DNA methylation data for identification of epigenetic targets of resveratrol in triple negative breast cancer cells.
ABSTRACT: Previous studies revealed that some bioactive food components have anti-cancer effects. However epigenetic effects of dietary compound resveratrol are largely unknown in breast cancer cells (M.A. Dawson, T. Kouzarides, 2012) . Here we provide novel data and comparisons of DNA methylation status of promoter gene regions in response to resveratrol treatment at 24 h and 48 h versus untreated MDA-MB-231 breast cancer cells. DNA methylation changes were measured using Array-PRIMES method (aPRIMES) followed by whole-genome hybridization using human DNA methylation promoter microarray NimbleGen HG18 Refseq Promoter 3×720 K array. Our data were associated to corresponding changes in mRNA expression in a set of cancer-related genes. Using gene ontology analysis we also identify cancer-related cellular processes and pathways that can be epigenetically reprogramed by resveratrol. Data in this article are associated to the research articles "Methylation Landscape of Human Breast Cancer Cells in Response to Dietary Compound Resveratrol". Medina Aguilar et al., PLoS ONE 11(6): e0157866. doi:10.1371/journal.pone.0157866 2016 (A.R. Medina, P.C. Pérez, L.A. Marchat, P. Gariglio, M.J. García, C.S. Rodríguez, G.E. Ruíz, et al., 2016) ; and "Resveratrol inhibits cell cycle progression by targeting Aurora kinase A and Polo-like kinase 1 in breast cancer cells" in Oncology Reports. Medina Aguilar et al., 2016 Jun; 35(6):3696-704. doi: 10.3892/or.2016.4728 (A.R. Medina, P. Gariglio, M.J. García, O.E. Arechaga, S.N. Villegas, C.M. Martínez et al., 2016) .
Project description:DNA synthesis and homologous recombination can be used to simplify molecular cloning and to make synthetic biology easily accessible (M.J. Czar et al., 2009). However, the design of overlapping DNA fragments to construct large molecules is time-consuming and requires verification of several parameters to ensure that fragment synthesis is attainable, given the restrictions found in chemical synthesis of DNA. OVERFRAG is a web-based tool that generates overlapping DNA fragments to assemble either in yeast cells by Gap Repair (H. Ma et al., 1987) or in vitro by (D.G. Gibson et al., 2009) and In-Fusion (B. Zhu et al., 2007) methods. The fragments generated are suitable for chemical synthesis and molecular assembly. Some possible uses include cDNA cloning, design of chimeric antibodies and synthetic biology applications. Web tool is freely available at http://www.each.usp.br/digiampietri/overfrag.
Project description:Progenitor cells in the medial ganglionic eminence (MGE) and preoptic area (PoA) give rise to GABAergic inhibitory interneurons that are distributed in the forebrain, largely in the cortex, hippocampus, and striatum. Two previous studies suggest that clonally related interneurons originating from individual MGE/PoA progenitors frequently form local clusters in the cortex. However, Mayer et al. and Harwell et al. recently argued that MGE/PoA-derived interneuron clones disperse widely and populate different forebrain structures. Here, we report further analysis of the spatial distribution of clonally related interneurons and demonstrate that interneuron clones do not non-specifically disperse in the forebrain. Around 70% of clones are restricted to one brain structure, predominantly the cortex. Moreover, the regional distribution of clonally related interneurons exhibits a clear clustering feature, which cannot occur by chance from a random diffusion. These results confirm that lineage relationship influences the spatial distribution of inhibitory interneurons in the forebrain. This Matters Arising paper is in response to Harwell et al. (2015) and Mayer et al. (2015), published in Neuron. See also the response by Turrero García et al. (2016) and Mayer et al. (2016), published in this issue.
Project description:The quantitative proteomics data reported here pertain to the research article entitled "A Tandem Mass Tag (TMT) proteomic analysis during the early phase of experimental pancreatitis reveals new insights in the disease pathogenesis" (García-Hernández et al., 2018) . The development of acute pancreatitis (AP, an important pathological inflammatory state of the exocrine pancreas) would be based on early changes in protein expression and signaling pathways whose unmasking would be crucial for deciphering AP at the molecular level. We reported here a Tandem Mass Tag (TMT)-based proteomics analysis of rat subcellular fractions of the pancreas during the early phase of experimental AP, using a sixplex isobaric chemical labeling technique. We identified 997 unique proteins, of which 353 were significantly different (22, 276 or 55 in both, the soluble or the membrane fractions, respectively). Accordingly, using TMT proteomics and bioinformatic tools, in García-Hernández et al., 2018-  we were able to detect significant changes in protein expression related to many pathobiological pathways of AP as from the early phase of the disease, including some changes never described before in this disease. Proteomics data are publicly available in ProteomeXchange via PRIDE through the identifier PXD007096.
Project description:The capitellid polychaete genus Dodecaseta McCammon & Stull, 1978 is relocated in Notodasus Fauchald, 1972. Two species are redescribed based on examination of type material and three new combinations are proposed: Notodasus oraria (McCammon & Stull, 1978), N. eibyejacobseni (Green, 2002). N. fauchaldi (Green, 2002). N. kristiani (García-Garza et al., 2009), is synonymized under N. oraria. Some comments on Dasybranchus lumbricoides Grube, 1878 are included.
Project description:Two sister species of Loneura, from Valle del Cauca, Colombia, are here described and illustrated. They constitute a new species group that modifies the scheme of classification, proposed earlier for the genus by García Aldrete et al. (2011b). The new group is characterized by having the central sclerite of the male hypandrium with four posterior projections. A key to the males of Group II is included. The types are deposited in the Entomological Museum of the Universidad del Valle. Colombia may prove to be the most species rich area for Loneura.
Project description:The original version of this article (Bartolo-Aguilar et al. 2017) was written and published including the first construction strategy of pLGC09, but not the final one. This error was pointed out by a reader and an analysis of sequences of parts of the plasmid corroborated this. The final construction strategy was reanalysed and confirmed the error. This error affected the text, Table 2, Fig. 1 and Additional files, but did not affect the results and conclusions stated in the paper. The authors regret that this error occurred in the original publication of the article. The corrected text, Table 2 and Fig. 1, and Additional files (Additional file 1. Construction strategy of pLGC09 and Additional file 2. Plasmid pLGC09) are given in this correction.
Project description:The data presented in this article describe the physical state of the triamcinolone acetonide (TA) in nanosuspension stabilized with polyvinyl alcohol (PVA) and poloxamer 407 (PL). The data were assessed by X-ray spectroscopy, ATR Fourier transforms infrared spectroscopy measurements (FTIR), and Differential scanning calorimetry (DSC) analysis. PVA, PL and polymeric mixture (PVA and PL) were compared with nanosuspension and the interactions between drug triamcinolone acetonide and polymers were studied. The data are related and are complementary to the research article entitle "Improved release of triamcinolone acetonide from medicated soft contact lenses loaded with drug nanosuspensions" (García-Millán et al., 2017) .
Project description:In this data article we provide different field parameters of an agricultural irrigated system under Mediterranean conditions. These parameters represent the response of variables related to soil functionality to different cover crops. Soil and plant samples were taken from fallow and cover crops treatments over the course of 10 years, with most variables measured every other year. This ample database provides reliable information to design sustainable agricultural practices under Mediterranean conditions. Researchers, policy makers and farmers are interested in the final outcome of this dataset. The data are associated with the research article entitled "Cover crops to mitigate soil degradation and enhance soil functionality in irrigated land" (García-González et al., 2018) .
Project description:Aberrant DNA methylation is a frequent epigenetic alteration in cancer cells that has emerged as a pivotal mechanism for tumorigenesis. Accordingly, novel therapies targeting the epigenome are being explored with the aim to restore normal DNA methylation patterns on oncogenes and tumor suppressor genes. A limited number of studies indicate that dietary compound resveratrol modulates DNA methylation of several cancer-related genes; however a complete view of changes in methylome by resveratrol has not been reported yet. In this study we performed a genome-wide survey of DNA methylation signatures in triple negative breast cancer cells exposed to resveratrol. Our data showed that resveratrol treatment for 24 h and 48 h decreased gene promoter hypermethylation and increased DNA hypomethylation. Of 2476 hypermethylated genes in control cells, 1,459 and 1,547 were differentially hypomethylated after 24 h and 48 h, respectively. Remarkably, resveratrol did not induce widespread non-specific DNA hyper- or hypomethylation as changes in methylation were found in only 12.5% of 27,728 CpG loci. Moreover, resveratrol restores the hypomethylated and hypermethylated status of key tumor suppressor genes and oncogenes, respectively. Importantly, the integrative analysis of methylome and transcriptome profiles in response to resveratrol showed that methylation alterations were concordant with changes in mRNA expression. Our findings reveal for the first time the impact of resveratrol on the methylome of breast cancer cells and identify novel potential targets for epigenetic therapy. We propose that resveratrol may be considered as a dietary epidrug as it may exert its anti-tumor activities by modifying the methylation status of cancer -related genes which deserves further in vivo characterization.
Project description:Background: Cellular retinoic acid binding protein 2 (CRABP2) mediates retinoic acid/RA anti-cancer pathways. Resveratrol effectively reverses RA tolerance and upregulates CRABP2 expression of anaplastic thyroid cancer cell line THJ-11T. As DNA methylation is responsible for CRABP2 silencing, the CRABP2 methylation status of THJ-11T cells and the demethylating effect of resveratrol on this gene are elucidated. Materials and methods: The statuses of CRABP2 expression and methylation and the levels of DNA methyltransferases (DNMTs) DNMT1, DNMT3A, and DNMT3B of THJ-11T cells were examined before and after resveratrol treatment via multiple experimental methods. The human medulloblastoma UW228-2 cell line was cited as the control of CRABP2 methylation and gemcitabine as the demethylator control. Results: RT-PCR, immunocytochemical staining and Western blotting showed that resveratrol significantly increased the CRABP2 expression and RA sensitivity of THJ-11T and UW228-2 cells. Bisulfite sequencing showed five CpG methylation sites at the CRABP2 promoter region of both cell lines, which were partially (3/5) demethylated by resveratrol and totally (5/5) by gemcitabine. DNMT1, DNMT3A, and DNMT3B were reduced in UW228-2 cells and DNMT1 and DNMT3A were reduced in THJ-11T cells after resveratrol treatment in a time-related fashion. Conclusion: Resveratrol is able to erase CRABP2 methylation and can thereby increase the RA sensitivity of THJ-11T and UW228-2 cells. This study demonstrates the additional value of the natural polyphenolic compound resveratrol as a demethylator in cancer treatments.