21 research outputs found
Azacytidine and Decitabine Induce Gene-Specific and Non-Random DNA Demethylation in Human Cancer Cell Lines
The DNA methyltransferase inhibitors azacytidine and decitabine represent archetypal drugs for epigenetic cancer therapy. To characterize the demethylating activity of azacytidine and decitabine we treated colon cancer and leukemic cells with both drugs and used array-based DNA methylation analysis of more than 14,000 gene promoters. Additionally, drug-induced demethylation was compared to methylation patterns of isogenic colon cancer cells lacking both DNA methyltransferase 1 (DNMT1) and DNMT3B. We show that drug-induced demethylation patterns are highly specific, non-random and reproducible, indicating targeted remethylation of specific loci after replication. Correspondingly, we found that CG dinucleotides within CG islands became preferentially remethylated, indicating a role for DNA sequence context. We also identified a subset of genes that were never demethylated by drug treatment, either in colon cancer or in leukemic cell lines. These demethylation-resistant genes were enriched for Polycomb Repressive Complex 2 components in embryonic stem cells and for transcription factor binding motifs not present in demethylated genes. Our results provide detailed insights into the DNA methylation patterns induced by azacytidine and decitabine and suggest the involvement of complex regulatory mechanisms in drug-induced DNA demethylation
Antiproliferative Effects of DNA Methyltransferase 3B Depletion Are Not Associated with DNA Demethylation
Silencing of genes by hypermethylation contributes to cancer progression and has been shown to occur with increased frequency at specific genomic loci. However, the precise mechanisms underlying the establishment and maintenance of aberrant methylation marks are still elusive. The de novo DNA methyltransferase 3B (DNMT3B) has been suggested to play an important role in the generation of cancer-specific methylation patterns. Previous studies have shown that a reduction of DNMT3B protein levels induces antiproliferative effects in cancer cells that were attributed to the demethylation and reactivation of tumor suppressor genes. However, methylation changes have not been analyzed in detail yet. Using RNA interference we reduced DNMT3B protein levels in colon cancer cell lines. Our results confirm that depletion of DNMT3B specifically reduced the proliferation rate of DNMT3B-overexpressing colon cancer cell lines. However, genome-scale DNA methylation profiling failed to reveal methylation changes at putative DNMT3B target genes, even in the complete absence of DNMT3B. These results show that DNMT3B is dispensable for the maintenance of aberrant DNA methylation patterns in human colon cancer cells and they have important implications for the development of targeted DNA methyltransferase inhibitors as epigenetic cancer drugs
End of life care for frail older patients in family practice (ELFOP) – protocol of a longitudinal qualitative study on needs, appropriateness and utilisation of services
In search of the harbours: New evidence of Late Roman and Byzantine harbours of Ephesus
Ephesus (Greek name: Ephesos) in Western Turkey was an important harbour city during Antiquity. The progradation of the Kucuk Menderes delta has continuously shifted the coastline westwards. Thus, along with the delta progradation, new harbour sites had to be established in a western direction. Historical sources refer to different harbours. While much is known about the Roman and older ones, the exact location of the ports and the coastline in late Roman and Byzantine times is still an open question. This article presents the results of geoarchaeological research in the area located along the southern flank of the Kucuk Menderes graben near Ephesus. Sediments from cores were examined with geochemical, sedimentological, and microfaunal analyses. These data were combined with the study of ancient maps and satellite images. The chronological framework was rendered by AMS-C-14 ages and diagnostic ceramics. The farthermost inland shoreline dates from 5000 BC; since then, delta progradation has continuously shifted the shoreline westwards. canakgol, today a little lake to the west of the city of Ephesus is identified as the harbour site in late Roman and Byzantine times. This harbour persisted at least until the 16th century AD. Further, a landing site with a pier was discovered west of canakgol, presumably dating to the late Byzantine-Ottoman times. (C) 2013 Elsevier Ltd and INQUA. All rights reserved
S1753 EGCG, a Major Component of Green Tea Catechins Attenuates Inflammatory Responses in Two Different Mouse Colitis Models
Neolithic settlement sites in Western Turkey - palaeogeographic studies at cukurici Hoyuk and Arvalya Hoyuk
Cukurici Hoyuk and Arvalya Hoyuk are two prehistoric settlement mounds (tells) located in parallel striking valleys in the environs of Ephesus, W Turkey. They were studied with geoarchaeological methods in order to reconstruct their environmental setting, areal extension and distinct settlement phases, as well as the vegetation history. Both tells are situated on small ridges flanked by rivers and their alluvial plains which were suitable for cultivation. The Neolithic coastline was located at a distance of c. 15-2 km to the north. Cukurici Hoyuk covers an area of c. 200 m x 100 m; its strata have a total thickness of at least 8.50 m. The oldest remains, dating from the 7th millennium BC, represent an advanced Neolithic culture closely linked to the sea. The oldest foundations reveal that the site was intentionally chosen on the ridge within the still naturally wooded vegetated landscape. Other than Cukurici Hoyuk, Arvalya Hoyuk has not yet been excavated. However, geophysical measurements and corings revealed that it covers an area of c. 100 m x 60 m, and that it is constructed of several settlement layers with a total thickness of at least 3.50 m. Radar and geomagnetic images show building structures including fireplaces and pits, surrounded by a rampart-ditch construction as a potential enclosure. (C) 2015 Elsevier Ltd. All rights reserved
Late Holocene coastline and landscape changes to the west of Ephesus, Turkey
Palaeogeographical research regarding coastline and landscape changes has been conducted in the Kucuk Menderes graben and the environs of the ancient city of Ephesus in Western Turkey for a few decades. Based on geophysical data, multi-proxy and microfaunal analyses of sediment cores, 14C-AMS age estimates and diagnostic ceramics, this study presents for the first time results of an area close to the present coastline, where a Byzantine church is located on top of a small hill. The results reveal that this mica schist hill turned into an island during the 2nd/1st millennium BCE. It was reconnected to the mainland via a tombolo during the 5th century CE. Drill cores and geophysical measurements surrounding the hill show massive stone layers which were deposited intentionally during the 5th/6th century CE when the Byzantine church was built. Geophysical images point to wall structures in the surroundings of the hill. The area to the northeast hosts a small harbour site. When the coastline continued to shift further to the west, this site was still connected to the sea by the Kucuk Menderes river. (C) 2017 Elsevier Ltd and INQUA. All rights reserved
Intestinal parasites from public and private latrines and the harbour canal in Roman Period Ephesus, Turkey (1st c. BCE to 6th c. CE)
To improve our knowledge of the parasite species affecting the inhabitants of Roman period Asia Minor, we analysed faecal material from Ephesus, Turkey. Mineralised material from the drain from a private house latrine (3rd c. CE), sediment samples from the sewer drain of a public communal latrine (6th c. CE), and sediment from the harbour canal (ca. 1st c. BCE to ca. 6th c. CE) were studied for the presence of intestinal parasites. Samples were viewed by light microscopy for helminth eggs, and commercial enzyme-linked immunosorbent assay (ELISA) kits were used to test for protozoal parasites that cause dysentery. Eggs of roundworm were found in the public latrine, whipworm in the house latrine, and both whipworm and roundworm in the harbour canal. Sequential sampling of the harbour core suggests that whipworm was by far the most common parasite throughout the Roman period, and there was no clear evidence for change in parasite species over the centuries. Whipworm and roundworm are both spread by the contamination of food and drink by human faeces. Despite the large number of travellers to Ephesus, as the capital of its province and a major port city in the Roman Empire, there was a surprising lack of diversity in parasite species found. This is especially apparent when we consider that ten species of intestinal parasite have been found across the Roman Empire. This is the first Roman site to be directly assessed for differences between infection in individuals using private latrines, public latrines, and mixed town effluent (in the harbour) at the same site
Human-environment interaction in the hinterland of Ephesos - As deduced from an in-depth study of Lake Belevi, west Anatolia
Lacustrine sediments are important archives for high resolution palaeoenvironmental reconstructions of the Holocene. Despite the density of ancient cities and settlements along the western coast of Turkey, the archives from coastal lakes in this area have until now not been recognized to their fullest potential and are, therefore, only poorly studied. The exceptional geo-bio-archive of Lake Belevi is located close to the ancient city of Ephesos in western Turkey. Two sediment cores have been analysed using geochemical, sedimentological, microfaunal, palynological, and archaeoparasitological methods. The in-depth study of these Holocene deposits is supported by a robust age-depth model that used 33 radiocarbon dates and tephrochronology. The results reveal the existence of a freshwater lake in the Early Holocene which turned brackish when the rising sea level connected it with the sea. The delta evolution of the Kucuk Menderes led to the reestablishment of a freshwater lake. The natural vegetation was represented by open oak woodlands. There are hints for first agricultural activities in the environs of Belevi as early as 8000 cal yr BP. Intensive cultivation of Olea is proven since 3000 cal yr BP. Starting during the 3rd millennium BP, the human impact with enhanced deforestation activities and correlative high sedimentation rates is attested for sites such as Belevi (Ephesos), Elaia (Pergamon) and Miletos. For the first time, tephra from the eruption of Minoan Santorini has been identified in the environs of Ephesos. This ash covered the vegetation by a thick layer, wherefore low-growing plants were strongly affected. The comparison between the results from the quasi natural area of Lake Belevi and the area around the city of Ephesos gives insights into the development and use of the landscapes, the environmental changes as well as the duration and intensity of the human impact. (C) 2020 Elsevier Ltd. All rights reserved
The hypermethylation phenotype is maintained in DNMT3B knockout cells.
<p>(A) Heatmap based on Infinium 27 k data illustrating the methylation levels of 67 CIMP marker genes in HCT-116 colon cancer cells and HCT-116 DNMT3B knockout cells (3BKO). (B) Boxplot illustrating methylation levels of 67 CIMP marker genes. Lines in boxes denote medians, boxes the interquartile range, and whiskers the 2.5th and 97.5th percentiles, respectively. (C) Heatmap based on Infinium 27 k data illustrating the methylation levels of 543 hypermethylated PRC2 target genes in HCT-116 colon cancer cells and HCT-116 DNMT3B knockout cells (3BKO). (D) Boxplot illustrating methylation levels of PRC2 target genes. AVB, Average Beta value.</p