We investigated the genomic DNA methylation profile of prostate cancer in transgenic adenocarcinoma of the mouse prostate (TRAMP) cancer model and to analyze the crosstalk among targeted genes and the related functional pathways. Methods: Prostate DNA samples from 24-week-old TRAMP and C57BL/6 male mice were isolated. The DNA methylation profiles were analyzed by methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing (MeDIP-seq)...
2018: Cell & Bioscience
https://www.readbyqxmd.com/read/29344312/an-endogenous-vaccine-based-on-fluorophores-and-multivalent-immunoadjuvants-regulates-tumor-micro-environment-for-synergistic-photothermal-and-immunotherapy
#8
Ling Li, Suleixin Yang, Linjiang Song, Yan Zeng, Tao He, Ning Wang, Chuan Yu, Tao Yin, Li Liu, Xiawei Wei, Qinjie Wu, Yuquan Wei, Li Yang, Changyang Gong
Recently, near-infrared (NIR) light-based photothermal therapy (PTT) has been widely applied in cancer treatment. However, in most cases, the tissue penetration depth of NIR light is not sufficient and thus photothermal therapy is unable to completely eradicate deep, seated tumors inevitably leading to recurrence of the tumor. Due to this significant limitation of NIR, improved therapeutic strategies are urgently needed. Methods: We developed an endogenous vaccine based on a novel nanoparticle platform for combinatorial photothermal ablation and immunotherapy...
2018: Theranostics
https://www.readbyqxmd.com/read/29344148/identification-of-potentially-critical-differentially-methylated-genes-in-nasopharyngeal-carcinoma-a-comprehensive-analysis-of-methylation-profiling-and-gene-expression-profiling
#9
Lian Hui, Jingru Zhang, Xiaoxu Ding, Xing Guo, Xuejun Jang
The present study aimed to identify potentially critical differentially methylated genes associated with the progression of nasopharyngeal carcinoma (NPC). Methylation profiling data of GSE62336 deposited in the Gene Expression Omnibus database were used to identify differentially methylated regions (DMRs) and differentially methylated CpG islands (DMIs). Concurrently, differentially expressed genes (DEGs) were identified using a meta-analysis of three gene expression datasets (GSE53819, GSE13597 and GSE12452)...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29343995/humanmethylation450k-array-identified-biomarkers-predict-tumour-recurrence-progression-at-initial-diagnosis-of-high-risk-non-muscle-invasive-bladder-cancer
#10
Mark O Kitchen, Richard T Bryan, Richard D Emes, Christopher J Luscombe, K K Cheng, Maurice P Zeegers, Nicholas D James, Lyndon M Gommersall, Anthony A Fryer
Background: High-risk non-muscle invasive bladder cancer (HR-NMIBC) is a clinically unpredictable disease. Despite clinical risk estimation tools, many patients are undertreated with intra-vesical therapies alone, whereas others may be over-treated with early radical surgery. Molecular biomarkers, particularly DNA methylation, have been reported as predictive of tumour/patient outcomes in numerous solid organ and haematologic malignancies; however, there are few reports in HR-NMIBC and none using genome-wide array assessment...
2018: Biomarkers in Cancer
https://www.readbyqxmd.com/read/29342962/functional-analyses-of-runx3-and-camkiin%C3%AE-in-ovarian-cancer-cell-lines-reveal-tumor-suppressive-functions-for-camkiin%C3%AE-and-dichotomous-roles-for-runx3-transcript-variants
#11
Karolin Heinze, Daniel Kritsch, Alexander S Mosig, Matthias Dürst, Norman Häfner, Ingo B Runnebaum
(1) Background: Epithelial ovarian cancer (EOC) is the most lethal cancer of the female reproductive system. In an earlier study, we identified multiple genes as hypermethylated in tumors of patients with poor prognosis. The most promising combination of markers to predict a patient's outcome was CaMKIINα and RUNX3. Aim of this study was to functionally validate the importance of both genes. (2) Methods: IC50 measurements, cell cycle distribution-, proliferation, and migration experiments were conducted after transgene overexpression in two EOC cell lines...
January 15, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29342954/a-built-in-cpg-adjuvant-in-rsv-f-protein-dna-vaccine-drives-a-th1-polarized-and-enhanced-protective-immune-response
#12
Yao Ma, Yue-Ying Jiao, Yun-Zhou Yu, Nan Jiang, Ying Hua, Xiu-Juan Zhang, Yuan-Hui Fu, Xiang-Lei Peng, Yan-Peng Zheng, Larry J Anderson, Jin-Sheng He
Human respiratory syncytial virus (RSV) is the most significant cause of acute lower respiratory infection in children. However, there is no licensed vaccine available. Here, we investigated the effect of five or 20 copies of C-Class of CpG ODN (CpG-C) motif incorporated into a plasmid DNA vaccine encoding RSV fusion (F) glycoprotein on the vaccine-induced immune response. The addition of CpG-C motif enhanced serum binding and virus-neutralizing antibody responses in BALB/c mice immunized with the DNA vaccines...
January 15, 2018: Viruses
https://www.readbyqxmd.com/read/29342280/epigenetic-differentiation-of-natural-populations-of-lilium-bosniacum-associated-with-contrasting-habitat-conditions
#13
V Zoldoš, I Biruš, E Muratovic, Z Šatovic, A Vojta, O Robin, F Pustahija, F Bogunic, V Vicic Bockor, S Siljak-Yakovlev
Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats. One population was growing under habitual ecological conditions for this species and the other two were growing under stress associated with high altitude and serpentine soil. Amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analyses revealed that the three populations did not differentiate genetically, but were clearly separated in the three distinct clusters according to DNA methylation profiles...
January 12, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29342273/hypermethylation-of-eif4e-promoter-is-associated-with-early-onset-of-gastric-cancer
#14
Yuqiu Ge, Qin Wu, Gaoxiang Ma, Wei Shao, Hanting Liu, Qiang Zhang, Junyi Xin, Yao Xue, Mulong Du, Qinghong Zhao, Meilin Wang, Haiyan Chu, Zhengdong Zhang
Although gastric cancer (GC) in young adults (≤ 45 years) accounts for fewer than 10% of newly diagnosed cases, the young patients are more likely to have advanced disease at presentation compared with elderly patients. Previous studies have identified that the DNA methylation of genomes are different during aging. Our study aimed to explore the association between DNA methylation and the onset of GC. We applied Illumina HumanMethylation450 BeadChip to examine methylation expression profiles and compared methylation expression patterns in five early onset GC patients and seven elderly patients...
January 12, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/29341861/genome-wide-survey-reveals-dynamic-effects-of-folate-supplement-on-dna-methylation-and-gene-expression-during-c2c12-differentiation
#15
Yi Li, Qiang Feng, Miao Guo, Yuding Wang, Yunliang Jiang, Jinyi Xing
Folic acid supplements during pregnancy can prevent neural tube defects and other developmental abnormalities. Here, we explored the effects of folate supplement on gene expression and DNA methylation during C2C12 differentiation. Based on the folic acid concentration, this study comprised three groups: low folate (L), normal folate (N), and high-folate supplement (H). Our analyses revealed that differentiation and the mRNA expression of myogenin in C2C12 cell were enhanced by folic acid, however, the overall methylation percentage in myogenin promoter between different treatment groups was not significantly different (P>0...
January 12, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29341476/a-rare-male-patient-with-classic-rett-syndrome-caused-by-mecp2_e1-mutation
#16
Narumi Tokaji, Hiromichi Ito, Tomohiro Kohmoto, Takuya Naruto, Rizu Takahashi, Aya Goji, Tatsuo Mori, Yoshihiro Toda, Masako Saito, Shoichiro Tange, Kiyoshi Masuda, Shoji Kagami, Issei Imoto
Rett syndrome (RTT) is a severe neurodevelopmental disorder typically affecting females. It is mainly caused by loss-of-function mutations that affect the coding sequence of exon 3 or 4 of methyl-CpG-binding protein 2 (MECP2). Severe neonatal encephalopathy resulting in death before the age of 2 years is the most common phenotype observed in males affected by a pathogenic MECP2 variant. Mutations in MECP2 exon 1 affecting the MeCP2_e1 isoform are relatively rare causes of RTT in females, and only one case of a male patient with MECP2-related severe neonatal encephalopathy caused by a mutation in MECP2 exon 1 has been reported...
January 17, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29341152/meta-analysis-of-the-prognostic-value-of-cpg-island-methylator-phenotype-in-gastric-cancer
#17
REVIEW
A G M T Powell, S Soul, A Christian, W G Lewis
BACKGROUND: CpG island methylator phenotype (CIMP) has been identified as a distinct molecular subtype of gastric cancer, yet associations with survival are conflicting. A meta-analysis was performed to estimate the prognostic significance of CIMP. METHODS: Embase, MEDLINE, PubMed, PubMed Central and Cochrane databases were searched systematically for studies related to the association between CIMP and survival in patients undergoing potentially curative resection for gastric cancer...
January 2018: British Journal of Surgery
https://www.readbyqxmd.com/read/29340450/therapeutic-drug-monitoring-of-benznidazole-and-nifurtimox-a-systematic-review-and-quality-assessment-of-published-clinical-practice-guidelines
#18
Mario Javier Olivera, Johana Alexandra Fory, Antonio José Olivera
The pharmacological management of adults with chronic-phase Chagas disease is challenging despite it being the recent focus of extensive research. One of the challenges in the current clinical practice guidelines (CPGs) landscape is the existence of non-evidence-based recommendations for the use of laboratory tests in treatment monitoring. This study aimed to systematically assess the quality and consistency of recommendations of CPGs on the pharmacological management of adults with chronic-phase Chagas disease...
November 2017: Revista da Sociedade Brasileira de Medicina Tropical
https://www.readbyqxmd.com/read/29340066/clinicopathological-and-prognostic-significance-of-sdc1-overexpression-in-breast-cancer
#19
Xiangrong Cui, Xuan Jing, Qin Yi, Chunlan Long, Jie Tian, Jing Zhu
Background: Breast cancer is the leading cause of cancer death among global women, and its early diagnosis and treatment are very urgent. Syndecan-1 (SDC1) is a heparin sulfate proteoglycan, which has been linked with the prognosis and treatment response in a various tumor type. To investigate whether SDC1 can serve as a prognostic indictor in breast cancer, bioinformatic analyses were performed in the present study. Methods: SDC1 expression was assessed using Oncomine analysis...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339976/detection-of-dioxin-induced-demethylation-of-mouse-cyp1a1-gene-promoter-by-a-new-labeling-method-for-short-dna-fragments-possessing-5-methylcytosine-at-the-end
#20
Hisaka Kurita, Toshiki Aiba, Toshiyuki Saito, Seiichiroh Ohsako
Environmental factors stimulate alteration of DNA methylation level. Investigation of the genome-wide DNA methylation status is important for environmental health studies. We here designed a genomic DNA amplification and labeling protocol using a methylation-sensitive restriction enzyme HinP1 I. This method can specifically amplify genomic DNA fragments possessing methyl-CpG at the end. The fragments are a relatively short size and dominantly located on CpG-islands. By using the samples prepared by this method, a dioxin-induced change in the methylation level of the mouse Cyp1a1 promoter was successfully evaluated using oligonucleotide probes covalently bound onto a glass plate...
2018: Genes and Environment: the Official Journal of the Japanese Environmental Mutagen Society
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