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https://www.readbyqxmd.com/read/29676944/integration-of-clinical-variables-for-the-prediction-of-late-distant-recurrence-in-patients-with-estrogen-receptor-positive-breast-cancer-treated-with-5-years-of-endocrine-therapy-cts5
#1
Mitch Dowsett, Ivana Sestak, Meredith M Regan, Andrew Dodson, Giuseppe Viale, Beat Thürlimann, Marco Colleoni, Jack Cuzick
Purpose Estimating risk of late distant recurrence (DR) is an important goal for managing women with hormone receptor-positive breast cancer after 5 years of endocrine treatment without recurrence. We developed and validated a simple clinicopathologic tool (Clinical Treatment Score post-5 years [CTS5]) to estimate residual risk of DR after 5 years of endocrine treatment. Patients and Methods The ATAC (Arimidex, Tamoxifen, Alone or in Combination) data set (N = 4,735) was used to create a prognostic score for post-5-year risk of DR...
April 20, 2018: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/29672730/the-importance-of-costoclavicular-space-on-possible-compression-of-the-subclavian-artery-in-the-thoracic-outlet-region-a-radio-anatomical-study
#2
Tevfik Kaplan, Ayhan Comert, Ali Firat Esmer, Gökçe Kaan Ataç, Halil Ibrahim Acar, Bulent Ozkurt, Ibrahim Tekdemir, Serdar Han
OBJECTIVES: The purposes of this study were to identify possible compression points along the transit route of the subclavian artery and to provide a detailed anatomical analysis of areas that are involved in the surgical management of the thoracic outlet syndrome (TOS). The results of the current study are based on measurements from cadavers, computed tomography (CT) scans and dry adult first ribs. METHODS: The width and length of the interscalene space and the width of the costoclavicular passage were measured on 18 cervical dissections in 9 cadavers, on 50 dry first ribs and on CT angiography sections from 15 patients whose conditions were not related to TOS...
April 16, 2018: Interactive Cardiovascular and Thoracic Surgery
https://www.readbyqxmd.com/read/29649445/chromatin-accessibility-based-characterization-of-the-gene-regulatory-network-underlying-plasmodium-falciparum-blood-stage-development
#3
Christa Geeke Toenhake, Sabine Anne-Kristin Fraschka, Mahalingam Shanmugiah Vijayabaskar, David Robert Westhead, Simon Jan van Heeringen, Richárd Bártfai
Underlying the development of malaria parasites within erythrocytes and the resulting pathogenicity is a hardwired program that secures proper timing of gene transcription and production of functionally relevant proteins. How stage-specific gene expression is orchestrated in vivo remains unclear. Here, using the assay for transposase accessible chromatin sequencing (ATAC-seq), we identified ∼4,000 regulatory regions in P. falciparum intraerythrocytic stages. The vast majority of these sites are located within 2 kb upstream of transcribed genes and their chromatin accessibility pattern correlates positively with abundance of the respective mRNA transcript...
April 11, 2018: Cell Host & Microbe
https://www.readbyqxmd.com/read/29649436/atac-ing-transcriptional-mysteries-in-malaria-parasites
#4
Catherine J Merrick
Ever since Plasmodium intraerythrocytic development was reported to proceed via an unusual "hardwired" transcriptional cascade, the control of gene transcription in malaria parasites has been an area of intense investigation. In this issue of Cell Host & Microbe, Toenhake et al. (2018) illuminate this intriguing issue by applying ATAC sequencing.
April 11, 2018: Cell Host & Microbe
https://www.readbyqxmd.com/read/29625068/chromatin-accessibility-dynamics-during-chemical-induction-of-pluripotency
#5
Shangtao Cao, Shengyong Yu, Dongwei Li, Jing Ye, Xuejie Yang, Chen Li, Xiaoshan Wang, Yuanbang Mai, Yue Qin, Jian Wu, Jiangping He, Chunhua Zhou, He Liu, Bentian Zhao, Xiaodong Shu, Chuman Wu, Ruiping Chen, Waiyee Chan, Guangjin Pan, Jiekai Chen, Jing Liu, Duanqing Pei
Despite its exciting potential, chemical induction of pluripotency (CIP) efficiency remains low and the mechanisms are poorly understood. We report the development of an efficient two-step serum- and replating-free CIP protocol and the associated chromatin accessibility dynamics (CAD) by assay for transposase-accessible chromatin (ATAC)-seq. CIP reorganizes the somatic genome to an intermediate state that is resolved under 2iL condition by re-closing previously opened loci prior to pluripotency acquisition with gradual opening of loci enriched with motifs for the OCT/SOX/KLF families...
April 5, 2018: Cell Stem Cell
https://www.readbyqxmd.com/read/29618724/global-dynamics-of-stage-specific-transcription-factor-binding-during-thymocyte-development
#6
Tomonori Hosoya, Ricardo D'Oliveira Albanus, John Hensley, Greggory Myers, Yasuhiro Kyono, Jacob Kitzman, Stephen C J Parker, James Douglas Engel
In vertebrates, multiple transcription factors (TFs) bind to gene regulatory elements (promoters, enhancers, and silencers) to execute developmental expression changes. ChIP experiments are often used to identify where TFs bind to regulatory elements in the genome, but the requirement of TF-specific antibodies hampers analyses of tens of TFs at multiple loci. Here we tested whether TF binding predictions using ATAC-seq can be used to infer the identity of TFs that bind to functionally validated enhancers of the Cd4, Cd8, and Gata3 genes in thymocytes...
April 4, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29610331/evolutionary-emergence-of-the-rac3b-rfng-sgca-regulatory-cluster-refined-mechanisms-for-hindbrain-boundaries-formation
#7
Joaquín Letelier, Javier Terriente, Ivan Belzunce, Adria Voltes, Cristian Alberto Undurraga, Rocio Polvillo, Lucie Devos, Juan J Tena, Ignacio Maeso, Sylvie Retaux, José Luis Gomez-Skarmeta, Juan R Martínez-Morales, Cristina Pujades
Developmental programs often rely on parallel morphogenetic mechanisms that guarantee precise tissue architecture. While redundancy constitutes an obvious selective advantage, little is known on how novel morphogenetic mechanisms emerge during evolution. In zebrafish, rhombomeric boundaries behave as an elastic barrier, preventing cell intermingling between adjacent compartments. Here, we identify the fundamental role of the small-GTPase Rac3b in actomyosin cable assembly at hindbrain boundaries. We show that the novel rac3b / rfng / sgca regulatory cluster, which is specifically expressed at the boundaries, emerged in the Ostariophysi superorder by chromosomal rearrangement that generated new cis -regulatory interactions...
April 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29605855/defining-regulatory-elements-in-the-human-genome-using-nucleosome-occupancy-and-methylome-sequencing-nome-seq
#8
Suhn Kyong Rhie, Shannon Schreiner, Peggy J Farnham
NOMe-seq (nucleosome occupancy and methylome sequencing) identifies nucleosome-depleted regions that correspond to promoters, enhancers, and insulators. The NOMe-seq method is based on the treatment of chromatin with the M.CviPI methyltransferase, which methylates GpC dinucleotides that are not protected by nucleosomes or other proteins that are tightly bound to the chromatin (GpCm does not occur in the human genome and therefore there is no endogenous background of GpCm ). Following bisulfite treatment of the M...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29605854/assay-for-transposase-accessible-chromatin-atac-seq-to-chart-the-open-chromatin-landscape-of-human-pancreatic-islets
#9
Helena Raurell-Vila, Mireia Ramos-Rodríguez, Lorenzo Pasquali
The regulatory mechanisms that ensure an accurate control of gene transcription are central to cellular function, development and disease. Such mechanisms rely largely on noncoding regulatory sequences that allow the establishment and maintenance of cell identity and tissue-specific cellular functions.The study of chromatin structure and nucleosome positioning allowed revealing transcription factor accessible genomic sites with regulatory potential, facilitating the comprehension of tissue-specific cis-regulatory networks...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29603380/identification-of-chromatin-accessible-domains-in-non-alcoholic-steatohepatitis-derived-hepatocellular-carcinoma
#10
Mekonnen Lemma Dechassa, Volodymyr Tryndyak, Aline de Conti, Wenming Xiao, Frederick A Beland, Igor P Pogribny
Non-alcoholic steatohepatitis (NASH) is becoming one of the major causes of hepatocellular carcinoma (HCC) in the United States and Western countries; however, the molecular mechanisms associated with NASH-related liver carcinogenesis are not well understood. In the present study, we investigated cancer-associated chromatin alterations using a model that resembles the development of NASH-related HCC in humans. An assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) identified 1,677 tumor-specific chromatin-accessible regions in NASH-derived HCC tissue samples...
March 30, 2018: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/29590483/building-capacity-for-complementary-and-integrative-medicine-through-a-large-cross-agency-acupuncture-training-program-lessons-learned-from-a-military-health-system-and-veterans-health-administration-joint-initiative-project
#11
Richard Niemtzow, John Baxter, Rollin M Gallagher, Arnyce Pock, Kathryn Calabria, David Drake, Kevin Galloway, Joan Walter, Richard Petri, Thomas Piazza, Stephen Burns, Lew Hofmann, John Biery, Chester Buckenmaier
Introduction: Complementary and integrative medicine (CIM) use in the USA continues to expand, including within the Military Health System (MHS) and Veterans Health Administration (VHA). To mitigate the opioid crisis and provide additional non-pharmacological pain management options, a large cross-agency collaborative project sought to develop and implement a systems-wide curriculum, entitled Acupuncture Training Across Clinical Settings (ATACS). Materials and Methods: ATACS curriculum content and structure were created and refined over the course of the project in response to consultations with Subject Matter Experts and provider feedback...
March 26, 2018: Military Medicine
https://www.readbyqxmd.com/read/29588064/the-evaluation-of-the-effects-of-steroid-treatment-on-the-tumor-and-peritumoral-edema-by-dwi-and-mr-spectroscopy-in-brain-tumors
#12
Cahit Kural, Gokce Kaan Atac, Ozkan Tehli, Ilker Solmaz, Caglar Temiz, Irgen Hodaj, Yusuf Izci
OBJECTIVE: To investigate the effects of dexamethasone on brain tumor and peritumoral edema by different sequences of magnetic resonance imaging (MRI). MATERIALS AND METHODS: MRI was performed in 28 patients with brain tumor. Patients were divided into the 3 groups based on the histological diagnosis; Group I: high-grade glial tumor, Group II: low-grade glial tumor, and Group III: brain metastasis. The measurements of peritumoral edema volume and apparent diffusion coefficient (ADC) values were performed while the peak areas of cerebral metabolites were measured by spectroscopy in groups I and II...
March 13, 2018: Neurologia i Neurochirurgia Polska
https://www.readbyqxmd.com/read/29579120/hsv-1-induced-disruption-of-transcription-termination-resembles-a-cellular-stress-response-but-selectively-increases-chromatin-accessibility-downstream-of-genes
#13
Thomas Hennig, Marco Michalski, Andrzej J Rutkowski, Lara Djakovic, Adam W Whisnant, Marie-Sophie Friedl, Bhaskar Anand Jha, Marisa A P Baptista, Anne L'Hernault, Florian Erhard, Lars Dölken, Caroline C Friedel
Lytic herpes simplex virus 1 (HSV-1) infection triggers disruption of transcription termination (DoTT) of most cellular genes, resulting in extensive intergenic transcription. Similarly, cellular stress responses lead to gene-specific transcription downstream of genes (DoG). In this study, we performed a detailed comparison of DoTT/DoG transcription between HSV-1 infection, salt and heat stress in primary human fibroblasts using 4sU-seq and ATAC-seq. Although DoTT at late times of HSV-1 infection was substantially more prominent than DoG transcription in salt and heat stress, poly(A) read-through due to DoTT/DoG transcription and affected genes were significantly correlated between all three conditions, in particular at earlier times of infection...
March 26, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29572403/genome-wide-mapping-of-dna-accessibility-and-binding-sites-for-creb-and-c-ebp-%C3%AE-in-vasopressin-sensitive-collecting-duct-cells
#14
Hyun Jun Jung, Viswanathan Raghuram, Jae Wook Lee, Mark A Knepper
Background Renal water excretion is controlled by vasopressin, in part through regulation of the transcription of the aquaporin-2 gene ( Aqp2 ). Methods To identify enhancer regions likely to be involved in the regulation of Aqp2 and other principal cell-specific genes, we used several next generation DNA-sequencing techniques in a well characterized cultured cell model of collecting duct principal cells (mpkCCD). To locate enhancers, we performed the assay for transposase-accessible chromatin using sequencing (ATAC-Seq) to identify accessible regions of DNA and integrated the data with data generated by chromatin immunoprecipitation followed by next generation DNA-sequencing (ChIP-Seq) for CCCTC binding factor (CTCF) binding, histone H3 lysine-27 acetylation, and RNA polymerase II...
March 23, 2018: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29569683/computed-tomography-use-in-minor-head-injury-attitudes-and-practices-of-emergency-physicians-neurosurgeons-and-radiologists-in-turkey
#15
Ebru Özan, Gökçe Kaan Ataç
BACKGROUND: We aimed to determine the attitudes and practices of emergency physicians (EPs), neurosurgeons, and radiologists in Turkey regarding computed tomography (CT) use for adults with minor head injury (MHI). METHODS: This cross-sectional study was conducted between August 2015 and October 2016 after obtaining the approval of the institutional ethical committee. The purpose of this study was disclosed to the participants prior to beginning the survey. The study was performed conducting a questionnaire via e-mail on three groups of participants including EPs, neurosurgeons, and radiologists...
March 2018: Ulusal Travma Ve Acil Cerrahi Dergisi, Turkish Journal of Trauma & Emergency Surgery: TJTES
https://www.readbyqxmd.com/read/29561703/chromium-disrupts-chromatin-organization-and-ctcf-access-to-its-cognate-sites-in-promoters-of-differentially-expressed-genes
#16
Andrew VonHandorf, Francisco Javier Sánchez-Martín, Jacek Biesiada, Hongxia Zhang, Xiang Zhang, Mario Medvedovic, Alvaro Puga
Hexavalent chromium compounds are well-established respiratory carcinogens used in industrial processes. While inhalation exposure constitutes an occupational risk affecting mostly chromium workers, environmental exposure from drinking water is a widespread gastrointestinal cancer risk, affecting millions of people throughout the world. Cr(VI) is genotoxic, forming protein-Cr-DNA adducts and silencing tumor suppressor genes, but its mechanism of action at the molecular level is poorly understood. Our prior work using FAIRE showed that Cr(VI) disrupted the binding of transcription factors CTCF and AP-1 to their cognate chromatin sites...
March 21, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29558892/global-analysis-of-primary-mesenchyme-cell-cis-regulatory-modules-by-chromatin-accessibility-profiling
#17
Tanvi Shashikant, Jian Ming Khor, Charles A Ettensohn
BACKGROUND: The developmental gene regulatory network (GRN) that underlies skeletogenesis in sea urchins and other echinoderms is a paradigm of GRN structure, function, and evolution. This transcriptional network is deployed selectively in skeleton-forming primary mesenchyme cells (PMCs) of the early embryo. To advance our understanding of this model developmental GRN, we used genome-wide chromatin accessibility profiling to identify and characterize PMC cis-regulatory modules (CRMs)...
March 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29545397/molecular-transitions-in-early-progenitors-during-human-cord-blood-hematopoiesis
#18
Shiwei Zheng, Efthymia Papalexi, Andrew Butler, William Stephenson, Rahul Satija
Hematopoietic stem cells (HSCs) give rise to diverse cell types in the blood system, yet our molecular understanding of the early trajectories that generate this enormous diversity in humans remains incomplete. Here, we leverage Drop-seq, a massively parallel single-cell RNA sequencing (scRNA-seq) approach, to individually profile 20,000 progenitor cells from human cord blood, without prior enrichment or depletion for individual lineages based on surface markers. Our data reveal a transcriptional compendium of progenitor states in human cord blood, representing four committed lineages downstream from HSC, alongside the transcriptional dynamics underlying fate commitment...
March 15, 2018: Molecular Systems Biology
https://www.readbyqxmd.com/read/29539636/the-cis-regulatory-dynamics-of-embryonic-development-at-single-cell-resolution
#19
Darren A Cusanovich, James P Reddington, David A Garfield, Riza M Daza, Delasa Aghamirzaie, Raquel Marco-Ferreres, Hannah A Pliner, Lena Christiansen, Xiaojie Qiu, Frank J Steemers, Cole Trapnell, Jay Shendure, Eileen E M Furlong
Understanding how gene regulatory networks control the progressive restriction of cell fates is a long-standing challenge. Recent advances in measuring gene expression in single cells are providing new insights into lineage commitment. However, the regulatory events underlying these changes remain unclear. Here we investigate the dynamics of chromatin regulatory landscapes during embryogenesis at single-cell resolution. Using single-cell combinatorial indexing assay for transposase accessible chromatin with sequencing (sci-ATAC-seq), we profiled chromatin accessibility in over 20,000 single nuclei from fixed Drosophila melanogaster embryos spanning three landmark embryonic stages: 2-4 h after egg laying (predominantly stage 5 blastoderm nuclei), when each embryo comprises around 6,000 multipotent cells; 6-8 h after egg laying (predominantly stage 10-11), to capture a midpoint in embryonic development when major lineages in the mesoderm and ectoderm are specified; and 10-12 h after egg laying (predominantly stage 13), when each of the embryo's more than 20,000 cells are undergoing terminal differentiation...
March 14, 2018: Nature
https://www.readbyqxmd.com/read/29522192/esatac-an-easy-to-use-systematic-pipeline-for-atac-seq-data-analysis
#20
Zheng Wei, Wei Zhang, Huan Fang, Yanda Li, Xiaowo Wang
Summary: ATAC-seq is rapidly emerging as one of the major experimental approaches to probe chromatin accessibility genome-wide. Here, we present "esATAC", a highly integrated easy-to-use R/Bioconductor package, for systematic ATAC-seq data analysis. It covers essential steps for full analyzing procedure, including raw data processing, quality control and downstream statistical analysis such as peak calling, enrichment analysis and transcription factor footprinting. esATAC supports one command line execution for preset pipelines, and provides flexible interfaces for building customized pipelines...
March 7, 2018: Bioinformatics
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